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Whole Genome Analysis of the OsGRF Gene Family Encoding Plant-Specific Putative Transcription Activators in Rice (Oryza sativa L.)
Abstract
OsGRF1 (Oryza sativa GROWTH-REGULATING FACTOR1) is a rice gene encoding a putative novel transcriptional regulator. We identified and characterized eleven homologs of OsGRF1 in the rice genome. All twelve OsGRF proteins have two highly conserved regions, the QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys) domains, and sequences reminiscent of transcription factors. OsGRF genes were preferentially expressed in young and growing tissues, and applied gibberellic acid (GA3) enhanced the expression of seven OsGRF genes. In situ hybridization showed high levels of OsGRF1 transcripts in the shoot apical meristem and in cells surrounding the vasculature of the intercalary meristem. In a GAL4-based yeast assay, the C-terminal region of OsGRF1 was found to have transactivation activity. These results indicate that OsGRF1 acts as a transcriptional activator. Based on the in situ expression pattern of OsGRF1, we postulate that it may be involved in regulating vegetative growth in rice.
... These genes have played important roles in the evolution of plants. Nine genes have been identified in Arabidopsis thaliana [2], 11 in Oryza sativa [3], 25 in Nicotiana benthamiana [4], and eight in Sorghum bicolor [5]. GRF has been confirmed to be involved in plant growth and development. ...
... GRF determines cell volume, positively regulates leaf size, and participates in chloroplast proliferation, photosynthesis, and osmotic stress [6,7]. Therefore, it is important to explore the function of GRFs in plant growth and genetic improvement [3]. ...
... To obtain an understanding of the phylogenetic relationships of the AmGRF gene family, we merged the nine GRF proteins of A. thaliana and 12 GRF proteins of O. sativa with the nine protein sequences of AmGRF [3]. Next, we used the Muscle program for multiple sequence alignment and constructed an evolutionary tree of the AmGRF gene family system using the MEGA-X11 software [18]. ...
Background
Astragalus membranaceus is a plant of the Astragalus genus, which is used as a traditional Chinese herbal medicine with extremely high medicinal and edible value. Astragalus mongholicus, as one of the representative medicinal materials with the same origin of medicine and food, has a rising market demand for its raw materials, but the quality is different in different production areas. Growth-regulating factors (GRF) are transcription factors unique to plants that play important roles in plant growth and development. Up to now, there is no report about GRF in A. mongholicus.
Methods and results
This study conducted a genome-wide analysis of the AmGRF gene family, identifying a total of nine AmGRF genes that were classified into subfamily V based on phylogenetic relationships. In the promoter region of the AmGRF gene, we successfully predicted cis-elements that respond to abiotic stress, growth, development, and hormone production in plants. Based on transcriptomic data and real-time quantitative polymerase chain reaction (qPCR) validation, the results showed that AmGRFs were expressed in the roots, stems, and leaves, with overall higher expression in leaves, higher expression of AmGRF1 and AmGRF8 in roots, and high expression levels of AmGRF1 and AmGRF9 in stems.
Conclusions
The results of this study provide a theoretical basis for the further exploration of the functions of AmGRFs in plant growth and development.
... The first plant GRF, OsGRF1, was previously identified in deepwater rice with high expression levels in internode intercalary meristem in response to GA3 [3]. Currently, members of GRFs have also been identified in several other plant species: 9 in A. thaliana, 12 in O. sativa, 17 in Brassica rapa, 15 in Lactuca sativa, and 19 in Populus alba × P. glandulosa [5][6][7][13][14][15][16]. ...
... Numerous transcription factors have been identified in promoting cell proliferation of developing leaves, including GRF [2,17]. The expression analysis of GRFs in various plant species has shown that GRFs were preferentially expressed in growing and developing tissues characterized by robust cell division, such as early flower buds, shoot tips with shoot apical meristem (SAM), and young leaves [5,[12][13][14]18,19]. The overexpression of AtGRF1, AtGRF2, or AtGRF5 in A. thaliana resulted in enhanced leaf growth and the development of transgenic plants with significantly larger leaves compared to those observed in the wild-type. ...
... The gene IDs of AtGRFs and OsGRFs were obtained from the Arabidopsis gene family information on the Tair website (https://www.arabidopsis.org/browse/genefamily/index.jsp accessed on 20 April 2024) and the research article published by Choi et al. [13], respectively. Other plant GRF protein sequences were downloaded from PLAZA_v5_dicots (https://bioinformatics.psb.ugent.be/plaza/versions/plaza_v5_dicots/ ...
The roots, stems, leaves, and seeds of Eucommia ulmoides contain a large amount of trans-polyisoprene (also known as Eu-rubber), which is considered to be an important laticiferous plant with valuable industrial applications. Eu-rubber used in industry is mainly extracted from leaves. Therefore, it is of great significance to identify genes related to regulating the leaf size of E. ulmoides. Plant growth-regulating factors (GRFs) play important roles in regulating leaf size, and their functions are highly conserved across different plant species. However, there have been very limited reports on EuGRFs until now. In this study, eight canonical EuGRFs with both QLQ and WRC domains and two putative eul-miR396s were identified in the chromosome-level genome of E. ulmoides. It is found that, unlike AtGRFs, all EuGRFs contain the miR396s binding site in the terminal of WRC domains. These EuGRFs were distributed on six chromosomes in the genome of E. ulmoides. Collinearity analysis of the E. ulmoides genome revealed that EuGRF1 and EuGRF3 exhibit collinear relationships with EuGRF2, suggesting that those three genes may have emerged via gene replication events. The collinear relationship between EuGRFs, AtGRFs, and OsGRFs showed that EuGRF5 and EuGRF8 had no collinear members in Arabidopsis and rice. Almost all EuGRFs show a higher expression level in growing and developing tissues, and most EuGRF promoters process phytohormone-response and stress-induced cis-elements. Moreover, we found the expression of EuGRFs was significantly induced by gibberellins (GA3) in three hours, and the height of E. ulmoides seedlings was significantly increased one week after GA3 treatment. The findings in this study provide potential candidate genes for further research and lay the foundation for further exploring the molecular mechanism underlying E. ulmoides development in response to GA3.
... These genes have played important roles in the evolution of plants. Nine genes have been identi ed in Arabidopsis thaliana (Kim et al., 2003), 11 in Oryza sativa (Choi et al., 2004), 25 in Nicotiana benthamiana (Zhang et al., 2018), and eight in Sorghum bicolor (Shi et al., 2022). GRF has been con rmed to be involved in plant growth and development. ...
... GRF determines cell volume, positively regulates leaf size, and participates in chloroplast proliferation, photosynthesis, and osmotic stress (Lu et al., 2023;Wang et al., 2023b). Therefore, it is important to explore the function of GRFs in plant growth and genetic improvement (Choi et al., 2004). ...
... To obtain an understanding of the phylogenetic relationships of the AmGRF gene family, we merged the nine GRF proteins of A. thaliana and 12 GRF proteins of O. sativa with the nine protein sequences of AmGRF (Choi et al., 2004). Next, we used the Muscle program for multiple sequence alignment and constructed an evolutionary tree of the AmGRF gene family system using the MEGA-X11 software (Kumar et al., 2016). ...
Background Astragalus membranaceus is a plant of the Astragalus genus, which is used as a traditional Chinese herbal medicine with extremely high medicinal and edible value.Astragalus mongholics, as one of the representative medicinal materials with the same origin of medicine and food, has a rising market demand for its raw materials, but the quality is different in different production areas. Growth-regulating factors are transcription factors unique to plants that play important roles in plant growth and development. Up to now, there is no report about GRF in A. mongholics.
Methods and results This study conducted a genome-wide analysis of the AmGRF gene family, identifying a total of nine AmGRF genes that were classified into subfamily V based on phylogenetic relationships. In the promoter region of the AmGRF gene, we successfully predicted cis-elements that respond to abiotic stress, growth, development, and hormone production in plants. Based on transcriptomic data and real-time quantitative polymerase chain reaction (qPCR) validation, the results showed that AmGRFs were expressed in the roots, stems, and leaves, with overall higher expression in leaves, higher expression ofAmGRF1 and AmGRF8 in roots, and high expression levels of AmGRF1and AmGRF9 in stems.
Conclusions The results of this study provide a theoretical basis for the further exploration of the functions of AmGRFsin plant growth and development.
... Growth-regulating factors (GRFs) are an unique class of plant-specific transcription factors involved in regulating the growth and development of plant cotyledons, leaves, stems, roots, flowers, and seeds, as well as biotic and abiotic stress response processes. The first identified growth-regulatory factor was OsGRF1 in rice [6], and subsequently the GRF family was gradually recognized in various plants, such Arabidopsis, rice, tomato, tobacco, poplar and wheat [7][8][9][10][11][12]. These findings indicate that GRF genes are mainly expressed in the meristem of plants and plays an essential role in plant growth and development. ...
... These findings indicate that GRF genes are mainly expressed in the meristem of plants and plays an essential role in plant growth and development. Generally, the members of GRFs in terrestrial plants ranges from 8-20, for instance, 9 in Arabidopsis, 12 in rice, 14 in maize, and 17 in Chinese cabbage [7,8,13]. Typical GRF proteins contain one conserved QLQ (glutamine-leucine-glutamine, Glu-Leu-Glu) damain and one or two conserved WRC (tryptophanarginine-cysteine, Trp-Arg-Cys) domains at the N-terminus [14]. ...
... Gibberellin (GA) regulates diverse aspects of plant growth and development [18]. Previous studies have shown that GA 3 treatment induces up-regulation of OsGRF1/2/3/7/10/12 and represses the expression of OsGRF9 in rice, but results in reduced expression of most GRFs in cabbage [8,13]. In addition, the effects of phytohormone including brassinolide (BR) and cytokinin (CK) on expression of GRF genes have also been reported. ...
Background
Citrus is one of the most valuable fruits worldwide and an economic pillar industry in southern China. Nevertheless, it frequently suffers from undesirable environmental stresses during the growth cycle, which severely restricts the growth, development and yield of citrus. In plants, the growth-regulating factor (GRF) family of transcription factors (TF) is extensively distributed and plays an vital part in plant growth and development, hormone response, as well as stress adaptation. However, the systematic identification and functional analysis of GRF TFs in citrus have not been reported.
Results
Here, a genome-wide identification of GRF TFs was performed in Citrus sinensis, 9 members of CsGRFs were systematically identified and discovered to be scattered throughout 5 chromosomes. Subsequently, physical and chemical properties, phylogenetic relationships, structural characteristics, gene duplication events, collinearity and cis-elements of promoter were elaborately analyzed. In particular, the expression patterns of the CsGRF genes in response to multiple phytohormone and abiotic stress treatments were investigated. Predicated on this result, CsGRF04, which exhibited the most differential expression pattern under multiple phytohormone and abiotic stress treatments was screened out. Virus-induced gene silencing (VIGS) technology was utilized to obtain gene silenced plants for CsGRF04 successfully. After the three stress treatments of high salinity, low temperature and drought, the CsGRF04-VIGS lines showed significantly reduced resistance to high salinity and low temperature stresses, but extremely increased resistance to drought stress.
Conclusions
Taken together, our findings systematically analyzed the genomic characterization of GRF family in Citrus sinensis, and excavated a CsGRF04 with potential functions under multiple abiotic stresses. Our study lay a foundation for further study on the function of CsGRFs in abiotic stress and hormone signaling response.
... The QLQ domain interacts with the SYT N-terminal homology domain (SNH) of GRF-interacting factors (GIFs) to form a functional GRF-GIF complex [3]. The amino acid sequence of the WRC domain is more highly conserved than QLQ, containing a nuclear localization signal domain and a C3H-type zinc finger domain, which can be combined with the cis-acting elements of downstream genes to regulate the temporal and spatial expression of genes [4]. Compared with the N-terminus, the C-terminus of the GRF protein varies widely: motifs such as TQL (Thr, Gln, Leu), GGPL (Gly, Gly, Pro, Leu) and FFD (Phe, Phe, Asp) often appear in the C-terminal end of the protein, although these are not highly conserved [5,6]. ...
... Based on motif analysis, motif 1 (WRC) and motif 2 (QLQ) were found in all LuGRF proteins ( Figure 2C), and there are different conserved protein motifs in LuGRF proteins. The differences between these subfamilies demonstrate the functional diversity of GRF members [4,5,32]. As shown in Figure 2B, WRC is closely related to other motifs, and it is possible that this domain plays a role in DNA binding. ...
... Flax GRF C-terminal protein can bind to cis-acting elements of downstream genes to regulate the temporal and spatial expression of genes [10]. The N-terminal and C-terminal domains of flax GRF protein participate in plant growth and development [4]. ...
Flax is an important cash crop globally with a variety of commercial uses. It has been widely used for fiber, oil, nutrition, feed and in composite materials. Growth regulatory factor (GRF) is a transcription factor family unique to plants, and is involved in regulating many processes of growth and development. Bioinformatics analysis of the GRF family in flax predicted 17 LuGRF genes, which all contained the characteristic QLQ and WRC domains. Equally, 15 of 17 LuGRFs (88%) are predicted to be regulated by lus-miR396 miRNA. Phylogenetic analysis of GRFs from flax and several other well-characterized species defined five clades; LuGRF genes were found in four clades. Most LuGRF gene promoters contained cis-regulatory elements known to be responsive to hormones and stress. The chromosomal locations and collinearity of LuGRF genes were also analyzed. The three-dimensional structure of LuGRF proteins was predicted using homology modeling. The transcript expression data indicated that most LuGRF family members were highly expressed in flax fruit and embryos, whereas LuGRF3, LuGRF12 and LuGRF16 were enriched in response to salt stress. Real-time quantitative fluorescent PCR (qRT-PCR) showed that both LuGRF1 and LuGRF11 were up-regulated under ABA and MeJA stimuli, indicating that these genes were involved in defense. LuGRF1 was demonstrated to be localized to the nucleus as expected for a transcription factor. These results provide a basis for further exploration of the molecular mechanism of LuGRF gene function and obtaining improved flax breeding lines.
... proteins. Most GRFs contain unique QLQ (Glu-Leu-Glu, glutamine, leucine, glutamine) and WRC (Trp-Arg-Cys, tryptophan, arginine, cysteine) domains in the N-terminal region [1,3,6,8]. The WRC domain can be combined with the cis-acting regions of downstream genes to regulate their expression. ...
... The WRC domain can be combined with the cis-acting regions of downstream genes to regulate their expression. The QLQ domain can interact with the SNH domain in the GIF protein to form a transcription activator [3,6,8,9]. ...
... Gain or loss events of exons or introns provide structural and functional differences [38]. From the gene structure of each group of responses, most of the PgGRF genes have similar structures, and most of the PgGRF genes have two to four introns/exons, which are similar to those of rice and Arabidopsis [6,8]. Previous reports showed that suppressed OsGRF3, OsGRF4 and OsGRF5 in clade B could cause plant dwarfing, delayed growth and inflorescence formation [39]. ...
Background
Panax ginseng is a perennial herb and one of the most widely used traditional medicines in China. During its long growth period, it is affected by various environmental factors. Past studies have shown that growth-regulating factors (GRFs) and GRF-interacting factors (GIFs) are involved in regulating plant growth and development, responding to environmental stress, and responding to the induction of exogenous hormones. However, GRF and GIF transcription factors in ginseng have not been reported.
Results
In this study, 20 GRF gene members of ginseng were systematically identified and found to be distributed on 13 chromosomes. The ginseng GIF gene family has only ten members, which are distributed on ten chromosomes. Phylogenetic analysis divided these PgGRFs into six clades and PgGIFs into two clades. In total, 18 of the 20 PgGRFs and eight of the ten PgGIFs are segmental duplications. Most PgGRF and PgGIF gene promoters contain some hormone- and stress- related cis-regulatory elements. Based on the available public RNA-Seq data, the expression patterns of PgGRF and PgGIF genes were analysed from 14 different tissues. The responses of the PgGRF gene to different hormones (6-BA, ABA, GA3, IAA) and abiotic stresses (cold, heat, drought, and salt) were studied. The expression of the PgGRF gene was significantly upregulated under GA3 induction and three weeks of heat treatment. The expression level of the PgGIF gene changed only slightly after one week of heat treatment.
Conclusions
The results of this study may be helpful for further study of the function of PgGRF and PgGIF genes and lay a foundation for further study of their role in the growth and development of Panax ginseng.
... WRC is a kind of plant-specific motif, which is responsible for the interaction between transcription factors and DNA in the nucleus. It contains a DNA-binding nucleus localization signal region and zinc finger structure (C-X9-C-X10-C-X2-H), which regulates the expression of downstream target genes [2,4,5,8,25]. However, research on the GRF gene family in M. dodecandrum has not been reported. ...
... Some genes were involved in the growth regulation of meristem, embryo, and seed growth. The previous studies show that the expression level of the GRF gene family in growing zones is significantly higher than that in mature tissues [3,4,24], such as the OsGRFs in rice being strongly expressed in buds, immature leaves, and flower buds [25]. The expression of the GRF gene family is highest in the tender organ of Camellia sinensis, followed by the stems and immature leaves, and is hardly expressed in the root and mature flower [3]. ...
... The expression of the GRF gene family is highest in the tender organ of Camellia sinensis, followed by the stems and immature leaves, and is hardly expressed in the root and mature flower [3]. In M. dodecandrum, the expression analysis according to RT-qPCR and transcriptome data of the GRF gene family showed that most MdGRFs were highly expressed in stem, flower bud, and small fruit, while MdGRFs were nearly not expressed in mature flower, root, and mature fruit, which is similar to previous studies on other species [3,25]. The high expression in the tender organ of the GRF gene family in M. dodecandrum indicated that MdGRFs may play an important role in regulating the development of plants. ...
Growth-regulating factor (GRF) is a kind of transcription factor unique to plants, playing an important role in the flowering regulation, growth, and development of plants. Melastoma dodecandrum is an important member of Melastomataceae, with ornamental, medicinal, and edible benefits. The identification of the GRF gene family in M. dodecandrum can help to improve their character of flavor and continuous flowering. The members of the GRF gene family were identified from the M. dodecandrum genome, and their bioinformatics, selective pressure, and expression patterns were analyzed. The results showed that there were 20 GRF genes in M. dodecandrum. Phylogenetic analysis showed that the 71 GRF genes from M. dodecandrum, Arabidopsis thaliana, Camellia sinensis, and Oryza sativa can be divided into three clades and six subclades. The 20 GRF genes of M. dodecandrum were distributed in twelve chromosomes and one contig. Furthermore, the gene structure and motif analysis showed that the intron and motif within each clade were very similar, but there were great differences among different clades. The promoter contained cis-acting elements related to hormone induction, stress, and growth and development. Different transcriptomic expression of MdGRFs indicated that MdGRFs may be involved in regulating the growth and development of M. dodecandrum. The results laid a foundation for further study on the function and molecular mechanism of the M. dodecandrum GRF gene family.
... There are two conserved domains involved in GRF proteins: QLQ (Gln, Leu, and Gln) and WRC (Trp, Arg, and Cys), and both of them are located in the N-terminal region [4,5]. The QLQ domain and the GRF-interacting factor (GIF) act upon each other, and it is also known as an important protein-protein interaction domain [6,7]. The WRC domain contains a zinc finger motif and a functional nuclear localization signal that plays a role in DNA binding [6]. ...
... The QLQ domain and the GRF-interacting factor (GIF) act upon each other, and it is also known as an important protein-protein interaction domain [6,7]. The WRC domain contains a zinc finger motif and a functional nuclear localization signal that plays a role in DNA binding [6]. The C-terminal of GRF is variable and contains several low conservative motifs [5,8]. ...
... OsGRF1 is the first member of the identified GRF family, which is isolated from rice and plays a crucial role in gibberellin (GA)-induced stem elongation [4]. The GRF genes have recently been identified and characterized at genomewide levels in many plant species, including Arabidopsis [9], rice [6], maize [5], tomato [8], soybean [2], cotton [10], and tea [11]. ...
Background: Growth regulating factors (GRFs) are transcription factors that regulate diverse biological and physiological processes in plants, including growth, development, and abiotic stress. Although GRF family genes have been studied in a variety of plant species, knowledge about the identification and expression patterns of GRF in sugarcane (Saccharum spp.) is still lacking.
Results: In the present study, a comprehensive analysis was conducted in the genome of wild sugarcane (Saccharum spontaneum) and 10 SsGRF genes were identified and characterized. The phylogenetic relationship, gene structure, and expression profiling of these genes were analyzed entirely under both regular growth and low-nitrogen stress conditions. Phylogenetic analysis suggested that the 10 SsGRF members were categorized into six clusters. Gene structure analysis indicated that the SsGRF members in the same group were greatly conserved. Expression profiling demonstrated that most SsGRF genes were extremely expressed in immature tissues, implying their critical roles in sugarcane growth and development. Expression analysis based on transcriptome data and real-time quantitative PCR verification revealed that GRF1 and GRF3 were distinctly differentially expressed in response to low-nitrogen stress, which meant that they were additional participated in sugarcane stress tolerance.
Conclusions: Our study provides a scientific basis for the potential functional prediction of SsGRF and will be further scrutinized by examining their regulatory network in sugarcane development and abiotic stress response, and ultimately facilitating their application in cultivated sugarcane breeding.
... The N-terminal of GRF proteins is highly conserved, containing a QLQ (QX 3 LX 2 Q) domain and a WRC (CX 9 CX 10 CX 2 H) domain. The QLQ domain was found to interact with the SNH domain of GRF-Interacting Factor (GIF) and participated in the activation or repression of the downstream genes, whereas the WRC domain contained a nuclear localization signal region (NLS) and a zinc finger responsible for the recognition and binding of downstream genes (Choi et al. 2004;Horiguchi et al. 2005;Kim et al. 2003;Kim and Kende 2004). Different from the conserved N-terminals, the C-terminals of GRFs are extremely varied, and possess the transcriptional activation activity (Choi et al. 2004;Kim and Kende 2004). ...
... The QLQ domain was found to interact with the SNH domain of GRF-Interacting Factor (GIF) and participated in the activation or repression of the downstream genes, whereas the WRC domain contained a nuclear localization signal region (NLS) and a zinc finger responsible for the recognition and binding of downstream genes (Choi et al. 2004;Horiguchi et al. 2005;Kim et al. 2003;Kim and Kende 2004). Different from the conserved N-terminals, the C-terminals of GRFs are extremely varied, and possess the transcriptional activation activity (Choi et al. 2004;Kim and Kende 2004). ...
... In rice, OsGRF1 was strongly expressed in shoot apical meristem and intercalary meristem, and functioned in the regulation of leaf, stem and grain development (Van der Knaap et al. 2000). OsGRF1,OsGRF2,OsGRF3,OsGRF7,OsGRF8,OsGRF10 and OsGRF12 were involved in gibberellin (GA)-induced stem elongation (Choi et al. 2004). OsGRF3 and OsGRF10 can bind to the promoter of Oskn2 gene in the KNOX gene family and repress the expression of Oskn2 to regulate rice architecture (Kuijt et al. 2014). ...
Key message
Identification, characterization and osmotic stress responsive expression of growth-regulating factor genes in grape.
Abstract
The growth and fruit production of grape vine are severely affected by adverse environmental conditions. Growth-regulating factors (GRFs) play a vital role in the regulation of plant growth, reproduction and stress tolerance. However, their biological functions in fruit vine crops are still largely unknown. In the present study, a total number of nine VvGRFs were identified in the grape genome. Phylogenetic and collinear relationship analysis revealed that they formed seven subfamilies, and have gone through three segmental duplication events. All VvGRFs were predicted to be nucleic localized and contained both the conserved QLQ and WRC domains at their N-terminals, one of the typical structural features of GRF proteins. Quantitative real-time PCR analyses demonstrated that all VvGRFs, with a predominant expression of VvGRF7, were constitutively expressed in roots, leaves and stems of grape plants, and showed responsive expression to osmotic stress. Further growth phenotypic analysis demonstrated that ectopic expression of VvGRF7 promoted the growth and sensitivity of transgenic Arabidopsis plants to osmotic stress. Our findings provide important information for the future study of VvGRF gene functions, and potential gene resources for the genetic breeding of new fruit vine varieties with improved fruit yield and stress tolerance.
... GRFs have two conserved domains: QLQ (Gln-Q, Leu-L, Gln-Q) and WRC (Trp-W, Arg-R, Cys-C), in the N-terminal region. The QLQ domain contains sites for interaction with GRF-interacting factors (GIFs) , while the WRC domain contains a DNA-binding motif and a nuclear localization signal (Choi et al., 2004). The QLQ domains are more conservative than the WRC domains (van der Knaap et al., 2000). ...
... The identification and function of the GRF gene family has been studied in a variety of plants, including Arabidopsis (9) (Kim et al., 2003), soybean (22) (Chen et al., 2019), rice (12) (Choi et al., 2004), apple (16) , mulberry (10) (Rukmangada et al., 2018), wheat (8) (Zan et al., 2020), and foxtail millet (Chen and Ge, 2022). However, studies on the GRF gene family in alfalfa are limited. ...
... The GRF family contains QLQ and WRC conserved domains at the N-terminus, and the WRC region contains DNA-binding motifs and nuclear localization signal regions, which can combine with the cis-acting regions of downstream genes to regulate the expression of such genes . The QLQ domain can combine with GIF to form a transcriptional activator and play a regulatory role (Choi et al., 2004). These 27 genes were verified to contain QLQ and WRC domains (Supplementary Figure 1); therefore, they were finally identified as GRF family members. ...
Growth-regulating factors (GRFs) play crucial roles in plant growth and stress response. To date, there have been no reports of the analysis and identification of the GRF transcription factor family in alfalfa. In this study, we identified 27 GRF family members from alfalfa (Medicago sativa L.) “Xinjiang Daye”, and analyzed their physicochemical properties. Based on phylogenetic analysis, these MsGRFs were divided into five subgroups, each with a similar gene structure and conserved motifs. MsGRFs genes are distributed on 23 chromosomes, and all contain QLQ and WRC conserved domains. The results of the collinearity analysis showed that all MsGRFs are involved in gene duplication, including multiple whole-genome duplication or segmental duplication and a set of tandem duplication, indicating that large-scale duplication is important for the expansion of the GRF family in alfalfa. Several hormone-related and stress-related cis-acting elements have been found in the promoter regions of MsGRFs. Some MsGRFs were highly expressed in young leaves and stems, and their expression decreased during development. In addition, the leaf size of different varieties was found to vary, and MsGRF1 to 4, MsGRF18 to 20, and MsGRF22 to 23 were differentially expressed in large and small leaf alfalfa varieties, suggesting that they are critical in the regulation of leaf size. The results of this study can benefit further exploration of the regulatory functions of MsGRFs in growth and development, and can identify candidate genes that control leaf size development.
... Studies have shown that OsGRF1 has multiple functions. The OsGRF1 gene is involved in regulating growth at the juvenile stage, and may be involved in the regulation of heading in rice as well [1,6]. There is a close relationship between plant hormones and GRFs in plant growth and development. ...
... To date, GRFs have been identified in multiple species. Among them are nine GRFs in Arabidopsis [5], thirteen in tobacco [7], twelve in rice [6], sixteen in apple, and thirty in wheat [13]. ...
... In the present study, we identified fifteen GRF genes from Zanthoxylum armatum genome. The structural features of ZaGRF proteins contained QLQ and WRC domains, which are similar to those of the GRF proteins of Arabidopsis and rice [5,6]. Although the Gln-Leu-Gln residues of the QLQ domain are absolutely conserved in ZaGRFs, this feature is absent in ZaGRF2 due to the substitution of Leu by Phe. ...
Growth-regulating factors (GRFs) are plant-specific transcription factors that play an important role in plant growth and development. In this study, fifteen GRF gene members containing QLQ and WRC domains were identified in Zanthoxylum armatum. Phylogenetic and collinearity analysis showed that ZaGRFs were closely related to CsGRFs and AtGRFs, and distantly related to OsGRFs. There are a large number of cis-acting elements related to hormone response and stress induction in the GRF gene promoter region of Z. armatum. Tissue-specific expression analysis showed that except for ZaGRF7, all the ZaGRFs were highly expressed in young parts with active growth and development, including terminal buds, seeds, and young flowers, suggesting their key roles in Z. armatum growth and development. Eight ZaGRFs were selected to investigate the transcriptional response to auxin, gibberellin and drought treatments. A total of six ZaGRFs in the NAA treatment, four ZaGRFs in the GA3 treatment, and six ZaGRFs in the PEG treatment were induced and significantly up-regulated. Overexpression of ZaGRF6 increased branching and chlorophyll content and delayed senescence of transgenic Nicotiana benthamiana. ZaGRF6 increased the expression of CRF2 and suppressed the expression of ARR4 and CKX1, indicating that ZaGRF6 is involved in cytokinin metabolism and signal transduction. These research results lay a foundation for further analysis of the GRF gene function of Z. armatum and provide candidate genes for growth, development, and stress resistance breeding of Z. armatum.
... The QLQ domain can interact with GRF Interaction Factor (GIF) to exert their functions [4]. The WRC domain functions in DNA binding and transcription factors targeting the nucleus, which consist of a C3H motif for DNA binding and a nuclear localization signal (NLS) [5]. The C-terminal region of GRF is variable when compared with the conservative amino acid residues in the N-terminal region, and this region has the transactivation activity [4][5][6][7]. ...
... The WRC domain functions in DNA binding and transcription factors targeting the nucleus, which consist of a C3H motif for DNA binding and a nuclear localization signal (NLS) [5]. The C-terminal region of GRF is variable when compared with the conservative amino acid residues in the N-terminal region, and this region has the transactivation activity [4][5][6][7]. In addition, several other motifs, such as TQL (Thr, Gln, Leu) and FFD (Phe, Phe, Asp), are usually present in the C-terminal region of GRFs, although they are not highly conservative [8]. ...
... (accessed on 1 January 2020), respectively. To identify all putative GRF transcription factor proteins in each genome assembly, the conserved domains of the GRF protein (PF08879 for WRC domain and PF08880 for QLQ domain) [5] of Hidden Markov Model (HMM) profiles were downloaded from the Pfam protein family database (https://pfam.xfam.org/) (accessed on 11 September 2020). ...
Growth Regulatory Factors (GRF) are plant-specific transcription factors that play critical roles in plant growth and development as well as plant tolerance against stress. In this study, a total of 16 GRF genes were identified from the genomes of Medicago truncatula and Medicago sativa. Multiple sequence alignment analysis showed that all these members contain conserved QLQ and WRC domains. Phylogenetic analysis suggested that these GRF proteins could be classified into five clusters. The GRF genes showed similar exon-intron organizations and similar architectures in their conserved motifs. Many stress-related cis-acting elements were found in their promoter region, and most of them were related to drought and defense response. In addition, analyses on microarray and transcriptome data indicated that these GRF genes exhibited distinct expression patterns in various tissues or in response to drought and salt treatments. In particular, qPCR results showed that the expression levels of gene pairs MtGRF2-MsGRF2 and MtGRF6-MsGRF6 were significantly increased under NaCl and mannitol treatments, indicating that they are most likely involved in salt and drought stress tolerance. Collectively, our study is valuable for further investigation on the function of GRF genes in Medicago and for the exploration of GRF genes in the molecular breeding of highly resistant M. sativa.
... In addition, some GRF transcription factors may also contain non-conservative domains, such as TQL, FFD, and GGPL, in the C-terminal [6]. Since the discovery of the first GRF in rice [7], a large number of GRF TFs have been isolated and identified [7][8][9][10][11][12][13], e.g., the model plant Arabidopsis thaliana has 9 GRFs [3], the tomato has 13 [14], Brachypodium distachyon has 10 [4], rice has 11 [9], and tobacco has 25 [15]. ...
... In addition, some GRF transcription factors may also contain non-conservative domains, such as TQL, FFD, and GGPL, in the C-terminal [6]. Since the discovery of the first GRF in rice [7], a large number of GRF TFs have been isolated and identified [7][8][9][10][11][12][13], e.g., the model plant Arabidopsis thaliana has 9 GRFs [3], the tomato has 13 [14], Brachypodium distachyon has 10 [4], rice has 11 [9], and tobacco has 25 [15]. ...
... Eight non-redundant protein sequences containing typical QLQ and WRC domains were obtained and renamed NuGRF1~NuGRF8. The number of GRF genes was less than that of most plants, such as A. thaliana (9), O. sativa (12), and Nymphaea colorata (9). The number of amino acids ranged from 349 to 604 aa, with the smallest one belonging to NuGRF6 and the largest belonging to NuGRF1 (Table 1). ...
Sacred lotus (Nelumbo nucifera) is an aquatic perennial plant with essential food, ornamental, and pharmacological value. Growth-regulating factor (GRF) is a transcription factor (TF) family that plays an important role in regulating the growth and development of plants. In this study, a comprehensive analysis of the GRF family in N. nucifera was performed, and its role in N. nucifera development was studied. A total of eight GRF genes were identified in the N. nucifera genome. Phylogenetic analysis divided the 38 GRF genes into six clades, while the NuGRFs only contained five clades. The analyses of gene structures, motifs, and cis-acting regulatory elements of the GRF gene family were performed. In addition, the chromosome location and collinearity were analyzed. The expression pattern based on transcriptomic data and real-time reverse transcription-quantitative PCR (qRT-PCR) revealed that the GRF genes were expressed in multiple organs and were abundant in actively growing tissues, and the expression levels decreased as the age of N. nucifera increased. Then, 3D structures of the NuGRF proteins were predicted by homology modeling. Finally, the subcellular localization of GRF1 was ascertained in the tobacco leaf through a vector. Therefore, this study provides a comprehensive overview of the GRF TF family in N. nucifera.
... These transcription factors regulate the expression of specific target genes in different tissues, cells, and respond to different external or internal stimuli. The GROWTH-REGU-LATING FACTOR (GRF) family is reported to be a type of plant-specific transcription factor family (Van der Knaap et al., 2000;Kim et al., 2003;Choi et al., 2004;Omidbakhshfard et al., 2015). The rice (Oryza sativa L.) OsGRF1 was the first member found to be involved in stem and leaf development (Van der Knaap et al., 2000). ...
... The rice (Oryza sativa L.) OsGRF1 was the first member found to be involved in stem and leaf development (Van der Knaap et al., 2000). To date, various studies have identified the GRF family members in different plant species, of which 9 and 12 GRFs are found in Arabidopsis (Kim et al., 2003) and rice (Choi et al., 2004), respectively. Majority of the plant GRFs are characterized by two highly conserved domains (QLQ and WRC) at the N terminal regions. ...
... Majority of the plant GRFs are characterized by two highly conserved domains (QLQ and WRC) at the N terminal regions. The QLQ domain is mainly responsible for protein-protein interactions, and the WRC domain is reported to be involved in DNA binding of the downstream target for expression regulation (Van der Knaap et al., 2000;Kim et al., 2003;Choi et al., 2004;Zhang et al., 2008). Various C-terminal regions may intercede the functional differences among GRF family members. ...
GROWTH-REGULATING FACTORs (GRFs) are plant-specific transcription factors that play important roles in the regulating plant growth, development, and tolerance to stresses. However, there has been no in-depth research on the GRF genes and their roles in apple. A total of sixteen GRF genes were identified in the apple genome (GDDH13 V1.1), that expressed differentially in various tissues, in which the highest expression levels were observed particularly in shoot tips and apical buds. Among MdGRFs, the MdGRF11 was cloned and further investigated. Overexpression of the MdGRF11 in Arabidopsis plants promoted flowering, root elongation and leaf size. Further investigation indicated that MdGRF11 interacts with key flower genes FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1). The transient assays demonstrated that MdGRF11 represses the expression of knotted-like homeobox (MdKNOX19). Furthermore, MdTFL1 can compete with MdFT1 for complex formation with MdGRF11 to regulate the expression of MdKNOX19. Taken together, our results suggest that MdGRF11 protein is involved in fine-tuning of the floral transition possibly through interaction with the MdFT1 and MdTFL1 proteins.
... GRF1 helps gibberellic acid (GA) to elongate stems (7). GRF2 regulates leaf size and is highly expressed in leaves (11). The KNOX gene and GRF3 regulate meristems (12), GRF4 regulates grain size and yield (13). GRF5 aids floral organogenesis (14), while chilling stress is coordinated by GRF6 (15). ...
... Leaf development is regulated by GRF7 and GRF8 (16). Young inflorescences express GRF10 and GRF11, which regulate floral growth (14) and GRF12 is expressed during GA-mediated shoot development (11). Rice is grown in a variety of conditions, including anaerobic (flood-irrigated rice), rainfed, and aerobic (upland rice). ...
Background: Growth-regulating factors (GRFs) are crucial in rice for controlling plant growth and development. Among
... The first GRF gene, OsGRF1, was identified in deepwater rice (Oryza sativa L.), and its induction by gibberellic acid (GA) affects stem elongation [3]. Numerous GRF genes have been identified in Brassica rapa L. [4], rice [5], Zea mays L. [6], Cucumis sativus [7], and Arabidopsis thaliana [8]. GRFs function in regulating the growth of leaves [8] and act as positive regulators of cell proliferation [9] to influence the shape and size of leaves [10]. ...
... GRF proteins consist of two highly conserved domains in their N-terminal regions: WRC and QLQ [14]. The QLQ domain, composed of Gln-Leu-Gln and neighboring residues, functions in protein-protein interactions [3,14,15], while the WRC domain contains a zinc finger structure and a nuclear localization signal region [5]. GRF proteins interact with GRF-INTERACTOR (GIF) to form a transcriptional complex, functioning in various aspects of plant growth and development [10,14]. ...
... For example, 7 of the 9 At-GRF genes regulate the root meristem, whereas 2 of the 12 OsGRF genes are expressed in the root. 11 In L. leptolepis, downregulating the expression of LaGRFs reduced the rooting rate, suggesting that LaGRFs might positively regulate the rooting of L. leptolepis. 12 In Populus, PTGRF1/2D was mainly expressed in the pericyclic and apical root positions, indicating that these genes participated in root formation. ...
... Using the GAL4 system in O. sativa, OsGRF1 was shown to fuse with the GAL4 DNA binding domain, thereby activating the HIS reporter gene and allowing yeast cells to grow on histidinedeficient medium. 11 A transcriptional activation experiment was used to verify the transcriptional activation activity of ArGRF1. The results indicated that ArGRF1 can activate the transcription of HIS reporter genes. ...
Rooting and root development in Acer rubrum have important effects on overall growth. A. rubrum does not take root easily in natural conditions. In this study, the mechanisms of the miR396b- GRF1 module underlying rooting regulation in A. rubrum were studied. The subcellular localization and transcriptional activation of miR396b and its target gene growth regulating factor 1 ( GRF1) were investigated. These experiments showed that GRF1 was localized in the nucleus and had transcriptional activation activity. Functional validation experiments in transgenic plants demonstrated that overexpression of Ar-miR396b inhibited adventitious root growth, whereas overexpression of ArGRF1 increased adventitious root growth. These results help clarify the molecular regulatory mechanisms underlying adventitious root growth in A. rubrum and provide some new insights into the rooting rate in this species.
... Recently, the GRF families in Arabidopsis thaliana [17], Oryza sativa [18], Saccharum [19], Spirodela polyrhiza [20], Triticum aestivum L. [21], Zanthoxylum armatum DC. [22], Lettuce [23], and Medicago truncatula [24] have been identified and extensively studied. Previous studies have reported on the moso bamboo GRF family; however, these studies were based on the first version of the genome sequencing data [25,26]. ...
... In the moso bamboo genome, a total of 24 PheGRFs containing QLQ and WRC domains were identified, which is significantly higher compared to wheat (18), Zea mays (17), O. sativa (12), Arabidopsis (9), and Brachypodium (12) [21,30,31]. Despite having a genome size similar to Z. mays (2300 Mb) [32], moso bamboo (2021 Mb) has a smaller genome size than wheat (Triticeae) (17 Gb) [33], but larger than A. thaliana (164 Mb), B. distachyon (300 Mb), and O. sativa (441 Mb) [34][35][36]. ...
Growth-regulating factors (GRFs) play an important role in regulating plant organ development, acting primarily as positive regulators of cell proliferation. However, research on the evolutionary history and expression patterns of the moso bamboo GRF family has been limited. In this study, a total of 24 GRFs have been identified in the Moso bamboo genome, and they have been categorized into four subfamilies. Estimation of the divergence time of paralogous gene pairs provided evidence supporting the significant contribution of recent whole-genome duplication events in the expansion of the GRF gene family. Sliding window analysis revealed that coding regions of a few PheGRFs, including the WRC and QLQ domains, may have undergone positive selection, possibly due to the redundant functions of paralogous genes. Coexpression network analysis further revealed the regulatory role of miR396 and various lncRNAs in controlling PheGRF expression. Based on the analysis of tissue-specific expression patterns using transcriptome sequencing, qRT-PCR results, and in situ hybridization, it was observed that most GRFs, particularly PheGRF6a and PheGRF9b, exhibited high levels of accumulation in the moso bamboo shoot. This suggests that the involvement of most PheGRF genes may be crucial for the growth and development of the bamboo shoot. A yeast two-hybrid screening revealed interactions between PheGRF9b and several proteins associated with plant growth and development, including PH02Gene11097.t1 (GIF3), PH02Gene37618.t (Phytochrome B), and PH02Gene01921.t3 (WD40). Based on transcriptome expression analysis, it was observed that a substantial number of PheGRFs exhibited significant variations under cold or drought stress treatments, and most of these genes were found to be downregulated, suggesting their role as abiotic stress-responsive genes. Our findings offer new insights into the GRF family of moso bamboo and provide some experimental evidence to support further gene functional validation research of PheGRF.
... GRFs are a unique family of TFs involved in plant growth, development, and stress responses (Lee et al., 2015). Since the discovery of OsGRF1 in rice (Oryza sativa) in 2000 (Knaap et al., 2000), additional GRF family genes have been identified in various plant species, including Arabidopsis thaliana (Kim et al., 2003), Brassica rapa , Brassica napus (Ma et al., 2017), Cucumis sativus (Zhou et al., 2018), Solanum lycopersicum (Khatun et al., 2017), Nicotiana tabacum , O. sativa (Choi et al., 2004), Zea mays (Wu et al., 2014), Triticum aestivum Linn. , and Arachis hypogaea (Zhao et al., 2019). ...
... In the present study, 17 BcGRF genes were identified based on whole-genome sequencing data analysis of flowering Chinese cabbage. The GRF gene family in flowering Chinese cabbage is more diverse than that in A. thaliana (9 genes) (Kim et al., 2003), Camellia japonica (6 genes) (Wu et al., 2017), C. sativus (8 genes) (Zhou et al., 2018), Brachypodium sylvaticum (10 genes) (Filiz et al., 2014), O. sativa (12 genes) (Choi et al., 2004), S. lycopersicum (13 genes) (Khatun et al., 2017), and Z. mays (14 genes) (Wu et al., 2014), but less diverse than that in B. napus (35 genes) (Ma et al., 2017), T. aestivum (30 genes) , A. hypogaea (24 genes) (Zhao et al., 2019), and Nicotiana tabacum (25 genes) . This variation indicates that the GRF family underwent extensive (A) The RT-qPCR-based expression profiles of BcGRF8 in various tissues. ...
Growth-regulating factors (GRFs) are a unique family of transcription factors with well-characterized functions in plant growth and development. However, few studies have evaluated their roles in the absorption and assimilation of nitrate. In this study, we characterized the GRF family genes of flowering Chinese cabbage (Brassica campestris), an important vegetable crop in South China. Using bioinformatics methods, we identified BcGRF genes and analyzed their evolutionary relationships, conserved motifs, and sequence characteristics. Through genome-wide analysis, we identified 17 BcGRF genes distributed on seven chromosomes. A phylogenetic analysis revealed that the BcGRF genes could be categorized into five subfamilies. RT-qPCR analysis showed that BcGRF1, 8, 10, and 17 expression clearly increased in response to nitrogen (N) deficiency, particularly at 8 h after treatment. BcGRF8 expression was the most sensitive to N deficiency and was significantly correlated with the expression patterns of most key genes related to N metabolism. Using yeast one-hybrid and dual-luciferase assays, we discovered that BcGRF8 strongly enhances the driving activity of the BcNRT1.1 gene promoter. Next, we investigated the molecular mechanism by which BcGRF8 participates in nitrate assimilation and N signaling pathways by expressing it in Arabidopsis. BcGRF8 was localized in the cell nucleus and BcGRF8 overexpression significantly increased the shoot and root fresh weights, seedling root length, and lateral root number in Arabidopsis. In addition, BcGRF8 overexpression considerably reduced the nitrate contents under both nitrate-poor and -rich conditions in Arabidopsis. Finally, we found that BcGRF8 broadly regulates genes related to N uptake, utilization, and signaling. Our results demonstrate that BcGRF8 substantially accelerates plant growth and nitrate assimilation under both nitrate-poor and -rich conditions by increasing the number of lateral roots and the expression of genes involved in N uptake and assimilation, providing a basis for crop improvement.
... In addition, the stable contribution of these candidate genes to panicle-related traits in multiple environments could be used as the optimal loci for marker-assisted selection in order to improve the yield in foxtail millet. [28] Protein content, sterility or low fertility, gelatinization temperature, amylose content, seed setting rate, grain width, grain length, floral organ development characteristics, and total starch content LGS1; GLW2(LOC_Os02g47280) [29] Grain shape, ear length, grain size, grain yield, seed drop, cold tolerance, grain width, grain length, plant dry weight, 1000-grain weight, plant cell size, plant fresh weight, and nitrogen use efficiency Si1g34880 1 40.251-40.252 PL_q1-2 OsMKK4; SMG1 (LOC_Os02g54600) [30] Plant height, grain size, panicle type, filled grains per panicle, grain width, grain length, lignin content, cytokinin content, diterpenoid phytoalexin content, and 1000-grain weight [38] Internode length, leaf width, leaf length, grain yield, leaf inclination, floral organ development characteristics, auxin content, 1000-grain weight, and plant cell size [39] Plant height, male sterility, seed morphology and anatomy, ear length, tiller number, lemma morphology and anatomy, seed setting rate, and primary branch number [40] Vegetative growth potential, seed setting rate, photosynthetic capacity, and spikelet fertility [53] Morphological and anatomical characters of root, plant height, leaf angle, panicle type, seed setting rate, grain width, grain thickness, and 1000-grain weight Chr: chromosome. ...
... These candidate genes regulate panicle-and yield-related traits in rice through multiple pathways including plant growth regulators (GAs, e.g., brassinolide and auxin), photoperiod, flower and panicle development, photosynthesis, etc. For example, OsGRF4 (Si1g31910) [29], OsARF19 (Si4g23080) [38], OsSAUR45 (Si6g23990) [45], GSE5(Si3g11190) [34,60], and VLN2 (Si9g39120) [53] were all involved in the synthesis or transduction of GA, brassinolide, and auxin to regulate flower, panicle, and grain development. In addition, DTH7 (Si2g43940) [33], OsMADS6 (Si1g27910) [28], OsNF-YA4 (Si9g12860) [51], OsFKF1 (Si8g15190) [50], and DFO1 (Si5g01910) [39] affected grain morphology and grain weight by participating in photoperiod or directly regulating flower development and panicle formation in rice. ...
Panicle traits are important factors affecting yield, and their improvement has long been a critical goal in foxtail millet breeding. In order to understand the genetic basis of panicle formation, a large-scale genome-wide association study (GWAS) was performed in this study for six panicle-related traits based on 706,646 high-polymorphism SNP loci in 407 accessions. As a result, 87 quantitative trait loci (QTL) regions with a physical distance of less than 100 kb were detected to be associated with these traits in three environments. Among them, 27 core regions were stably detected in at least two environments. Based on rice–foxtail millet homologous comparison, expression, and haplotype analysis, 27 high-confidence candidate genes in the QTL regions, such as Si3g11200 (OsDER1), Si1g27910 (OsMADS6), Si7g27560 (GS5), etc., affected panicle-related traits by involving multiple plant growth regulator pathways, a photoperiod response, as well as panicle and grain development. Most of these genes showed multiple effects on different panicle-related traits, such as Si3g11200 affecting all six traits. In summary, this study clarified a strategy based on the integration of GWAS, a homologous comparison, and haplotype analysis to discover the genomic regions and candidate genes for important traits in foxtail millet. The detected QTL regions and candidate genes could be further used for gene clone and marker-assisted selection in foxtail millet breeding.
... In recent years, the GRF transcription factor family has been identified in Arabidopsis (Kim et al. 2003), rice (Choi et al. 2004), maize (Zhang et al. 2008), cabbage (Wang et al. 2014), citrus (Liu et al. 2016), rape (Ma et al. 2017), cucumber (Yong et al. 2018), and other plant species. M. truncatula is widely grown as fodder and pasture worldwide. ...
... Phylogenetic analysis of the GRF protein from 12 species (including M. truncatula, Arabidopsis, Oryza sativa, Fragaria vesca, Zea mays, Arachis hypogaea, Populus trichocarpa, Triticum aestivum, Brachypodium distachyon, Phyllostachys edulis, Lotus japonicus, and Solanum lycopersicum) showed that MtGRFs shared greater similarity with LjGRFs and AhGRFs than other species (Fig. S1), which was consistent with their evolutionary relationships: M. truncatula, Arachis hypogaea, and Lotus japonicus are all leguminous plants. Previous studies have shown that the expression of GRFs in developing tissues is much higher than that in mature tissues (Khatun et al. 2017;Shi et al. 2019;Choi et al. 2004;Zhang et al. 2018;Ma et al. 2017). In this study, MtGRFs showed significantly higher expression in shoot apical meristems (SAM) than other tissues (Fig. 3), which was also found in wheat (Huang et al. 2021). ...
Growth-regulating factor (GRF) exerts important functions related to plant development and stress response. However, in Medicago truncatula, the GRF family has not been comprehensively analyzed at the genome level. This study identified eight MtGRF genes (containing both QLQ and WRC domains) in the M. truncatula genome, and no duplicate events occurred between these genes. Gene expression analysis showed that MtGRFs exhibited the highest expression in shoot apical meristems (SAM) followed by seeds, flowers, roots, etc. MtGRF2-6 and MtGRF8 were induced by GA, IAA, and ABA, and MtGRF2 and MtGRF5 also responded to MeJA. Additionally, eight, five, and seven MtGRF genes were differentially expressed under drought, salt, and cold stress, respectively. Five MtGRF genes (MtGRF1, 2, 6, 7, and 8) responded to all three types of stresses, especially MtGRF8, the expression of which was inhibited under drought, salt, and cold stress. These results indicated that MtGRF8 may be a negative regulator of the stress response. Degradome analysis showed that all eight MtGRFs were the target genes of Mt-miR396, and MtGRF4 may be jointly regulated by Mt-miR396 and other microRNAs. These results will contribute to the understanding of the GRF family in M. truncatula.
... Since then, there has been extensive work on the identification and evolutionary analysis of the GRF gene family in various plant species. So far, researchers have identified nine GRF members in Arabidopsis thaliana [3], 12 in Oryza sativa [4], 14 in Zea mays [5], 10 in Brachypodium distachyon [6], 30 in Triticum aestivum [7], 35 in Brassica napus [8], 22 in Glycine max [9], and 10 in Jatropha curcus [10]. ...
... Numerous studies on GRF members in plants demonstrated that there are two highly conserved domains (QLQ and WRC) present in the N-terminal. The QLQ (Gln, Leu, Gln, IPR014978) domain, present on the SW12/SNF2 protein, is specific for protein-protein interaction, while WRC (Trp, Arg, Cys, IPR014977) is a plant-specific domain that possesses a C3H motif for DNA binding [4,11]. In contrast to the conserved nature of the N-terminal, the C-terminal in GRFs is composed of variable amino acid residue and is responsible for transcriptional activation. ...
Growth-regulating factors (GRFs) encode plant-specific transcription factors that play a vital role in regulation of plant growth, development, and stress response. Although GRFs have been identified in various plants, there is no reported work available in Actinidia (commonly known as kiwifruit) so far. In the present study, we identified 22 GRF genes on A. chinensis (hereafter A. chinensis is referred to as Ac, and GRF genes in A. chinensis are referred to as AcGRF) distributed on 17 chromosomes and one contig, and 26 GRF genes in A. eriantha (hereafter A. eriantha is referred to as Ae, and GRF genes in A. eriantha are referred to as AeGRF) distributed on 21 chromosomes. Phy-logenetic analysis showed that kiwifruit GRF proteins were clustered into five distinct groups. Additionally , kiwifruit GRFs showed motif composition and gene structure similarities within the same group. Synteny analysis showed that whole-genome duplication played a key role in the expansion of the GRF family in kiwifruit. The higher expression levels of kiwifruit GRFs in young tissues and under stress conditions indicated their regulatory role in kiwifruit growth and development. We observed two genes in Ae (AeGRF6.1, AeGRF 6.2) and two genes in Ac (AcGRF 6.1, AeGRF 6.2) significantly upregulated in different RNA-seq datasets. The presence of conserved protein structures and cis-regulatory elements caused functional divergence in duplicated gene pairs. The subcellular localization indicated the presence of kiwifruit GRFs in the nucleus of the plant cell. Protein-protein interaction analysis predicted AtGIF protein orthologs for AcGRFs and AeGRFs. Taken together, we systematically analyzed the characterization of kiwifruit GRF family members for their potential role in kiwifruit development and Pseudomonas syringae pv. actinidiae (Psa.) invasion response. Further functional studies of kiwifruit GRFs in plant growth, development, and stress response will provide valuable insights for kiwifruit breeders.
... They named it the Growth-Regulating Factor (GRF). GRF is a highly conserved plant-specific transcription factor that typically contains two conserved domains: WRC (Trp, Arg, and Cys) and QLQ (Gln, Leu, and Gln) [100,101]. GRF interacts with its partner, GRF-Interacting Factor (GIF), which contains an SNH domain that interacts with the QLQ domain of GRF, forming a protein complex. This complex modulates the expression of downstream target genes, thereby regulating various aspects of plant growth and development [102][103][104]. ...
Establishing plant regeneration systems and efficient genetic transformation techniques plays a crucial role in plant functional genomics research and the development of new crop varieties. The inefficient methods of transformation and regeneration of recalcitrant species and the genetic dependence of the transformation process remain major obstacles. With the advancement of plant meristematic tissues and somatic embryogenesis research, several key regulatory genes, collectively known as developmental regulators, have been identified. In the field of plant genetic transformation, the application of developmental regulators has recently garnered significant interest. These regulators play important roles in plant growth and development, and when applied in plant genetic transformation, they can effectively enhance the induction and regeneration capabilities of plant meristematic tissues, thus providing important opportunities for improving genetic transformation efficiency. This review focuses on the introduction of several commonly used developmental regulators. By gaining an in-depth understanding of and applying these developmental regulators, it is possible to further enhance the efficiency and success rate of plant genetic transformation, providing strong support for plant breeding and genetic engineering research.
... The N-termini of GRF proteins contain highly conserved QLQ and WRC domains [9]. The QLQ domain consists of the highly conserved Gln-Leu-Gln (QX 3 LX 2 Q) motif and its adjacent residues [5]; it performs transcriptional activation functions by interacting with the SNH domain in GIF proteins [10]. ...
Background
Plant growth-regulating factors (GRFs) and GRF-interacting factors (GIFs) interact with each other and collectively have important regulatory roles in plant growth, development, and stress responses. Therefore, it is of great significance to explore the systematic evolution of GRF and GIF gene families. However, our knowledge and understanding of the role of GRF and GIF genes during plant evolution has been fragmentary.
Results
In this study, a large number of genomic and transcriptomic datasets of algae, mosses, ferns, gymnosperms and angiosperms were used to systematically analyze the evolution of GRF and GIF genes during the evolution of plants. The results showed that GRF gene first appeared in the charophyte Klebsormidium nitens, whereas the GIF genes originated relatively early, and these two gene families were mainly expanded by segmental duplication events after plant terrestrialization. During the process of evolution, the protein sequences and functions of GRF and GIF family genes are relatively conservative. As cooperative partner, GRF and GIF genes contain the similar types of cis-acting elements in their promoter regions, which enables them to have similar transcriptional response patterns, and both show higher levels of expression in reproductive organs and tissues and organs with strong capacity for cell division. Based on protein–protein interaction analysis and verification, we found that the GRF–GIF protein partnership began to be established in pteridophytes and is highly conserved across different terrestrial plants.
Conclusions
These results provide a foundation for further exploration of the molecular evolution and biological functions of GRF and GIF genes.
... However, the expression patterns of different family members in the same species in response to GA differ. In rice, for example, OsGRF1,2,3,7,8,10 and 12 are upregulated after GA 3 treatment, whereas OsGRF9 is downregulated, with no effect on the expression levels of other members (Choi et al., 2004). A similar situation also existed after GA 3 treatment of Chinese cabbage leaves, with different levels of expression for each BrGRF member (Wang et al., 2014). ...
The role of GRF (Growth-regulating Factor) in regulating plant growth and development has been studied, but its potential role in regulating seed fertility remains unclear. PmGRF7 overexpression in tomatoes altered leaf morphology and pollen activity. Most importantly, genetically modified tomato plants had no offspring. PmGRF7 overexpression resulted in abnormal leaf morphology, and transgenic plants that produced seedless fruit or seeds only showed signs of abortion. Pollination of genetically modified tomatoes with wild-type tomato pollen still produced sterile seeds. Further research using bioinformatics tools and physiological index measurement showed that PmGRF7 induced a hormone pathway leading to seed sterility, and at the same time, it caused differential genes to be induced in the plant hormone signal transduction pathway, ribosome pathway, sphingolipid metabolism and other related pathways, leading to morphogenesis in plant leaves. Collectively, our research findings reveal a potential new mechanism by which PmGRF7 regulates seed fertility and leaf growth, and these findings are of potential application in molecular plant breeding.
... In rice plants, a complex of SLENDER RICE 1 (SLR1: rice DELLA) and OsIDD2 regulates the expression of miR396, whose target is growth-regulating factors (OsGRFs) [22]. The GRF family protein is a plant-specific transcription factor involved in many aspects of plant development and growth, including GA signaling and stem elongation [23][24][25][26]. These results indicate that the complex of IDD and DELLA proteins is primarily involved in the regulation of GA synthesis and signaling in angiosperms. ...
INDETERMINATE DOMAIN (IDD) proteins are plant-specific transcription factors that interact with GRAS proteins, such as DELLA and SHORT ROOT (SHR), to regulate target genes. The combination of IDD and DELLA proteins regulates genes involved in gibberellic acid (GA) synthesis and GA signaling, whereas the combination of IDD with the complex of SHR and SCARECROW, another GRAS protein, regulates genes involved in root tissue formation. Previous bioinformatic research identified seven IDDs, two DELLA, and two SHR genes in Physcomitrium patens, a model organism for non-vascular plants (bryophytes), which lack a GA signaling pathway and roots. In this study, DNA-binding properties and protein–protein interaction of IDDs from P. patens (PpIDD) were analyzed. Our results showed that the DNA-binding properties of PpIDDs were largely conserved between moss and seed plants. Four PpIDDs showed interaction with Arabidopsis DELLA (AtDELLA) proteins but not with PpDELLAs, and one PpIDD showed interaction with PpSHR but not with AtSHR. Moreover, AtIDD10 (JACKDAW) interacted with PpSHR but not with PpDELLAs. Our results indicate that DELLA proteins have modified their structure to interact with IDD proteins during evolution from moss lineage to seed plants, whereas the interaction of IDD and SHR was already present in moss lineage.
... Additionally, OSH15 and SH5 interact directly with CAD2 (cinnamyl alcohol dehydrogenase 2) chromatin to inhibit lignin content, leading to a reduced seed-shattering phenotype. GRF4 (Growth-Regulating Factor 4) encodes a growth-regulating factor that positively regulates grain shape and panicle length and negatively regulates seed shattering [74,80]. Ishii et al. [75] produced two backcross populations with reciprocal genetic backgrounds: cultivated rice Nipponbare with closed panicles and wild rice W630 with spreading panicles. ...
Seed shattering is an important trait that wild rice uses to adapt to the natural environment and maintain population reproduction, and weedy rice also uses it to compete with the rice crop. The loss of shattering is a key event in rice domestication. The degree of shattering is not only one of the main reasons for rice yield reduction but also affects its adaptability to modern mechanical harvesting methods. Therefore, it is important to cultivate rice varieties with a moderate shattering degree. In this paper, the research progress on rice seed shattering in recent years is reviewed, including the physiological basis, morphological and anatomical characteristics of rice seed shattering, inheritance and QTL/gene mapping of rice seed shattering, the molecular mechanism regulating rice seed shattering, the application of seed-shattering genes, and the relationship between seed-shattering genes and domestication.
... 2 Materials and methods 2.1 Data sources and sequence retrieval All protein sequences of pineapple were obtained from the Pineapple Genome Project (Ming et al., 2015). Sequences of nine A. thaliana GRF genes and 12 rice GRF genes were obtained from previous studies (Kim et al., 2003;Choi et al., 2004). The corresponding protein sequences were downloaded from the Arabidopsis Information Resource Library (TAIR) (http:// www.arabidopsis.org/) ...
Background:
Pineapple is the only commercially grown fruit crop in the Bromeliaceae family and has significant agricultural, industrial, economic, and ornamental value. GRF (growth-regulating factor) proteins are important transcription factors that have evolved in seed plants (embryophytes). They contain two conserved domains, QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys), and regulate multiple aspects of plant growth and stress response, including floral organ development, leaf growth, and hormone responses. The GRF family has been characterized in a number of plant species, but little is known about this family in pineapple and other bromeliads.
Main discoveries:
We identified eight GRF transcription factor genes in pineapple, and phylogenetic analysis placed them into five subfamilies (I, III, IV, V, VI). Segmental duplication appeared to be the major contributor to expansion of the AcGRF family, and the family has undergone strong purifying selection during evolution. Relative to that of other gene families, the gene structure of the GRF family showed less conservation. Analysis of promoter cis-elements suggested that AcGRF genes are widely involved in plant growth and development. Transcriptome data and qRT-PCR results showed that, with the exception of AcGRF5, the AcGRFs were preferentially expressed in the early stage of floral organ development and AcGRF2 was strongly expressed in ovules. Gibberellin treatment significantly induced AcGRF7/8 expression, suggesting that these two genes may be involved in the molecular regulatory pathway by which gibberellin promotes pineapple fruit expansion.
Conclusion:
AcGRF proteins appear to play a role in the regulation of floral organ development and the response to gibberellin. The information reported here provides a foundation for further study of the functions of AcGRF genes and the traits they regulate.
... Moreover, miR396 cleavage sites were identified in five putative GRF genes via degradome sequencing. All these genes contain a DNA-targeting WRC domain [31,32] and a QLQ domain, that recruits ATP-dependent DNA translocase Switch/Sucrose Non-fermenting (SWI/SNF) via interacting with GRF-interacting factor (GIF) [33,34], thereby remodeling chromatins. During primary thickening, stem cells in the shoot apical meristem produce rapidly dividing daughter cells. ...
MiR396 plays an essential role in various developmental processes. However, the miR396-mRNA molecular network in bamboo vascular tissue differentiation during primary thickening has not been elucidated. Here, we revealed that three of the five members from the miR396 family were overexpressed in the underground thickening shoots collected from Moso bamboo. Furthermore, the predicted target genes were up/down-regulated in the early (S2), middle (S3) and late (S4) developmental samples. Mechanistically, we found that several of the genes encoding protein kinases (PKs), growth-regulating factors (GRF), transcription factors (TFs), and transcription regulators (TRs) were the potential targets of miR396 members. Moreover, we identified QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys) d omains in five PeGRF homologs and a Lipase_3 domain and a K_trans domain in another two potential targets, where the cleavage targets were identified via degradome sequencing (p < 0.05). The sequence alignment indicated many mutations in the precursor sequence of miR396d between Moso bamboo and rice. Our dual-luciferase assay revealed that ped-miR396d-5p binds to a PeGRF6 homolog. Thus, the miR396-GRF module was associated with Moso bamboo shoot development. Fluorescence in situ hybridization localized miR396 in the vascular tissues of the leaves, stems, and roots of pot Moso bamboo seedlings at the age of two months. Collectively, these experiments revealed that miR396 functions as a regulator of vascular tissue differentiation in Moso bamboo. Additionally, we propose that miR396 members are targets for bamboo improvement and breeding.
... Since the discovery of the first Grf, they have been reported in various species. In particular, nine members of the Grf family have been identified in Arabidopsis thaliana [33,34], 14 in maize [35], and 12 in rice [36]. In Arabidopsis thaliana, Grf knockout mutants are characterized with smaller and narrower leaves compared to wild-type genotypes [33,37,38]. ...
The dwarfness in many triticale cultivars is provided by the dominant Ddw1 (Dominant dwarf 1) allele found in rye. However, along with conferring semi-dwarf phenotype to improve resistance to lodging, this gene also reduces grain size and weight and delays heading and flowering. Grf (Growth-regulating factors) genes are plant-specific transcription factors that regulate plant growth, including stem growth, in terms of length and thickness, and leaf and fruit size. In this work, we partially sequenced the rye gene ScGrf3 on chromosome 2R homologous to the wheat Grf3 gene, and found multiple polymorphisms in intron 3 and exon 4 complying with two alternative alleles (haplotypes ScGrf3-2Ra and ScGrf3-2Rb). For the identification of these, we developed a codominant PCR marker. Using a new marker, we studied the effect of ScGrf3-2R alleles in combination with the Ddw1 dwarf gene on economically valuable traits in F4 and F5 recombinant lines of spring triticale from the hybrid combination Valentin 90 x Dublet, grown in the Non-Chernozem zone for 2 years. Allele ScGrf3-2Ra was associated with greater thousand-grain weight, higher spike productivity, and earlier heading and flowering, which makes ScGrf3-2R a perspective compensator for negative effects of Ddw1 on these traits and increases prospects for its involvement in breeding semi-dwarf cultivars of triticale.
... The QLQ domain functions as a protein-protein interaction domain, which interacts with the conserved structure of other proteins to perform transcriptional activation [4,5]. The WRC domain contains a nuclear localization signal (NLS) motif and regulates the expression of downstream genes by binding to their cis-acting regions [6]. The OsGRF1 was the first identified GRF from Oryza sativa, which participates in the gibberellin (GA)-induced stem elongation [7]. ...
Growth-regulating factors (GRFs) are plant-specific transcription factors that play essential roles in regulating plant growth and stress response. The GRF gene families have been described in several terrestrial plants, but a comprehensive analysis of these genes in diverse aquatic species has not been reported yet. In this study, we identified 130 GRF genes in 13 aquatic plants, including floating plants (Azolla filiculoides, Wolffia australiana, Lemna minuta, Spirodela intermedia, and Spirodela polyrhiza), floating-leaved plants (Nymphaea colorata and Euryale ferox), submersed plants (Zostera marina, Ceratophyllum demersum, Aldrovanda vesiculosa, and Utricularia gibba), an emergent plant (Nelumbo nucifera), and an amphibious plant (Cladopus chinensis). The gene structures, motifs, and cis-acting regulatory elements of these genes were analyzed. Phylogenetic analysis divided these GRFs into five clusters, and ABRE cis-elements were highly enriched in the promoter region of the GRFs in floating plants. We found that abscisic acid (ABA) is efficient at inducing the turion of Spirodela polyrhiza (giant duckweed), accompanied by the fluctuated expression of SpGRF genes in their fronds. Our results provide information about the GRF gene family in aquatic species and lay the foundation for future studies on the functions of these genes.
... The GRF genes have been investigated in a number of main crops, including Zea mays (Zhang et al., 2008), Brassica napus (Liu et al., 2012), Brassica rapa , Oryza sativa (Choi et al., 2004;Kuijt et al., 2014;Luo et al., 2005), Gossypium hirsutum (Cao et al., 2020a;Chen et al., 2017), Brachypodium distachyon (Filiz et al., 2014) and Solanum lycopersicum (Khatun et al., 2017). We identified 8 GRF genes in the sorghum genome and illustrated that the gene family was conserved among different plant species. ...
Sorghum (Sorghum bicolor) is the fifth important cereal and an industrial energy crop in the world. Growth Regulation Factors (GRFs) play an important role in response to environmental stress, however, the knowledge of GRFs relating to the pest resistance is lacking. Here, we identified 8 GRF genes harboring the typical QLQ (glutamine, leucine, glutamine) and WRC (tryptophan, arginine, cysteine) domains in Sorghum, which could be classified into 4 clades through phylogenetic analysis. The SbGRF genes express in most tissues, while more than half of them express at the highest level in inflorescence. To further investigate their possible role in stress response, we analyzed the transcriptomics data. The results showed that SbGRFs could respond to the abiotic stresses including heat, salt and drought stress. Furthermore, combined the data with qRT-PCR, SbGRF1, 2, 4 and 7 were identified as dominant genes response to the aphid-induced stress. SSR markers close to these genes were also searched. Above all, we summarized the SbGRFs and provided their potential roles in aphid response.
Plants rely on complex regulatory mechanisms to ensure proper growth and development. As plants are sessile organisms, these mechanisms must be flexible enough to adapt to changes in the environment. GROWTH-REGULATING FACTORS (GRFs) are plant-specific transcription factors that act as a central hub controlling plant growth and development, which offer promising biotechnological applications to enhance plant performance. Here, we analyze the complex molecular mechanisms that regulate GRFs activity, and how their natural and synthetic variants can impact on plant growth and development. We describe the biological roles of the GRFs and examine how they regulate gene expression and contribute to the control of organ growth and plant responses to a changing environment. This review focuses on the premise that unlocking the full biotechnological potential of GRFs requires a thorough understanding of the various regulatory layers governing GRF activity, the functional divergence among GRF family members, and the gene networks that they regulate.
Background
Dendrobium, one of the largest genera in Orchidaceae, is popular not only for its aesthetic appeal but for its significant medicinal value. Growth-regulating factors (GRFs) play an essential role in plant growth and development. However, there is still a lack of information about the evolution and biological function analysis of the GRF gene family among Dendrobiumspecies.
Methods
Growth-regulating factors from Dendrobium officinale Kimura et Migo and Dendrobium chrysotoxum Lindl. were identified by HMMER and BLAST. Detailed bioinformatics analysis was conducted to explore the evolution and function of GRF gene family in D. officinale and D. chrysotoxum using genomic data, transcriptome data and qRT-PCR technology.
Results
Here, we evaluated the evolution of the GRF gene family based on the genome sequences of D. officinale and D. chrysotoxum. Inferred from phylogenetic trees, the GRF genes were classified into two clades, and each clade contains three subclades. Sequence comparison analysis revealed relatively conserved gene structures and motifs among members of the same subfamily, indicating a conserved evolution of GRF genes within Dendrobiumspecies. However, considering the distribution of orthologous DoGRFs and DcGRFs, and the differences in the number of GRFs among species, we suggest that the GRF gene family has undergone different evolutionary processes. A total of 361 cis-elements were detected, with 33, 141, and 187 related to plant growth and development, stress, and hormones, respectively. The tissue-specific expression of GRFs showed that DoGRF8 may have a significant function in the stem elongation of D. officinale. Moreover, four genes were up-regulated under Methyl-jasmonic acid/methyl jasmonate (MeJA) treatment, showing that DoGRFs and DcGRFs play a crucial role in stress response. These findings provide valuable information for further investigations into the evolution and function of GRF genes in D. officinale and D. chrysotoxum.
Leaf growth initiates in the peripheral region of the meristem at the apex of the stem, eventually forming flat structures. Leaves are pivotal organs in plants, serving as the primary sites for photosynthesis, respiration, and transpiration. Their development is intricately governed by complex regulatory networks. Leaf development encompasses five processes: the leaf primordium initiation, the leaf polarity establishment, leaf size expansion, shaping of leaf, and leaf senescence. The leaf primordia starts from the side of the growth cone at the apex of the stem. Under the precise regulation of a series of genes, the leaf primordia establishes adaxial-abaxial axes, proximal-distal axes and medio-lateral axes polarity, guides the primordia cells to divide and differentiate in a specific direction, and finally develops into leaves of a certain shape and size. Leaf senescence is a kind of programmed cell death that occurs in plants, and as it is the last stage of leaf development. Each of these processes is meticulously coordinated through the intricate interplay among transcriptional regulatory factors, microRNAs, and plant hormones. This review is dedicated to examining the regulatory influences of major regulatory factors and plant hormones on these five developmental aspects of leaves.
Cis-regulatory elements (CREs) fine-tune gene transcription in eukaryotes. CREs with sequence variations play vital roles in driving plant or crop domestication. However, how global sequence and structural variations are responsible for multi-level changes between indica and japonica rice (Oryza sativa) is still not fully elucidated. To address this, we conducted multi-omics studies using MH-seq (MNase hypersensitivity sequencing) in combination with RNA-seq, ChIP-seq and BS-seq between the japonica rice variety Nipponbare (NIP) and indica rice variety 93-11. We found that differential MHSs exhibited some distinct intrinsic genomic sequence features between NIP and 93-11. Notably, through MHS-GWAS integration, we found that key sequence variations may be associated with differences of agronomic traits between NIP and 93-11, which is partly achieved by MHSs harboring CREs. In addition, SV-derived differential MHSs caused by TE insertion, especially by non-common TEs among rice varieties, were associated with genes with distinct functions, indicating that TE driven gene neo- or subfunctionalization is mediated by changes of chromatin openness. This study thus provides insights into how sequence and genomic structural variations control agronomic traits of NIP and 93-11; it also provides genome editing targets for molecular breeding aiming at improving favorable agronomic properties.
Growth regulatory factors (GRF) are plant-specific transcription factors that play pivotal roles in growth and various abiotic stresses regulation. However, adaptive evolution of GRF gene family in land plants are still being elucidated. Here, we performed the evolutionary and expression analysis of GRF gene family from seven representative species. Extensive phylogenetic analyses and gene structure analysis revealed that the number of genes, QLQ domain and WRC domain identified in higher plants was significantly greater than those identified in lower plants. Besides, dispersed duplication and WGD/segmental duplication effectively promoted expansion of the GRF gene family. The expression patterns of GRF gene family and target genes were found in multiple floral organs and abundant in actively growing tissues. They were also found to be particularly expressed in response to various abiotic stresses, with stress-related elements in promoters, implying potential roles in floral development and abiotic stress. Our analysis in GRF gene family interaction network indicated the similar results that GRFs resist to abiotic stresses with the cooperation of other transcription factors like GIFs. This study provides insights into evolution in the GRF gene family, together with expression patterns valuable for future functional researches of plant abiotic stress biology.
High yield and stress resistance are the major prerequisites for successful crop cultivation, and can be achieved by modifying plant architecture. Evolutionarily conserved growth‐regulating factors (GRFs) control the growth of different tissues and organs of plants. Here, we provide a systematic overview of the expression patterns of GRF genes and the structural features of GRF proteins in different plant species. Moreover, we illustrate the conserved and divergent roles of GRFs, microRNA396 (miR396), and GRF‐interacting factors (GIFs) in leaf, root, and flower development. We also describe the molecular networks involving the miR396–GRF–GIF module, and illustrate how this module coordinates with different signaling molecules and transcriptional regulators to control development of different plant species. GRFs promote leaf growth, accelerate grain filling, and increase grain size and weight. We also provide some molecular insight into how coordination between GRFs and other signaling modules enhances crop productivity; for instance, how the GRF–DELLA interaction confers yield‐enhancing dwarfism while increasing grain yield. Finally, we discuss how the GRF–GIF chimera substantially improves plant transformation efficiency by accelerating shoot formation. Overall, we systematically review the conserved and divergent roles of GRFs and the miR396–GRF–GIF module in growth regulation, and also provide insights into how GRFs can be utilized to improve the productivity and nutrient content of crop plants.
Plant growth and development are dependent on complex regulatory networks to adapt various environments. The growth regulatory factor (GRF) and GRF-interacting factor (GIF) families have been shown to control growth in various plant species. There are growing evidences that GRFs and GIFs can improve crop genetic transformation efficiency. In this study, we identified and classified 17 ZmGRFs, 10 SiGRFs, 4 ZmGIFs and 3 SiGIFs in maize (Zea mays L.) and foxtail millet (Setaria italica L.) using updated genome data. Many ABREs (Abscisic Acid-responsive elements) were present in the promoter regions of GRFs by analysis, and the expression levels of ZmGRF4, 9, 12, 14 and ZmGIF2 were associated with the Abscisic Acid (ABA) response. Furthermore, ZmGRF9 showed collinearity with AtGRF5 between Arabidopsis and maize. ZmGRF9 conservatively interacts with ZmGIF 2, 3, and 4. As a result, we systematically identified GRF and GIF family members, analyzed the regulatory network, and found that exogenous ABA inhibited the expression of GRFs, regulating responses to stress in the environment.
Supplementary information:
The online version contains supplementary material available at 10.1007/s12298-022-01234-z.
Cotton fiber is one of the most important natural raw materials in the world textile industry. Improving fiber yield and quality has always been the main goal. MicroRNAs, as typical small noncoding RNAs, could affect fiber length during different stages of fiber development. Based on differentially expressed microRNA in the two interspecific backcross inbred lines (BILs) with a significant difference in fiber length, we identified the miR396 gene family in the two tetraploid cotton genomes and found MIR396b_D13 as the functional precursor to produce mature miR396 during the fiber elongation stage. Among 46 target genes regulated by miR396b, the GROWTH-REGULATING FACTOR 5 gene (GRF5, Gh_A10G0492) had a differential expression level in the two BILs during fiber elongation stage. The expression patterns indicated that the miR396b-GRF5 regulatory module has a critical role in fiber development. Furthermore, virus-induced gene silencing (VIGS) of miR396b significantly produced longer fiber than the wild type, and the expression level of GRF5 showed the reverse trends of the miR396b expression level. The analysis of co-expression network for the GRF5 gene suggested that a cytochrome P450 gene functions as an allene oxide synthase (Gh_D06G0089, AOS), which plays a critical role in jasmonate biosynthetic pathway. In conclusion, our results revealed that the miR396b-GRF5 module has a critical role in fiber development. These findings provide a molecular foundation for fiber quality improvement in the future.
Growth-regulating factor (GRF) is a transcription factor unique to plants that plays a crucial role in the growth, development and stress adaptation of plants. However, information on the GRFs related to salt stress in Populus davidiana × P. bolleana is lacking. In this study, we characterized the activity of PdbGRF1 in transgenic Populus davidiana × P. bolleana under salt stress. qRTPCR analyses showed that PdbGRF1 was highly expressed in young leaves and that the pattern of PdbGRF1 expression was significantly changed at most time points under salt stress, which suggests that PdbGRF1 expression may be related to the salt stress response. Moreover, PdbGRF1 overexpression enhanced tolerance to salt stress. A physiological parameter analysis showed that the overexpression of PdbGRF1 significantly decreased the contents of hydrogen peroxide (H2O2) and malondialdehyde (MDA) and increased the activities of antioxidant enzymes (SOD and POD) and the proline content. A molecular analysis showed that PdbGRF1 regulated the expression of PdbPOD17 and PdbAKT1 by binding to the DRE ('A/GCCGAC') in their respective promoters. Together, our results demonstrate that the binding of PdbGRF1 to DRE regulates genes related to stress tolerance and activates the associated physiological pathways, and these effects increase the ROS scavenging ability, reduce the degree of damage to the plasma membrane and ultimately enhance the salt stress response in Populus davidiana × P. bolleana.
Growth-regulating factors (GRFs) are plant-specific transcription factors, and their activities are regulated by miR396 and the GRF-GIF interaction. The miR396-GRFs/GIFs module determines organ size by regulating cell proliferation. However, it is largely unknown in cucumber. In this study, the CsmiR396-CsGRFs/CsGIFs module was investigated in cucumber. Five CsMIR396 loci (CsMIR396A-E), eight CsGRFs and two CsGIFs were identified. CsMIR396A-E was distributed within two clusters and coded three different mature CsmiR396, and all CsGRFs acted as the target of CsmiR396. Bioinformatic analyses showed that miR396s were classified into five types, while GRFs were classified into six groups in plants. The GRFs from group Ⅰ exhibited high diversity and harbored specific characteristics (truncated C-terminus or two WRC domains). qRT–PCR results showed that CsMIR396s (CsMIR396A, CsMIR396B and CsMIR396D) and mature CsmiR396 increased, whereas CsGRFs declined as leaf age increased. In contrast, CsMIR396E was highly expressed in young leaves and shoot tissue, and it was expressed in an age-independent pattern. Yeast two-hybrid assays showed that CsGRF3 strongly interacted with CsGIFs, while CsGRF5 weakly interacted with CsGIFs. Overexpression of CsGRF3 resulted in an enlarged organ size; in contrast, overexpression of CsGRF5, which belonged to group Ⅰ and harbored two WRC domains, resulted in a reduced organ size in Arabidopsis. Section analysis showed that cell proliferation was increased in CsGRF3OE plants, whereas it was decreased in CsGRF5OE plants. In summary, our results reveal the diversity of the CsmiR396-CsGRFs/CsGIFs module in cucumber, and that CsGRF3 and CsGRF5 play an opposite role in regulating cell proliferation.
Background: growth-regulating factors（GRFs）are plant-specific transcription factors that play an important role in plant growth and development, Although the GRF gene family has been identified in many species, a genome-wide analysis of this gene family in pineapple has not been reported. Results: In this study, 8 pineapple GRF genes (AcGRF) were identified and renamed according to their chromosomal locations.8 AcGRFs were divided into three main families and subgroups based on their structural and phylogenetic characteristics. Genomic collinearity analysis found that segmental duplication played a more important role in the expansion of the pineapple GRF gene family. GRF gene collinearity analysis and phylogenetic analysis provide deeper insights into the evolutionary characteristics of pineapple GRF genes. Transcriptome data and real-time quantitative PCR analysis revealed AcGRF gene expression patterns in various tissues and responses to different abiotic stresses and hormonal treatments. Conclusions: In this study, 8 GRF genes were identified in pineapple, and their coding gene structures, evolutionary characteristics, and expression patterns were analyzed. This systematic analysis provides a basis for further identification of pineapple GRF gene function.
Poplar is not only an important woody plant, but also a model species for molecular plant studies. We identified PagGRF11 (pAxG07Gg0005700), a homolog of the Arabidopsis AtGRF1 (AT4G37740) and AtGRF2 (AT2G22840) gene. We transformed the poplar clone “84K” with PagGRF11, and the transgenic overexpressed plants (PagGRF11-OE) showed plant height reduction (dwarfing), stem diameter increase, internode shortening, and larger leaf area. The Arabidopsis overexpression line grf-oe (Overexpression of PagGRF11 in Arabidopsis), mutant line atgrf (a loss-of-function mutant of the AtGRF1 gene of Arabidopsis thaliana), and mutant trans-complementary line atgrf+oe (overexpression of PagGRF11 in mutant plants (atgrf)) also showed different leaf size phenotypes. Further, tissue sections revealed that increased xylem production was the main cause of stem thickening. Transcriptome differential expression analysis of PagGRF11 overexpressed and control plants showed that PagGRF11 promoted CCCH39(C3H39) expression. The expression profile of CCCH39 in different tissues showed that it was highly expressed in xylem. Yeast single hybrid and instantaneous double luciferase assay results showed that PagGRF11 directly transcribed and activated CCCH39 expression through interaction with cis-acting element GARE (TCTGTTG), thus promoting xylem development. This is the first finding that GRF positively regulates xylem development through CCCH39 expression activation and further suggests that PagGRF11 is a potential target for increasing wood yield.
Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 non-transposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.
The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic, and statistical refinements permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is described for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position Specific Iterated BLAST (PSLBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities.
The cloning of genes encoding mammalian DNA binding transcription factors for RNA polymerase II has provided the opportunity
to analyze the structure and function of these proteins. This review summarizes recent studies that define structural domains
for DNA binding and transcriptional activation functions in sequence-specific transcription factors. The mechanisms by which
these factors may activate transcriptional initiation and by which they may be regulated to achieve differential gene expression
are also discussed.
The yeast SNF-SWI complex is required for transcriptional activation of diverse genes and has been shown to alter chromatin
structure. The complex has at least 10 components, including SNF2/SWI2, SNF5, SNF6, SWI1/ADR6, and SWI3, and has been widely
conserved in eukaryotes. Here we report the characterization of a new component. We identified proteins that interact in the
two-hybrid system with the N-terminal region of SNF2, preceding the ATPase domain. In addition to SWI3, we recovered a new
19-kDa protein, designated SNF11. Like other SNF/SWI proteins, SNF11 functions as a transcriptional activator in genetic assays.
SNF11 interacts with SNF2 in vitro and copurifies with the SNF-SWI complex from yeast cells. Using a specific antibody, we
showed that SNF11 coimmunoprecipitates with members of the SNF-SWI complex and that SNF11 is tightly and stoichiometrically
associated with the complex. Furthermore, SNF11 was detected in purified SNF-SWI complex by staining with Coomassie blue dye;
its presence previously went unrecognized because it does not stain with silver. SNF11 interacts with a 40-residue sequence
of SNF2 that is highly conserved, suggesting that SNF11 homologs exist in other organisms.
The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons,
a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST
programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering
the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program
that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining
statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using
this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration
as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST
is used to uncover several new and interesting members of the BRCT superfamily.
A barley gene encoding a novel DNA-binding protein (HRT) was identified by southwestern screening with baits containing a gibberellin phytohormone response element from an alpha-amylase promoter. The HRT gene contains two introns, the larger of which (5722 base pairs (bp)) contains a 3094-bp LINE-like element with homology to maize Colonist1. In vitro mutagenesis and zinc- and DNA-binding assays demonstrate that HRT contains three unusual zinc fingers with a CX8-9CX10CX2H consensus sequence. HRT is targeted to nuclei, and homologues are expressed in other plants. In vivo, functional tests in plant cells indicate that full-length HRT can repress expression from certain promoters including the Amy1/6-4 and Amy2/32 alpha-amylase promoters. In contrast, truncated forms of HRT containing DNA-binding domains can activate, or derepress, transcription from these promoters. Northern hybridizations indicate that HRT mRNA accumulates to low levels in various tissues. Roles for HRT in mediating developmental and phytohormone-responsive gene expression are discussed.
Expansins are a family of proteins capable of inducing stress relaxation of isolated cell walls. In earlier studies, we showed that the expression of expansin genes in deepwater rice (Oryza sativa L.) is regulated by developmental, hormonal and environmental stimuli. Here, we describe the spatial distribution pattern of expansin transcripts and proteins in tissues and organs of deepwater rice using in situ mRNA hybridization and immunohistochemical analysis. Expansin transcripts and proteins are present at high levels in the growing internodal epidermis, which has thick cell walls and acts, therefore, as a growth-limiting cell layer. Expansins are also concentrated in the differentiating vascular bundles of internodes. In the primary root, expansins are predominantly expressed in the tip region, particularly in the epidermis, differentiating vascular cylinder, and around the pericyle. Developing adventitious roots and lateral root primordia also contain high levels of expansin mRNA. In the shoot apex, expansin transcripts are abundant in the emerging leaf primordia. Our results indicate that expansins play an important role in the expansion and differentiation of plant tissues and organs.
Semiaquatic plants grow mostly in flood plains and along river beds and are adapted to survive partial submergence during periods of flooding. Among their adaptive features are the development of internal air channels (aerenchyma) that facilitate aeration of submerged organs and the capacity for rapid elongation when the plants become partially covered by floodwaters. In addition to its importance as a crop plant, deepwater rice is also excellent for studying basic aspects of plant growth. The growth response is induced by an environmental signal and is mediated by at least three interacting hormones, namely ethylene, ABA, and GA. Internodal elongation is based on increased cell-division activity and enhanced cell elongation in well-delineated zones of the internode. This allows one to study both processes of growth in an integrated manner. Also, the unusually high growth rates magnify growth-related cellular, physiological, biochemical, and molecular processes, thereby facilitating their analysis. In addition to yielding fundamental insights into the growth process, studies of internodal elongation in deepwater rice may ultimately help to identify genes that could confer at least limited elongation capacity onto modern, high-yielding cultivars.
Os-GRF1 (Oryza sativa-GROWTH-REGULATING FACTOR1) was identified in a search for genes that are differentially expressed in the intercalary meristem of deepwater rice (Oryza sativa L.) internodes in response to gibberellin (GA). Os-GRF1 displays general features of transcription factors, contains a functional nuclear localization signal, and has three regions with similarities to sequences in the database. One of these regions is similar to a protein interaction domain of SWI2/SNF2, which is a subunit of a chromatin-remodeling complex in yeast. The two other domains are novel and found only in plant proteins of unknown function. To study its role in plant growth, Os-GRF1 was expressed in Arabidopsis. Stem elongation of transformed plants was severely inhibited, and normal growth could not be recovered by the application of GA. Our results indicate that Os-GRF1 belongs to a novel class of plant proteins and may play a regulatory role in GA-induced stem elongation.
Several eukaryotic transcription factors such as Sp1 or Oct1 contain glutamine-rich domains that mediate transcriptional activation. In human cells, promoter-proximally bound glutamine-rich activation domains activate transcription poorly in the absence of acidic type activators bound at distal enhancers, but synergistically stimulate transcription with these remote activators. Glutamine-rich activation domains were previously reported to also function in the fission yeast Schizosaccharomyces pombe but not in the budding yeast Saccharomyces cerevisiae, suggesting that budding yeast lacks this pathway of transcriptional activation. The strong interaction of an Sp1 glutamine-rich domain with the general transcription factor TAF(II)110 (TAF(II)130), and the absence of any obvious TAF(II)110 homologue in the budding yeast genome, seemed to confirm this notion. We reinvestigated the phenomenon by reconstituting in the budding yeast an enhancer-promoter architecture that is prevalent in higher eukaryotes but less common in yeast. Under these conditions, we observed that glutamine-rich activation domains derived from both mammalian and yeast transcription factors activated only poorly on their own but strongly synergized with acidic activators bound at the remote enhancer position. The level of activation by the glutamine-rich activation domains of Sp1 and Oct1 in combination with a remote enhancer was similar in yeast and human cells. We also found that mutations in a glutamine-rich domain had similar phenotypes in budding yeast and human cells. Our results show that glutamine-rich activation domains behave very similarly in yeast and mammals and that their activity in budding yeast does not depend on the presence of a TAF(II)110 homologue.
GAGA is a nuclear protein encoded by the Trithorax-like gene in Drosophila that is expressed in at least two isoforms generated by alternative splicing. By means of its specific interaction with DNA, GAGA has been involved in several nuclear transactions including regulation of gene expression. Here we have studied the GAGA(519) isoform as a transcription factor. In vitro, the transactivation domain has been assigned to the 93 C-terminal residues that correspond to a glutamine-rich domain (Q-domain). It presents an internal modular structure and acts independently of the rest of the protein. In vivo, in Drosophila SL2 cells, Q-domain can transactivate reporter genes either in the form of GAGA or Gal4BD-Q fusions, whereas a GAGA mutant deleted of the Q-domain cannot. Our results give support to the notion that GAGA can function as a transcription activating factor.
An extensive effort of the International Rice Genome Sequencing Project (IRGSP) has resulted in rapid accumulation of genome sequence, and >137 Mb has already been made available to the public domain as of August 2001. This requires a high-throughput annotation scheme to extract biologically useful and timely information from the sequence data on a regular basis. A new automated annotation system and database called Rice Genome Automated Annotation System (RiceGAAS) has been developed to execute a reliable and up-to-date analysis of the genome sequence as well as to store and retrieve the results of annotation. The system has the following functional features: (i) collection of rice genome sequences from GenBank; (ii) execution of gene prediction and homology search programs; (iii) integration of results from various analyses and automatic interpretation of coding regions; (iv) re-execution of analysis, integration and automatic interpretation with the latest entries in reference databases; (v) integrated visualization of the stored data using web-based graphical view. RiceGAAS also has a data submission mechanism that allows public users to perform fully automated annotation of their own sequences. The system can be accessed at http://RiceGAAS.dna.affrc.go.jp/.
The genome of the japonica subspecies of rice, an important cereal and model monocot, was sequenced and assembled by whole-genome
shotgun sequencing. The assembled sequence covers 93% of the 420-megabase genome. Gene predictions on the assembled sequence
suggest that the genome contains 32,000 to 50,000 genes. Homologs of 98% of the known maize, wheat, and barley proteins are
found in rice. Synteny and gene homology between rice and the other cereal genomes are extensive, whereas synteny with Arabidopsis is limited. Assignment of candidate rice orthologs to Arabidopsis genes is possible in many cases. The rice genome sequence provides a foundation for the improvement of cereals, our most
important crops.
We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp.indica, by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional
coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and
most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences.
We collected and completely sequenced 28,469 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. Nipponbare. Through homology searches of publicly available sequence data, we assigned tentative protein functions to
21,596 clones (75.86%). Mapping of the cDNA clones to genomic DNA revealed that there are 19,000 to 20,500 transcription units
in the rice genome. Protein informatics analysis against the InterPro database revealed the existence of proteins presented
in rice but not in Arabidopsis. Sixty-four percent of our cDNAs are homologous to Arabidopsis proteins.
Deepwater rice (Oryza sativa L.) responds to partial submergence by rapid elongation of the internodes. The elongation of intact plants was measured during 7 days of submergence using angular transducers. Growth rates began to increase within 3 to 4 h upon submergence and peaked after 3 days; they were higher in the light than in the dark. The composition of the gas phase in the internodal air spaces was analyzed at different times after partial submergence. In the light, the O2 concentrations in internal gas compartments of intact plants dropped initially, but recovered largely within 90 min. During longer periods of submergence, the internal O2 concentration followed a diurnal pattern with O2 levels being lower during the night than during the day. An O2 gradient was found from the apical parts of the plant near the water surface to the basal parts of the shoot.
Concentrations of CO2 changed with a pattern inverse to that of the O2concentrations. The level of ethylene in the internodal lacunae increased upon submergence and reached 1μl-liter⁻¹ after 72 h. It was higher at the end of the dark period than during the day.
The gas exchange of the submerged parts of the plant seems to depend mainly on mass flow of air from the atmosphere to the root system. Mass flow through this pathway was determined at different pressure gradients and was compared to the intake of air into plants as established in earlier investigations. A significant decrease in gas flow resistance found during 7 days of submergence may constitute a long-term adaptation to flooding.
An extensive effort of the International Rice Genome Sequencing Project (IRGSP) has resulted in rapid accumulation of genome
sequence, and >137 Mb has already been made available to the public domain as of August 2001. This requires a high-throughput
annotation scheme to extract biologically useful and timely information from the sequence data on a regular basis. A new automated
annotation system and database called Rice Genome Automated Annotation System (RiceGAAS) has been developed to execute a reliable
and up-to-date analysis of the genome sequence as well as to store and retrieve the results of annotation. The system has
the following functional features: (i) collection of rice genome sequences from GenBank; (ii) execution of gene prediction
and homology search programs; (iii) integration of results from various analyses and automatic interpretation of coding regions;
(iv) re-execution of analysis, integration and automatic interpretation with the latest entries in reference databases; (v)
integrated visualization of the stored data using web-based graphical view. RiceGAAS also has a data submission mechanism
that allows public users to perform fully automated annotation of their own sequences. The system can be accessed at http://RiceGAAS.dna.affrc.go.jp/.
Many transcription factors contain proline- or glutamine-rich activation domains. Here it is shown that simple homopolymeric stretches of these amino acids can activate transcription when fused to the DNA binding domain of GAL4 factor. In vitro, activity increased with polymer length, whereas in cell transfection assays maximal activity was achieved by 10 to 30 glutamines or about 10 prolines. Similar results were obtained when glutamine stretches were placed within a [GAL4]-VP16 chimeric protein. Because these stretches are encoded by rapidly evolving triplet repeats (microsatellites), they may be the main cause for modulation of transcription factor activity and thus result in subtle or overt genomic effects.
Maize Dof1, one of the plant-specific Dof transcription factors, is involved in light-regulated gene expression. To elucidate the molecular mechanism underlying the activity of Dof1, in vivo functional analyses were carried out using transient expression assays with maize mesophyll protoplasts. The results suggest that the Dof domain alone, the region conserved among Dof factors, can mediate interaction with DNA in vivo and distinct Dof1 activities in greening and etiolated protoplasts. A region rich in basic amino acids was identified as a nuclear localization signal. Deletion analysis defined the transcriptional activation domain of 48 amino acids located in the C-terminus of Dof1. This activation domain was also found to be functional in both human cells and yeast, implying that Dof1 may stimulate transcription through a mechanism evolutionarily conserved among eukaryotes. A computer homology search with known transcription factors revealed that the activation domain of Dof1 displayed only a limited similarity to Activation domain II of animal transcription factor GATA-4. Mutational analysis revealed the critical role of a tryptophan residue within the activation domain of Dof1, as had been shown in Activation domain II of GATA-4.
Fourteen putative rice (Oryza sativa) beta-expansin genes, Os-EXPB1 through Os-EXPB14, were identified in the expressed sequence tag and genomic databases. The DNA and deduced amino acid sequences are highly conserved in all 14 beta-expansins. They have a series of conserved C (cysteine) residues in the N-terminal half of the protein, an HFD (histidine-phenylalanine-aspartate) motif in the central region, and a series of W (tryptophan) residues near the carboxyl terminus. Five beta-expansin genes are expressed in deepwater rice internodes, with especially high transcript levels in the growing region. Expression of four beta-expansin genes in the internode was induced by treatment with gibberellin and by wounding. The wound response resulted from excising stem sections or from piercing pinholes into the stem of intact plants. The level of wound-induced beta-expansin transcripts declined rapidly 5 h after cutting of stem sections. We conclude that the expression of beta-expansin genes is correlated with rapid elongation of deepwater rice internodes, it is induced by gibberellin and wounding, and wound-induced beta-expansin mRNA appears to turn over rapidly.
Expansins were first identified as cell-wall-loosening proteins that, at least in part, mediate pH-dependent extension of the plant cell wall and growth of the cell. More recently, it has been realized that expansins belong to two protein families, the alpha-and beta-expansins, and that they appear to be involved in regulating, besides cell expansion, a variety of plant processes, including morphogenesis, softening of fruits, and growth of the pollen tube of grasses through the stigma and the style. The Arabidopsis genome contains 26 alpha-expansin genes and the rice genome at least 26. There are more beta-expansin genes in monocots than in dicots, at least 14 in rice and five in Arabidopsis. Expansin genes are differentially regulated by environmental and hormonal signals, and hormonal regulatory elements have been found in their promoter regions. An analysis of exon/intron structure led to the hypothesis that alpha-and beta-expansins evolved from a common ancestral gene.
The Pro-rich regions, found in a subset of plant bZIP transcription factors, including G-box-binding factors (GBFs) of Arabidopsis thaliana, are thought to be deeply involved in transcriptional regulation. However, the molecular mechanisms of the Pro-rich region-mediated transcriptional regulation are still largely unknown. Here we report evidence showing that two closely related Arabidopsis proteins, designated GPRI1 and GPRI2, containing a GARP DNA-binding domain, are likely partners of one or more GBFs. The results of yeast two-hybrid assays and in vitro binding assays indicated that GPRI1 can interact with the Pro-rich regions of GBF1 and GBF3. GPRI2 interacted with the Pro-rich region of GBF1. GPRI1 and GPRI2 transactivated transcription in yeast. In GPRI1 the region responsible for this activation was mapped in the N-terminal third of the protein. Transient assays showed that in Arabidopsis cells not only the N-terminal but also the C-terminal regions of GPRI1 can function as a separable activation domain. GPRI1 and GPRI2 may function in some promoters in concert with a GBF through interaction with its Pro-rich region to enhance the transcriptional level of the corresponding genes.
Previously, we identified a novel rice gene, GROWTH-REGULATING FACTOR1 (OsGRF1), which encodes a putative transcription factor that appears to play a regulatory role in stem elongation. We now describe the GRF gene family of Arabidopsis thaliana (AtGRF), which comprises nine members. The deduced AtGRF proteins contain the same characteristic regions--the QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys) domains--as do OsGRF1 and related proteins in rice, as well as features indicating a function in transcriptional regulation. Most of the AtGRF genes are strongly expressed in actively growing and developing tissues, such as shoot tips, flower buds, and roots, but weakly in mature stem and leaf tissues. Overexpression of AtGRF1 and AtGRF2 resulted in larger leaves and cotyledons, as well as in delayed bolting of the inflorescence stem when compared to wild-type plants. In contrast, triple insertional null mutants of AtGRF1-AtGRF3 had smaller leaves and cotyledons, whereas single mutants displayed no changes in phenotype and double mutants displayed only minor ones. The alteration of leaf growth in overexpressors and triple mutants was based on an increase or decrease in cell size, respectively. These results indicate that AtGRF proteins play a role in the regulation of cell expansion in leaf and cotyledon tissues.
We have shown previously that ethylene, which accumulates in the air spaces of submerged stem sections of rice (Oryza sativa L. cv "Habiganj Aman II"), is involved in regulating the growth response caused by submergence. The role of gibberellins in the submergence response was studied using tetcyclacis (TCY), a new plant growth retardant, which inhibits gibberellin biosynthesis. Stem sections excised from plants that had been watered with a solution of 1 micromolar TCY for 7 to 10 days did not elongate when submerged in the same solution or when exposed to 1 microliter per liter ethylene in air. Gibberellic acid (GA(3)) at 0.3 micromolar overcame the effect of TCY and restored the rapid internodal elongation in submerged and ethylene-treated sections to the levels observed in control sections that had not been treated with TCY. The effect of 0.01 to 0.2 micromolar GA(3) on internodal elongation was enhanced two- to eight-fold when 1 microliter per liter ethylene was added to the air passing through the chamber in which the sections were incubated. GA(3) and ethylene caused a similar increase in cell division and cell elongation in rice internodes. Thus, ethylene may cause internodal elongation in rice by increasing the activity of endogenous GAs. In internodes from which the leaf sheath had been peeled off, growth in response to submergence, ethylene and GA(3) was severely inhibited by light.
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(Received March 23, 2004; Accepted April 14, 2004)
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