Publications (27)118.88 Total impact
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Article: Molecular cloning, characterization, and stress-responsive expression of genes encoding glycine-rich RNA-binding proteins in Camelina sativa L.
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ABSTRACT: Camelina sativa L. is an oil-seed crop that has potential for biofuel applications. Although the importance of C. sativa as a biofuel crop has increased in recent years, reports demonstrating the stress responsiveness of C. sativa and characterizing the genes involved in stress response of C. sativa have never been published. Here, we isolated and characterized three genes encoding glycine-rich RNA-binding proteins (GRPs) from camelina: CsGRP2a, CsGRP2b, and CsGRP2c. The three CsGRP2 proteins were very similar in amino acid sequence and contained a well-conserved RNA-recognition motif at the N-terminal region and glycine-rich domain at the C-terminal region. To understand the functional roles of CsGRP2s under stress conditions, we investigated the expression patterns of CsGRP2s under various environmental stress conditions. The expressions of the three CsGRP2s were highly up-regulated under cold stress. The expression of CsGRP2a was up-regulated under salt or dehydration stress, whereas the transcript levels of CsGRP2b and CsGRP2c were decreased under salt or dehydration stress conditions. The three CsGRP2s had the ability to complement cold-sensitive Escherichia coli mutants at low temperatures and harbored transcription anti-termination and nucleic acid-melting activities, indicating that the CsGRP2s possess RNA chaperone activity. The CsGRP2a protein was localized to both the nucleus and the cytoplasm. Expression of CsGRP2a in cold-sensitive Arabidopsis grp7 mutant plants resulted in decreased electrolyte leakage at freezing temperatures. Collectively, these results suggest that the stress-responsive CsGRP2s play a role as an RNA chaperone during the stress adaptation process in camelina.Plant Physiology and Biochemistry 04/2013; 68C:44-51. · 2.84 Impact Factor -
Article: MYB46-Mediated Transcriptional Regulation of Secondary Wall Biosynthesis.
Molecular Plant 08/2012; 5(5):961-3. · 5.55 Impact Factor -
Article: MYB46 directly regulates the gene expression of secondary wall-associated cellulose synthases in Arabidopsis.
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ABSTRACT: Cellulose is the most abundant biopolymer on Earth. In the secondary cell walls of Arabidopsis, three cellulose synthases (CESA4, CESA7, and CESA8) are necessary for cellulose production. Little is known about how the expression of these CESA genes is regulated. We recently identified a cis-regulatory element ('M46RE') recognized by MYB46, which is a master switch for secondary wall formation in Arabidopsis. A genome-wide survey of promoter sequences for the M46RE led to a hypothesis that MYB46 may function as a direct regulator of all three secondary wall-associated cellulose synthases, CESA4, CESA7 and CESA8. We tested this hypothesis using several lines of experimental evidence. All of the three CESA genes are highly upregulated in both constitutive and inducible over-expression of MYB46 in planta. Using a steroid receptor-based inducible activation system, we show that MYB46 directly activates the transcription of the three CESA genes. We then used electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) analysis to confirm that MYB46 protein directly binds the promoters of the three CESA genes both in vitro and in vivo. Furthermore, ectopic upregulation of MYB46 resulted in a significant increase of crystalline cellulose content in Arabidopsis. Taken together, we identify MYB46 as a transcription factor that directly regulates all three secondary wall-associated CESA genes. Yeast-one hybrid screening identified additional transcription factors that regulate the CESAs. However, none of the putative regulators appears to be regulated by MYB46 (Ko et al., 2009; Kim et al., 2012), suggesting multifaceted nature of the transcriptional regulation of secondary wall cellulose biosynthesis. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.The Plant Journal 08/2012; · 6.16 Impact Factor -
Article: Biotechnological improvement of lignocellulosic feedstock for enhanced biofuel productivity and processing
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ABSTRACT: Secondary walls have recently drawn research interest as a primary source of sugars for liquid biofuel production. Secondary walls are composed of a complex mixture of the structural polymers cellulose, hemicellulose, and lignin. A matrix of hemicellulose and lignin surrounds the cellulose component of the plant’s cell wall in order to protect the cell from enzymatic attacks. Such resistance, along with the variability seen in the proportions of the major components of the mixture, presents process design and operating challenges to the bioconversion of lignocellulosic biomass to fuel. Expanding bioenergy production to the commercial scale will require a significant improvement in the growth of feedstock as well as in its quality. Plant biotechnology offers an efficient means to create “targeted” changes in the chemical and physical properties of the resulting biomass through pathway-specific manipulation of metabolisms. The successful use of the genetic engineering approach largely depends on the development of two enabling tools: (1) the discovery of regulatory genes involved in key pathways that determine the quantity and quality of the biomass, and (2) utility promoters that can drive the expression of the introduced genes in a highly controlled manner spatially and/or temporally. In this review, we summarize the current understanding of the transcriptional regulatory network that controls secondary wall biosynthesis and discuss experimental approaches to developing-xylem-specific utility promoters. KeywordsSecondary wall–Biomass feedstock–Biofuel–Transcriptional regulator–Utility promoterPlant Biotechnology Reports 04/2012; 5(1):1-7. · 1.19 Impact Factor -
Article: Tissue-type-specific transcriptome analysis identifies developing xylem-specific promoters in poplar.
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ABSTRACT: Plant biotechnology offers a means to create novel phenotypes. However, commercial application of biotechnology in crop improvement programmes is severely hindered by the lack of utility promoters (or freedom to operate the existing ones) that can drive gene expression in a tissue-specific or temporally controlled manner. Woody biomass is gaining popularity as a source of fermentable sugars for liquid fuel production. To improve the quantity and quality of woody biomass, developing xylem (DX)-specific modification of the feedstock is highly desirable. To develop utility promoters that can drive transgene expression in a DX-specific manner, we used the Affymetrix Poplar Genome Arrays to obtain tissue-type-specific transcriptomes from poplar stems. Subsequent bioinformatics analysis identified 37 transcripts that are specifically or strongly expressed in DX cells of poplar. After further confirmation of their DX-specific expression using semi-quantitative PCR, we selected four genes (DX5, DX8, DX11 and DX15) for in vivo confirmation of their tissue-specific expression in transgenic poplars. The promoter regions of the selected DX genes were isolated and fused to a β-glucuronidase (GUS)-reported gene in a binary vector. This construct was used to produce transgenic poplars via Agrobacterium-mediated transformation. The GUS expression patterns of the resulting transgenic plants showed that these promoters were active in the xylem cells at early seedling growth and had strongest expression in the developing xylem cells at later growth stages of poplar. We conclude that these DX promoters can be used as a utility promoter for DX-specific biomass engineering.Plant Biotechnology Journal 03/2012; 10(5):587-96. · 5.44 Impact Factor -
Article: Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis.
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ABSTRACT: While many aspects of primary cell wall have been extensively elucidated, our current understanding of secondary wall biosynthesis is limited. Recently, transcription factor MYB46 has been identified as a master regulator of secondary wall biosynthesis in Arabidopsis thaliana. To gain better understanding of this MYB46-mediated transcriptional regulation, we analyzed the promoter region of a direct target gene, AtC3H14, of MYB46 and identified a cis-acting regulatory motif that is recognized by MYB46. This MYB46-responsive cis-regulatory element (M46RE) was further characterized and shown to have an eight-nucleotide core motif, RKTWGGTR. We used electrophoretic mobility shift assay, transient transcriptional activation assay and chromatin immunoprecipitation analysis to show that the M46RE was necessary and sufficient for MYB46-responsive transcription. Genome-wide analysis identified that the frequency of M46RE in the promoters were highly enriched among the genes upregulated by MYB46, especially in the group of genes involved in secondary wall biosynthesis.Plant Molecular Biology 03/2012; 78(4-5):489-501. · 4.15 Impact Factor -
Article: Novel aspects of transcriptional regulation in the winter survival and maintenance mechanism of poplar.
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ABSTRACT: Temperate woody plants have developed sophisticated winter survival and maintenance mechanisms that enable them to adapt rapidly to the annual cycle of environmental changes. Here, we demonstrate notable aspects of the transcriptional regulation adopted by poplar in winter/dormancy, employing biochemical and whole transcriptome analysis, and showing high levels of transcriptional activity in a broad spectrum of genes during the dormancy period. A total of 3237 probe sets upregulated more than threefold in winter/dormancy stems over summer/active-growth stems were identified. As expected, genes related to cold hardiness and defense were over-represented. Carbohydrate biosynthesis and transport-related genes were also actively expressed in winter/dormancy stems. Further biochemical analyses verified the dormancy/winter transcription phenotype. More than 60% of the winter upregulated transcription factors (TFs) were related to either biotic or abiotic stress. This finding substantiates that the major transcriptional network of winter/dormancy stems is related to stress tolerance, such as dehydration, cold tolerance and defense. Furthermore, during winter/dormancy, preferential expression of genes involved in cell wall biosynthesis or modification, indirect transcriptional regulation (RNA metabolism) and chromatin modification/remodeling were observed. Taken together, these findings show that regulation of gene expression associated with winter survival and maintenance extends beyond control by promoter-binding TFs to include regulation at the post-transcriptional and chromatin levels.Tree Physiology 03/2011; 31(2):208-25. · 2.88 Impact Factor -
Article: Ectopic expression of MYB46 identifies transcriptional regulatory genes involved in secondary wall biosynthesis in Arabidopsis.
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ABSTRACT: MYB46 functions as a transcriptional switch that turns on the genes necessary for secondary wall biosynthesis. Elucidating the transcriptional regulatory network immediately downstream of MYB46 is crucial to our understanding of the molecular and biochemical processes involved in the biosynthesis and deposition of secondary walls in plants. To gain insights into MYB46-mediated transcriptional regulation, we first established an inducible secondary wall thickening system in Arabidopsis by expressing MYB46 under the control of dexamethasone-inducible promoter. Then, we used an ATH1 GeneChip microarray and Illumina digital gene expression system to obtain a series of transcriptome profiles with regard to the induction of secondary wall development. These analyses allowed us to identify a group of transcription factors whose expression coincided with or preceded the induction of secondary wall biosynthetic genes. A transient transcriptional activation assay was used to confirm the hierarchical relationships among the transcription factors in the network. The in vivo assay showed that MYB46 transcriptionally activates downstream target transcription factors, three of which (AtC3H14, MYB52 and MYB63) were shown to be able to activate secondary wall biosynthesis genes. AtC3H14 activated the transcription of all of the secondary wall biosynthesis genes tested, suggesting that AtC3H14 may be another master regulator of secondary wall biosynthesis. The transcription factors identified here may include direct activators of secondary wall biosynthesis genes. The present study discovered novel hierarchical relationships among the transcription factors involved in the transcriptional regulation of secondary wall biosynthesis, and generated several testable hypotheses.The Plant Journal 09/2009; 60(4):649-65. · 6.16 Impact Factor -
Article: Rootstock-induced dwarfing in cherries is caused by differential cessation of terminal meristem growth and is triggered by rootstock-specific gene regulation.
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ABSTRACT: Use of dwarfing rootstocks has dramatically increased the profitability of fruit production by reducing production costs, reduced chemical use and higher density plantings. Despite the importance of rootstock-induced dwarfing, the cause of this phenomenon is not known. Using two commercially available graft combinations consisting of a sweet cherry scion, 'Bing', on a dwarfing rootstock (Gi5) or a semi-vigorous rootstock (Gi6), we discovered that the difference in grafted tree height was due to a significantly earlier cessation of terminal meristem growth of the scion on Gi5 compared to Gi6 rootstock, rather than shorter metamer length. We then carried out cDNA-AFLP analysis to investigate differential gene expression between the two graft combinations. Transcript-derived fragments (TDFs) identified as differentially expressed were cloned and printed on microarrays for further confirmation of the differential expression. A total of 99 TDFs were identified as differentially expressed between the 'Bing'/Gi5 and 'Bing'/Gi6 samples, including genes involved in transcription regulation, brassinosteroid signaling, flavonoid metabolism and cell wall biosynthesis or modification. Rootstock vigor has a significant effect on gene expression at the scion and the graft union. Timing of the differential gene expression in the dwarf trees coincides with the earlier cessation of terminal shoot growth, suggesting that these differentially expressed genes may be involved in the dwarfing phenomenon.Tree Physiology 06/2009; 29(7):927-36. · 2.88 Impact Factor -
Article: Transcriptional profiles of the annual growth cycle in Populus deltoides.
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ABSTRACT: Cycling between vegetative growth and dormancy is an important adaptive mechanism in temperate woody plants. To gain insights into the underlying molecular mechanisms, we carried out global transcription analyses on stem samples from poplar (Populus deltoides Bartr. ex Marsh.) trees grown in the field and in controlled environments. Among seasonal changes in the transcriptome, up-regulation of defense-related genes predominated in early winter, whereas signaling-related genes were up-regulated during late winter. Cluster analysis of the differentially expressed genes showed that plants regulated seasonal growth by integrating environmental factors with development. Short day lengths induced some cold-associated genes without concomitant low temperature exposure, and enhanced the expression of some genes when combined with low temperature exposure. These mechanisms appear to maintain closer synchrony between cold hardiness and climate than would be achieved through responses to temperature alone.Tree Physiology 04/2008; 28(3):321-9. · 2.88 Impact Factor -
Article: Optimizing lignocellulosic feedstock for improved biofuel productivity and processing
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ABSTRACT: Liquid fuels from lignocellulosic materials, such as wood, offer an attractive alternative to fossil fuel. Lignocellulosic biomass is composed of a complex mixture of cellulose, hemicellulose, and lignin. As structural polymers, the matrix of hemicellulose and lignin surround the cellulose component of the plant cell wall to protect it against enzymatic attack. The resistance of this complex to enzymatic attack is a major impediment to commercial bioconversion of lignocellulosic biomass. Furthermore, proportional variability within the mixture of the three major components varies, depending on the species of feedstock used, growing site, climate, age, and the part of the plant harvested. This fact presents process design and operating challenges for the fermentation of sugars derived from lignocellulosic feedstocks. The essentially uncontrolled variability of biomass properties also presents major difificulties in understanding the fundamental processes involved in limiting the digestion of cell walls to fermentable sugars. Energy crops must be optimized for ‘low-input production’ systems and efficiency of pretreatment and hydrolysis to derive sugars for further fermentation to produce ethanol. Recent advances in the molecular biology of wood formation and cell-wall biosynthesis have provided new tools to tailor the biomass composition. This review summarizes recent advances in the understanding of the molecular mechanisms regulating the biochemical and developmental processes of woody biomass production. Potential areas of future research in optimizing lignocellulosic feedstock for bioenergy production are identified. © 2007 Society of Chemical Industry and John Wiley & Sons, LtdBiofuels Bioproducts and Biorefining 08/2007; 1(2):135 - 146. · 4.74 Impact Factor -
Article: ANAC012, a member of the plant-specific NAC transcription factor family, negatively regulates xylary fiber development in Arabidopsis thaliana.
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ABSTRACT: Vascular plants evolved to have xylem that provides physical support for their growing body and serves as a conduit for water and nutrient transport. In a previous study, we used comparative-transcriptome analyses to select a group of genes that were upregulated in xylem of Arabidopsis plants undergoing secondary growth. Subsequent analyses identified a plant-specific NAC-domain transcription factor gene (ANAC012) as a candidate for genetic regulation of xylem formation. Promoter-GUS analyses showed that ANAC012 expression was preferentially localized in the (pro)cambium region of inflorescence stem and root. Using yeast transactivation analyses, we confirmed the function of ANAC012 as a transcriptional activator, and identified an activation domain in the C terminus. Ectopic overexpression of ANAC012 in Arabidopsis (35S::ANAC012 plants) dramatically suppressed secondary wall deposition in the xylary fiber and slightly increased cell-wall thickness in the xylem vessels. Cellulose compositions of the cell wall were decreased in the inflorescent stems and roots of 35S::ANAC012 plants, probably resulting from defects in xylary fiber formation. Our data suggest that ANAC012 may act as a negative regulator of secondary wall thickening in xylary fibers.The Plant Journal 07/2007; 50(6):1035-48. · 6.16 Impact Factor -
Article: Global comparative transcriptome analysis identifies gene network regulating secondary xylem development in Arabidopsis thaliana.
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ABSTRACT: Our knowledge of the genetic control of wood formation (i.e., secondary growth) is limited. Here, we present a novel approach to unraveling the gene network regulating secondary xylem development in Arabidopsis, which incorporates complementary platforms of comparative-transcriptome analyses such as "digital northern" and "digital in situ" analysis. This approach effectively eliminated any genes that are expressed in either non-stem tissues/organs ("digital northern") or phloem and non-vascular regions ("digital in situ"), thereby identifying 52 genes that are upregulated only in the xylem cells of secondary growth tissues as "core xylem gene set". The proteins encoded by this gene set participate in signal transduction, transcriptional regulation, cell wall metabolism, and unknown functions. Five of the seven signal transduction-related genes represented in the core xylem gene set encode the essential components of ROP (Rho-related GTPase from plants) signaling cascade. Furthermore, the analysis of promoter sequences of the core xylem gene set identified a novel cis-regulatory element, ACAAAGAA. The functional significances of this gene set were verified by several independent experimental and bioinformatics methods.Molecular and General Genetics 01/2007; 276(6):517-31. · 2.63 Impact Factor -
Article: Upregulation of an Arabidopsis RING-H2 gene, XERICO, confers drought tolerance through increased abscisic acid biosynthesis.
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ABSTRACT: RING (really interesting new gene) zinc-finger proteins have important regulatory roles in the development of a variety of organisms. The XERICO gene encodes a small protein (162 amino acids) with an N-terminal trans-membrane domain and a RING-H2 zinc-finger motif located at the C-terminus. In silico gene-expression analysis indicated that XERICO is induced by salt and osmotic stress. Compared with wild-type (WT) Arabidopsis plants, transgenic plants overexpressing XERICO (35S::XERICO) exhibited hypersensitivity to salt and osmotic stress and exogenous abscisic acid (ABA) during germination and early seedling growth. When subjected to a drought treatment, transcriptional upregulation of a key ABA-biosynthesis gene, AtNCED3, was much faster and stronger in 35S::XERICO plants compared with WT plants. Further, upregulation of XERICO substantially increased cellular ABA levels. The adult 35S::XERICO plants, in contrast to early seedling growth, showed a marked increase in their tolerance to drought stress. Yeast two-hybrid screening indicated that XERICO interacts with an E2 ubiquitin-conjugating enzyme (AtUBC8) and ASK1-interacting F-box protein (AtTLP9), which is involved in the ABA-signaling pathway. Affymetrix GeneChip array analysis showed that the expressions of many of the genes involved in the biosynthesis of plant hormones (e.g. ethylene, brassinosteroid, gibberellic acid) were significantly changed in the 35S::XERICO plants. These results suggest that the homeostasis of various plant hormones might be altered in 35S::XERICO plants, possibly by overaccumulation of ABA.The Plant Journal 09/2006; 47(3):343-55. · 6.16 Impact Factor -
Article: Loss of function of COBRA, a determinant of oriented cell expansion, invokes cellular defence responses in Arabidopsis thaliana.
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ABSTRACT: An Arabidopsis T-DNA insertion mutant that results in complete loss-of-function of the COBRA gene has been identified. The COBRA gene encodes a putative glycosylphosphatidylinositol (GPI)-anchored protein that modulates cellulose deposition and oriented cell expansion in roots. The loss-of-function mutant allele (named "cob-5") exhibits abnormal cell growth throughout the entire plant body and accumulates massive amounts of stress response chemicals such as anthocyanins and callose. To gain further insight into the mechanism by which COBRA affects cell growth and physiology, the whole-genome gene expression profile of cob-5 plants was compared with that of wild-type plants. Consistent with the mutant phenotype, many genes involved in anthocyanin biosynthesis were up-regulated in the cob-5 plants, whereas genes involved in cell elongation were down-regulated. The most striking feature of the gene expression profile of cob-5 was the massive and co-ordinate induction of defence- and stress-related genes, many of which are regulated by the plant stress signal jasmonic acid (JA). Indeed, the cob-5 plants over-accumulated JA by nearly 8-fold compared with wild-type plants. Furthermore, induction of cell elongation defects in conditional allele cob-3 plants triggers the expression of a defence-responsive gene. These results provide potential clues to the mechanisms by which plant cells initially perceive biotic stress at the cell surface.Journal of Experimental Botany 02/2006; 57(12):2923-36. · 5.36 Impact Factor -
Article: Developmental and seasonal expression of PtaHB1, a Populus gene encoding a class III HD-Zip protein, is closely associated with secondary growth and inversely correlated with the level of microRNA (miR166).
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ABSTRACT: In contrast to our knowledge of the shoot apical meristem, our understanding of cambium meristem differentiation and maintenance is limited. Class III homeodomain leucine-zipper (HD-Zip) proteins have been shown to play a regulatory role in vascular differentiation. The hybrid aspen (Populus tremulaxPopulus alba) class III HD-Zip transcription factor (PtaHB1) and microRNA 166 (Pta-miR166) family were cloned from hybrid aspen using a combination of in silico and polymerase chain reaction methods. Expression analyses of PtaHB1 and Pta-miR166 were performed by Northern blot analysis. The expression of PtaHB1 was closely associated with wood formation and regulated both developmentally and seasonally, with the highest expression during the active growing season. Also, its expression was inversely correlated with the level of Pta-miR166. Pta-miR166-directed cleavage of PtaHB1 in vivo was confirmed using modified 5'-rapid amplification of cDNA ends (RACE). The expression of Pta-miR166 was much higher in the winter than in the growing seasons, suggesting seasonal and developmental regulation of microRNA in this perennial plant species.New Phytologist 02/2006; 169(3):469-78. · 6.64 Impact Factor -
Article: Transcriptome profiling of vertical stem segments provides insights into the genetic regulation of secondary growth in hybrid aspen trees.
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ABSTRACT: In order to better understand the genetic regulation of secondary growth in hybrid aspen (Populus tremula L.xP. alba L.), we carried out a series of cDNA-amplified fragment length polymorphism (AFLP)-based transcriptome analyses in vertical stem segments that represent a gradient of developmental stages with regard to secondary growth. This approach allowed us to screen >80% of the transcriptome expressed in six samples and identify genes differentially expressed with the progress of secondary growth, in a tissue-specific manner. Of the 76,800 transcript-derived fragments (TDFs) analyzed, 271 TDFs were selected and sequenced based on their differential expression patterns. Many of the xylem-up-regulated genes were involved in cell wall and lignin biosynthesis, while the bark-up-regulated genes had diverse functional roles. About 25% of the xylem-up-regulated TDFs analyzed were involved in the phenylpropanoid biosynthesis pathway, which produces the cell wall polymer lignin and various wood extractives. In addition, many of the TDFs showing secondary xylem-specific expression were annotated as genes not previously reported in Populus, including novel cell death proteins, cytoskeleton-interacting proteins, transporters and putative transcription factors.Plant and Cell Physiology 08/2005; 46(8):1213-25. · 4.70 Impact Factor -
Article: Large-scale computational analysis of poplar ESTs reveals the repertoire and unique features of expressed genes in the poplar genome
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ABSTRACT: Perennial woody plants differ from annual herbaceous plants in several ways and are expected to have evolved to adopt a unique repertoire and expression profiles of functional genes. Poplar, a model tree species for which a large number of ESTs are publicly available, was used to carry out a large-scale comparative analysis with the expressed sequences of eight plant species. First, we obtained 105,831 poplar ESTs from public databases and identified a set of 25,282 unigenes (i.e., tentative non-redundant sequences). The majority of the unigenes (56%) had significant matches to Arabidopsis genes. We then estimated poplar multigene families by counting the tBLASTX matches of each unigene against the poplar unigene dataset itself. Forty-seven percent of the 25,282 unigenes were subsequently organized into 3,481 multigene families 89% of which had less than five copy members. In poplar, protein kinases represent the largest family followed by GTP-binding proteins and Myb transcription factors. Several multigene families had a higher copy number in poplar than in Arabidopsis hinting potential lineage-specific proliferation of poplar protein families. Such expansion may be related to the adaptation of perennial poplars for the high degree of environmental stresses that affects growth and survival. Comparison of poplar unigenes with the Arabidopsis transcriptome revealed that genes involved in transcriptional regulation are the most divergent while metabolism-related genes are the most conserved.Molecular Breeding 12/2004; 14(4):429-440. · 2.85 Impact Factor -
Article: Arabidopsis whole-transcriptome profiling defines the features of coordinated regulations that occur during secondary growth.
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ABSTRACT: Secondary growth in the inflorescence stems of Arabidopsis plants was induced by a combination of short-day and long-day treatments. The induced stems were divided into three different stem developmental stages (i.e., immature, intermediate, and mature) with regard to secondary growth. Whole transcriptome microarrays were used to examine the changes in global gene expression occurring at the different stem developmental stages. Over 70% of the Arabidopsis transcriptome was expressed in the stem tissues. In the mature stems with secondary growth, 567 genes were upregulated 5-fold or higher and 530 were downregulated, when compared to immature stems (with no secondary growth) and 10-day old seedlings (with no inflorescence stem). The transcription phenotypes obtained from the stems at different developmental stages largely confirm the existing insights into the biochemical processes involved in the sequential events that lead to wood formation. The major difference found between the stems undergoing secondary growth and only primary growth was in the expression profiles of transcriptional regulation-and signal transduction-related genes. An analysis of several shoot apical meristem (SAM) activity-related gene expression patterns in the stems indicated that the genetic control of secondary meristem activity might be governed by a different mechanism from that of SAM. The current study established the expression patterns of many unknown genes and identified candidate genes that are involved in the genetic regulation of secondary growth. The findings described in this report should improve our understanding of the molecular mechanisms that regulate the growth and development of the stem.Plant Molecular Biology 06/2004; 55(3):433-53. · 4.15 Impact Factor -
Article: Plant body weight-induced secondary growth in Arabidopsis and its transcription phenotype revealed by whole-transcriptome profiling.
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ABSTRACT: Wood is an important raw material and environmentally cost-effective renewable source of energy. However, the molecular biology of wood formation (i.e. secondary growth) is surprisingly understudied. A novel experimental system was employed to study the molecular regulation of secondary xylem formation in Arabidopsis. First, we demonstrate that the weight carried by the stem is a primary signal for the induction of cambium differentiation and the plant hormone, auxin, is a downstream carrier of the signal for this process. We used Arabidopsis whole-transcriptome (23 K) GeneChip analysis to examine gene expression profile changes in the inflorescent stems treated for wood formation by cultural manipulation or artificial weight application. Many of the genes up-regulated in wood-forming stems had auxin responsive cis-acting elements in their promoter region, indicating auxin-mediated regulation of secondary growth. We identified 700 genes that were differentially expressed during the transition from primary growth to secondary growth. More than 40% of the genes that were up-regulated (>5x) were associated with signal transduction and transcriptional regulation. Biological significance of these regulatory genes is discussed in light of the induction and development of secondary xylem.Plant physiology 06/2004; 135(2):1069-83. · 6.53 Impact Factor
Top co-authors
Top Journals
Institutions
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2003–2012
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Michigan State University
- • Department of Horticulture
- • Department of Forestry
East Lansing, MI, USA
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2011
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Kyung Hee University
- Department of Plant and Environmental New Resources
Seoul, Seoul, South Korea
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