Shengcheng Han

• Beijing Normal University

Long noncoding RNAs (lncRNAs), which are a type of RNA exceeding 200 nucleotides and lack representative open reading frames (ORFs), have emerged as crucial regulatory molecules that modulate numerous growth processes in plants. While substantial progress has been made in understanding the functions and regulatory mechanisms of coding RNAs, the stu...

Background Transcription factors (TFs) are crucial regulators of plant growth, development, and resistance to environmental stresses. However, comprehensive understanding of the roles of TFs in speciation of Orinus, an extreme-habitat plant on the Qinghai-Xizang (Tibet) Plateau, is limited. Results Here, we identified 52 TF families, including 212...

Long non-coding RNAs (lncRNAs) are involved in plant biotic and abiotic stress responses, in which Ca²⁺ also plays a significant role. There is diversity in the regulation of different gene expressions by cytosolic Ca²⁺ ([Ca²⁺]cyt) and nucleosolic Ca²⁺ ([Ca²⁺]nuc). However, no studies have yet explored the interrelationship between lncRNAs and calc...

Intrinsically disordered proteins (IDPs) include two types of proteins: partial disordered regions (IDRs) and wholly disordered proteins (WDPs). Extensive studies focused on the proteins with IDRs, but less is known about WDPs because of their difficult-to-form folded tertiary structure. In this study, we developed a bioinformatics method for scree...

Intrinsically disordered proteins (IDPs) include two types of proteins: one contains partial disordered regions (IDRs), the other is wholly disordered proteins (WDPs). Extensive studies focused on the proteins with IDRs, but less is known about WDPs because of their difficult to form the folded tertiary structure. In this study, we developed a bioi...

Due to their immobility and possession of underground parts, plants have evolved various mechanisms to endure and adapt to abiotic stresses such as extreme temperatures, drought, and salinity. However, the contribution of long noncoding RNAs (lncRNAs) to different abiotic stresses and distinct rice seedling parts remains largely uncharacterized bey...

Simple Summary Orinus, a genus distributed in alpine regions of the Qinghai-Xizang (Tibet) Plateau (QTP), includes the following two species: O. thoroldii, predominantly in the western QTP at elevations between 3300 and 4700 m, and O. kokonoricus, in the eastern QTP at relatively low altitude between 2500 and 3400 m. However, the mechanism of long...

Many plants have the capability to accumulate anthocyanins for coloration, and anthocyanins are advantageous to human health. In the case of hulless barley (Hordeum vulgare L. var. nudum), investigation into the mechanism of anthocyanin formation is limited to the level of protein-coding genes (PCGs). Here, we conducted a comprehensive bioinformati...

Simple Summary Verticillium dahliae (Vd) is a kind of soil-borne filamentous fungus that can cause Verticillium wilt in many crops and serious damage to agricultural production. Vd 991 is a main pathogen of cotton Verticillium wilt. Previously, we isolated C17 mycosubtilin from Bacillus subtilis J15 (BS J15) broth and showed a significant inhibitor...

Microbial-plant interactions protect plants from external stimuli, releasing various elicitor that activate the plants defense response and regulate its growth. Bacillus subtilis BS-Z15 was screened from cotton inter-rhizosphere soil, antagonized various plant pathogens, and protected cotton against Verticillium dahliae. This study showed that the...

Long noncoding RNAs (lncRNAs) are distributed in various species and play critical roles in plant growth, development, and defence against stimuli. However, the lncRNA response to methyl jasmonate (MeJA) treatment has not been well characterized in Nicotiana tabacum Bright Yellow-2 (BY-2) cells, and their roles in plant defence remain elusive. Here...

Subtilisin-like proteases (SUBs), which are extensively distributed in three life domains, affect all aspects of the plant life cycle, from embryogenesis and organogenesis to senescence. To explore the role of SUBs in rice caryopsis development, we recharacterized the OsSUB gene family in rice (Oryza sativa ssp. japonica). In addition, investigatio...

Bacillus subtilis strain Z15 (BS-Z15) was isolated from the cotton field of Xinjiang, China, and characterized as an effective biocontrol agent antagonizing plant pathogen Verticillium dahliae 991 (VD-991). However, the chemical substance produced by BS-Z15 for resistance to VD-991 remains elusive. Here, a serial purification methods including HCl...

Rice calcium-dependent protein kinase 21 (OsCPK21) is specifically and highly expressed throughout reproductive development and plays a critical role in rice pollen development by indirectly regulating the MIKC*-type MADS box transcription factor. However, little is known about the function of OsCPK21 in rice caryopsis development. In this study, w...

Simple Summary Drought and salt stresses are the two major abiotic constraints on plant growth and development, as well as crop production. Previous studies have shown that several of 11 OsOSCAs complement hyperosmolality-induced [Ca²⁺]cytincreases (OICIcyt), salt stress-induced [Ca²⁺]cyt increases (SICIcyt), and the associated growth phenotype in...

Long noncoding RNAs (lncRNAs) play important regulatory roles in caryopsis development and grain size in rice. However, whether there exist differences in lncRNA expression between caryopses located on primary branches (CPB) and caryopses located on secondary branches (CSB) that contribute to their differential development remains elusive. Here, we...

Calcium acts as a universal secondary messenger that transfers developmental cues and stress signals for gene expression and adaptive growth. A prior study showed that abiotic stresses induce mutually independent cytosolic Ca²⁺ ([Ca²⁺]cyt) and nucleosolic Ca²⁺ ([Ca²⁺]nuc) increases in Arabidopsis thaliana root cells. However, gene expression networ...

Drought and salt are two major abiotic stresses that severely impact plant growth and development, as well as crop production. A previous study showed that OsOSCA1.4, one of eleven rice OSCAs (OsOSCAs), complements hyperosmolality-induced [Ca2+]cyt increases (OICIcyt), salt stress-induced [Ca2+]cyt increases (SICIcyt) and the associated growth phen...

Ethylene response factor (ERF) Group VII members generally function in regulating plant growth and development, abiotic stress response, and plant immunity in Arabidopsis. However, the detail regulatory mechanism by which Group VII ERFs mediate plant immune responses remains elusive. Here, we characterised ERF72, a member of the Group VII ERFs, as...

In plants, jasmonate ZIM-domain proteins (JAZs) act as critical regulators, interacting physically with transcription factors (TFs) and other transcriptional regulators to modulate jasmonate (JA)-responsive gene expression and participate in crosstalk with other hormone signalling pathways. Identifying novel JAZ-interacting proteins will provide ne...

Generally, the caryopses located on proximal secondary branches (CSB) have smaller grain size and slower and poorer filling rate than those on apical primary branches (CPB) in rice, which greatly limits the grain yield potential fulfillment. However, the key regulators determining the developmental differences between CPB and CSB remain elusive. He...

In rice (Oryza sativa), caryopses located on proximal secondary branches (CSBs) have smaller grain size and poorer grain filling than those located on apical primary branches (CPBs), greatly limiting grain yield. However, the molecular mechanism responsible for developmental differences between CPBs and CSBs remains elusive. In this transcriptome-w...

In plants, both hyperosmolality and salt stress induce cytosolic calcium increases within seconds, referred to as the hyperosmolality-induced [Ca²⁺]cyt increases, OICIcyt, and salt stress-induced [Ca²⁺]cyt increases, SICIcyt. Previous studies have shown that Arabidopsis reduced hyperosmolality-induced [Ca²⁺]i increase 1 (OSCA1.1) encodes a hyperosm...

Ca2+ acts as a universal second messenger in eukaryotes. In animals, a wide variety of environmental and developmental stimuli trigger Ca2+ dynamics in organelles, such as the cytoplasm, nucleus, and endoplasmic reticulum (ER). However, ER Ca2+ ([Ca2+]er) homeostasis and its contributions in cytosolic and/or nucleosolic Ca2+ dynamics in plants rema...

In flowering plants, pollen development is a critical step for reproductive success and necessarily involves complex genetic regulatory networks. Calcium-dependent protein kinases (CPKs) are plant-specific calcium sensors involved in the regulation of plant development and adaption to the environment; however, whether they play a role in regulating...

The phytohormones brassinosteroid (BR), auxin, and gibberellin (GA) regulate photomorphogenesis-related hypocotyl elongation in Arabidopsis via the cooperative interaction of BZR-ARF-PIF/DELLA (BAP/D) transcription factors/regulators. Moreover, ethylene activates the PIF3 or ERF1 pathway through EIN3/EIL1 to balance hypocotyl elongation in Arabidop...

The ERA (E. coli RAS-like protein)-related GTPase (ERG) is a nuclear-encoded GTPase with two conserved domains: a GTPase domain and a K Homology (KH) domain. ERG plays a vital role in early seed development in Antirrhinum majus. However, the mechanism that regulates seed development remains unclear. Blasting the genome sequence revealed two homolog...

The original image of Figure 6D. Western blot to detect the protein level of mitochondrial synthesized protein ATPase Subunit 6 in 1.5-DAP siliques of WT and aterg2-1 +/−. An equal amount of protein (10 μg) was loaded into each lane. Actin is used as the marker of the cytoplasm component.

WE-CLSM analysis of embryo development in WT and aterg2-1 +/− at 1.5 and 2.0 DAP.

Primer sequences used in this study.

Phylogenetic analysis of AtERGs and homologous proteins. Phylogenetic tree constructed using the predicted amino acid sequences of the 21 ERA homologous proteins in 14 species. ERA (NP_417061.1) and EcDER (double Era-like GTPase, AAC75564) were from E. coli; ERAL1 (NP_005693.1) from Homo sapiens; DrERA (NP_001122219.1) from Danio rerio; MmERA (NP_0...

Schematic of different AtERG2-eYFP constructs. The full-length and different truncated AtERG2 constructs were constructed with eYFP (green rectangles) attached to the C-terminal region. AtERG2 was divided into three different regions: 1–150 aa as the N-terminal of AtERG2 (AtERG2_N); 151–437 aa as the C-part of AtERG2 (AtERG2_C), which contains 151–...

The ovule development in WT and aterg2-1 +/− from before pollination (BP) to 2.0 DAP. The seeds were observed under a 40x objective DIC bright field microscope. “ec” = egg cells; “sy” = synergid cells; “pc” = the two polar nuclei; “cc” = central cells following the fusion of polar cells; “zy” = embryos in the zygote stage; “ea. gl” = embryos in the...

The calcium-dependent protein kinases (CDPKs) are a class of plant-specific kinase that directly bind Ca(2+) and mediate the calcium-signaling pathways to play important physiological roles in growth and development. The rice genome contains 31 CDPK genes, one of which, OsCPK21, is known to modulate the abscisic acid (ABA) and salt stress responses...

Calcium acts as a universal second messenger in both developmental processes and responses to environmental stresses. Previous research has shown that a number of stimuli can induce [Ca²⁺] increases in both the cytoplasm and nucleus in plants. However, the relationship between cytosolic and nucleosolic calcium signaling remains obscure. Here, we ge...

The change of [Ca2+]cyt or [Ca2+]nuc response to bathing medium as the stimuli in transgenic plants roots. (A) NES-YC transgenic lines. (B) NES-YC/PV-NES transgenic lines. (C) NES-YC/NLS-PV transgenic lines. (D) NLS-YC transgenic lines. (E) NLS-YC/NLS-PV transgenic lines. (F) NLS-YC/NES-PV transgenic lines. Each measurement was examined at about si...

The original image of Figure 1B: Western blot to detect the subcellular localization of PV-NES and NLS-PV in the transgenic Arabidopsis plants. An equal amount of protein (10 μg) was loaded into each lane. Histone is used as the marker of the nucleus component, and non-specific band as the marker of the cytoplasm component.

Schematics of the different PV constructs. Fusion proteins were constructed, consisting of PV with NES fused to the C-terminal region (i.e., PV-NES) and NLS to the N-terminal region (i.e., NLS-PV), and eYFP fused to the N-terminal of these two fusion proteins (i.e., eYFP-PV-NES and eYFP-NLS-PV). The 35S promoter sequence is indicated by the light-b...

The changes in CFP and CpVenus intensities that were used to calculate the apparent FRET efficiency. (A) 250-mM sorbitol treatment of the NES-YC transgenic lines shown in Figure 2B. (B) 125-mM NaCl treatment of the NES-YC transgenic lines shown in Figure 2D. (C) 250-mM sorbitol treatment of the NLS-YC transgenic lines shown in Figure 3B. (D) 125-mM...

Western blot to detect the PV levels in the WT and different transgenic plants. An equal amount of protein (10 μg) was loaded into each lane. The non-specific band is used as the marker of the loading control.

The transcription level of RD22 in response to the treatment with a high concentration of sorbitol and NaCl in 6-day-old seedlings of the WT, NES-PV, and NLS-PV plants, as detected via qRT-PCR. Error bars are SD, n = 3 biological replicates. ∗P < 0.05, ∗∗P < 0.001 (two-way ANOVA followed by Tukey’s multiple comparisons test).

The ERA ( E. coli RAS-like protein)-related GTPase (ERG) is a nuclear-encoded GTPase with two conserved domains: a GTPase domain and a K Homology domain. ERG plays a vital role in early seed development in Antirrhinum majus . However, the mechanism that regulates seed development remains unclear. Blasting the genome sequence revealed two homologies...

N-terminal-TM-C2 domain proteins (NTMC2), which share domain architecture and sequence similarity to synaptotagmins (Syts) in mammals and FAM62 (extended Syts) in metazoans, form a small gene family in plants. Previous studies showed that the Arabidopsis thaliana NTMC2 type 1.1 protein (NTMC2T1.1, named AtSyt1) possesses calcium- and membrane-bindi...

Hexokinase (HXK) as a moonlighting protein involves in glucose metabolism and signalling to regulate growth and development in plants. Therefore, the clarification for the structural properties of OsHXK7 (Oryza sativa Hexokinase 7) is essential to understand its role mechanism associated with the Glc signalling and metabolism. In this study, the st...

Jasmonates (JAs) are well-known regulators of stress, defence, and secondary metabolism in plants, with JA perception triggering extensive transcriptional reprogramming, including both activation and/or repression of entire metabolic pathways. We performed RNA sequencing based transcriptomic profiling of tobacco BY-2 cells before and after treatmen...

Glucose is the primary energy provider and the most important sugar-signalling molecule, regulating metabolites and modulating gene expression from unicellular yeast to multicellular plants and animals. Therefore, monitoring intracellular glucose levels temporally and spatially in living cells is an essential step for decoding the glucose signallin...

The growth and development of plants under drought stress depends mainly on the expression levels of various genes and modification of proteins. To clarify the molecular mechanism of drought-tolerance of plants, suppression subtractive hybridisation cDNA libraries were screened to identify drought-stress-responsive unigenes in Grimmia pilifera, and...

Summary on screening results of forward library ESTs cloned by SSH. (DOCX)

Specific primers sequences for RT-PCR of Grimmia pilifera. (DOCX)

Specific primers sequences for qRT-PCR expression analysis of drought stress-related genes in Arabidopsis. (DOCX)

Primers for PCR, cloning, and construction of vectors. (DOCX)

Reception of and response to exogenous and endogenous osmotic changes is important to sustain plant growth and development, as well as reproductive formation. Hyperosmolality-gated calcium-permeable channels (OSCA) were first characterised as an osmosensor in Arabidopsis and are involved in the perception of extracellular changes to trigger hyperos...

Arabidopsis synaptotagmin 2 (SYT2) has been reported to participate in an unconventional secretory pathway in somatic cells. Our results showed that SYT2 was expressed mainly in Arabidopsis thaliana L. pollen. The pollen of syt2 T-DNA and RNA interference mutant lines exhibited reduced total germination and impeded pollen tube growth. The expressio...

NTL transcription factors, containing three regions: the N-terminal NAC domain (ND), the middle regulation region (RR), and the C-terminal transmembrane domain (TM), belong to the tail-anchored proteins. Although these NTLs play numerous essential roles in plants, their subcellular distribution and the mechanism of translocation into the nucleus re...

Jasmonate (JA) zinc-finger expressed in inflorescence meristem (ZIM)-domain (JAZ) proteins are key regulators of the JA response in plants. Transcriptome profiling of tobacco BY-2 cells was used to identify 17 members of the NtJAZ family, which were divided into 12 distinct groups based on their predicted amino acid sequences and conserved domains....

Nicotine biosynthesis in tobacco (Nicotiana tabacum L.) is highly regulated by jasmonic acid (JA). Two nuclear loci, A and B (renamed NIC1 and NIC2) have been identified that mediate JA-inducible nicotine formation and total alkaloid accumulation. NIC2 was recently shown to be a cluster of seven genes encoding Apetala2/Ethylene-Response Factor (AP2...

ADP-ribosylation factors (ARFs) have been widely identified as being involved in regulation of cell differentiation, intracellular vesicle transport, and cytoskeleton organization in animals and plants. To systematically clarify the ARF gene family in rice, eight putative rice ARF genes (OsARFs) were detected by searching the rice genome database....

Tobacco (Nicotiana tabacum) is a member of the Solanaceae, one of the agronomically most important groups of flowering plants. We have performed an in silico analysis of 1.15 million gene-space sequence reads from the tobacco nuclear genome and report the detailed analysis of more than 2,500 tobacco transcription factors (TFs). The tobacco genome c...

Various signaling pathways rely on changes in cytosolic calcium ion concentration ([Ca2+]i). In plants, resting [Ca2+]i oscillates diurnally. We show that in Arabidopsis thaliana, [Ca2+]i oscillations are synchronized to extracellular Ca2+ concentration ([Ca2+]o) oscillations largely through the Ca2+-sensing receptor CAS. CAS regulates concentratio...

In plant cells, the plane of division is anticipated at the onset of mitosis by the presence of a preprophase band (PPB) of microtubules and F-actin at a cortical site that circumscribes the nucleus. During cytokinesis, the microtubule- and F-actin-based phragmoplast facilitates construction of a new cell wall and is guided to the forecast division...

Extracellular Ca(2+) (Ca(2+)(o)) is required for various physiological and developmental processes in animals and plants. In response to varied Ca(2+)(o) levels, plants maintain relatively constant internal Ca(2+) content, suggesting a precise regulatory mechanism for Ca(2+) homeostasis. However, little is known about how plants monitor Ca(2+)(o) s...

A hammerhead ribozyme (Rz) with long hybridizing arms targeting the mRNA of rice dwarf virus (RDV) segment 5 and a mutated nonfunctional ribozyme (mRz) were constructed. As predicted, Rz transcribed in vitro cleaved the target mRNA of RDV segment 5 into two fragments of 138 and 238 nucleotides in length. The Rz and mRz genes were each placed under...

Actin and myosin from pollen tubes ofLilium davidii were studied by using imrnunoblotting, Dot-Blot and myosin Ca2+ -ATPase analysis. On immunoblotting of the total soluble pollen tube proteins, anti-α-actin antibody labelled a polypeptide approximately 43 ku, which is considered to be the actin of lily. The mRNA encoding actin in ungerminated poll...