Developmental Stages In Arabidopsis Research Articles

Large-scale analyses of heat shock transcription factors and database construction based on whole-genome genes in horticultural and representative plants.

Heat shock transcription factor (Hsf) plays a critical role in regulating heat resistance. Here, 2950 Hsf family genes were identified from 111 horticultural and representative plants. More Hsf genes were detected in higher plants than in lower plants. Based on all Hsf genes, we constructed a phylogenetic tree, which indicated that Hsf genes of each branch evolved independently after species differentiation. Furthermore, we uncovered the evolutionary trajectories of Hsf genes by motif analysis. There were only six motifs (M1–M6) in lower plants, and then four novel motifs (M7–M10) appeared in higher plants. However, the motifs of some Hsf genes were lost in higher plants, indicating that Hsf genes have undergone sequence variation during their evolution. The number of Hsf genes lost was greater than the number of genes that were duplicated after whole-genome duplication in higher plants. The heat response network was constructed using 24 Hsf genes and 2421 downstream and 222 upstream genes of Arabidopsis. Further enrichment analysis revealed that Hsf genes and other transcription factors interacted with each other in the response to heat stress. Global expression maps were illustrated for Hsf genes under various abiotic and biotic stresses and several developmental stages in Arabidopsis. Syntenic and phylogenetic analyses were conducted using Hsf genes of Arabidopsis and the pan-genome of 18 Brassica rapa accessions. We also performed expression pattern analysis of Hsf and six Hsp family genes using expression values from different tissues and heat treatments in B. rapa. The interaction network between the Hsf and Hsp gene families was constructed in B. rapa, and several core genes were detected in the network. Finally, we constructed an Hsf database (http://hsfdb.bio2db.com) for researchers to retrieve Hsf gene family information. Therefore, our study will provide rich resources for the study of the evolution and function of Hsf genes.

Transcriptome analysis of gynoecium morphogenesis uncovers the chronology of gene regulatory network activity.

The gynoecium is the most complex organ formed by the flowering plants. It encloses the ovules, provides a surface for pollen contact and self-incompatibility reactions, allows pollen tube growth, and, post fertilization, develops into the fruit. Consequently, the regulation of gynoecium morphogenesis is complex and appropriate timing of this process in part determines reproductive success. However, little is known about the global control of gynoecium development, even though many regulatory genes have been characterized. Here, we characterized dynamic gene expression changes using laser-microdissected gynoecium tissue from four developmental stages in Arabidopsis. We provide a high-resolution map of global expression dynamics during gynoecium morphogenesis and link these to the gynoecium interactome. We reveal groups of genes acting together early and others acting late in morphogenesis. Clustering of co-expressed genes enables comparisons between the leaf, shoot apex, and gynoecium transcriptomes, allowing the dissection of common and distinct regulators. Furthermore, our results lead to the discovery of genes with putative transcription factor activity (B3LF1, -2, DOFLF1), which, when mutated, lead to impaired gynoecium expansion, illustrating that global transcriptome analyses reveal yet unknown developmental regulators. Our data show that genes encoding highly interacting proteins, such as SEPALLATA3, AGAMOUS, and TOPLESS, are expressed evenly during development but switch interactors over time, whereas stage-specific proteins tend to have fewer interactors. Our analysis connects specific transcriptional regulator activities, protein interactions, and underlying metabolic processes, contributing toward a dynamic network model for gynoecium development.

Silicon flow from root to shoot in pepper: a comprehensive in silico analysis reveals a potential linkage between gene expression and hormone signaling that stimulates plant growth and metabolism.

BackgroundSilicon (Si) is categorized as a quasi-essential element for plants thanks to the benefits on growth, development and metabolism in a hormetic manner. Si uptake is cooperatively mediated by Lsi1 and Lsi2. Nevertheless, Lsi channels have not yet been identified and characterized in pepper (Capsicum annuum), while genes involved in major physiological processes in pepper are Si-regulated. Furthermore, Si and phytohormones may act together in regulating plant growth, metabolism and tolerance against stress. Our aim was to identify potential synergies between Si and phytohormones stimulating growth and metabolism in pepper, based on in silico data.MethodsWe established a hydroponic system to test the effect of Si (0, 60, 125 and 250 mg L−1 Si) on the concentrations of this element in different pepper plant tissues. We also performed an in silico analysis of putative Lsi genes from pepper and other species, including tomato (Solanum lycopersicum), potato (Solanum tuberosum) and Arabidopsis thaliana, to look for cis-acting elements responsive to phytohormones in their promoter regions. With the Lsi1 and Lsi2 protein sequences from various plant species, we performed a phylogenetic analysis. Taking into consideration the Lsi genes retrieved from tomato, potato and Arabidopsis, an expression profiling analysis in different plant tissues was carried out. Expression of Si-regulated genes was also analyzed in response to phytohormones and different plant tissues and developmental stages in Arabidopsis.ResultsSi concentrations in plant tissues exhibited the following gradient: roots > stems > leaves. We were able to identify 16 Lsi1 and three Lsi2 genes in silico in the pepper genome, while putative Lsi homologs were also found in other plant species. They were mainly expressed in root tissues in the genomes analyzed. Both Lsi and Si-regulated genes displayed cis-acting elements responsive to diverse phytohormones. In Arabidopsis, Si-regulated genes were transcriptionally active in most tissues analyzed, though at different expressed levels. From the set of Si-responsive genes, the NOCS2 gene was highly expressed in germinated seeds, whereas RABH1B, and RBCS-1A, were moderately expressed in developed flowers. All genes analyzed showed responsiveness to phytohormones and phytohormone precursors.ConclusionPepper root cells are capable of absorbing Si, but small amounts of this element are transported to the upper parts of the plant. We could identify putative Si influx (Lsi1) and efflux (Lsi2) channels that potentially participate in the absorption and transport of Si, since they are mainly expressed in roots. Both Lsi and Si-regulated genes exhibit cis-regulatory elements in their promoter regions, which are involved in phytohormone responses, pointing to a potential connection among Si, phytohormones, plant growth, and other vital physiological processes triggered by Si in pepper.

Arabidopsis V-ATPase d2 Subunit Plays a Role in Plant Responses to Oxidative Stress.

Vacuolar-type H+-ATPase (V-ATPase), a multisubunit proton pump located on the endomembrane, plays an important role in plant growth. The Arabidopsis thaliana V-ATPase d subunit (VHA-d) consists of two isoforms; AtVHA-d1 and AtVHA-d2. In this study, the function of AtVHA-d2 was investigated. Histochemical analysis revealed that the expression of AtVHA-d1 and AtVHA-d2 was generally highly overlapping in multiple tissues at different developmental stages of Arabidopsis. Subcellular localization revealed that AtVHA-d2 was mainly localized to the vacuole. AtVHA-d2 expression was significantly induced by oxidative stress. Analysis of phenotypic and H2O2 content showed that the atvha-d2 mutant was sensitive to oxidative stress. The noninvasive microtest monitoring demonstrated that the net H+ influx in the atvha-d2 roots was weaker than that in the wild-type under normal conditions. However, oxidative stress resulted in the H+ efflux in atvha-d2 roots, which was significantly different from that in the wild-type. RNA-seq combined with qPCR analysis showed that the expression of several members of the plasma membrane H+-ATPase gene (AtAHA) family in atvha-d2 was significantly different from that in the wild-type. Overall, our results indicate that AtVHA-d2 plays a role in Arabidopsis in response to oxidative stress by affecting H+ flux and AtAHA gene expression.

Identification and Expression Analysis of Snf2 Family Proteins in Tomato (Solanum lycopersicum).

As part of chromatin-remodeling complexes (CRCs), sucrose nonfermenting 2 (Snf2) family proteins alter chromatin structure and nucleosome position by utilizing the energy of ATP, which allows other regulatory proteins to access DNA. Plant genomes encode a large number of Snf2 proteins, and some of them have been shown to be the key regulators at different developmental stages in Arabidopsis. Yet, little is known about the functions of Snf2 proteins in tomato (Solanum lycopersicum). In this study, 45 Snf2s were identified by the homologous search using representative sequences from yeast (S. cerevisiae), fruit fly (D. melanogaster), and Arabidopsis (A. thaliana) against the tomato genome annotation dataset. Tomato Snf2 proteins (also named SlCHRs) could be clustered into 6 groups and distributed on 11 chromosomes. All SlCHRs contained a helicase-C domain with about 80 amino acid residues and a SNF2-N domain with more variable amino acid residues. In addition, other conserved motifs were also identified in SlCHRs by using the MEME program. Expression profile analysis indicated that tomato Snf2 family genes displayed a wide range of expressions in different tissues and some of them were regulated by the environmental stimuli such as salicylic acid, abscisic acid, salt, and cold. Taken together, these results provide insights into the functions of SlCHRs in tomato.

Evolutionary variation and expression profiling of Isopentenyl transferase gene family in Arabidopsis thaliana L. and Oryza sativa L.

Cytokinin is widely known for its critical involvement in various processes of plant growth and development, such as cell division, differentiation, and nutrient metabolism. As a phytohormone, it also plays a vital role in the stress modulation mechanism of the plant. Isopentenyl transferase (IPT) is the key regulatory enzyme of cytokinin biosynthesis. In the present study, all the identified members of Arabidopsis and rice IPT family were analyzed in terms of their chromosomal location, exon-intron distribution, and sub-cellular localization. Based on structural variation and evolutionary conservancy, they could be broadly divided into two families- Adenylate IPT and t-RNA IPT. Further, expression of all AtIPT and OsIPT transcripts were analyzed based on publicly available microarray datasets. All AtIPT genes except AtIPT3 and AtIPT6 showed a high level of expression in all the developmental stages of Arabidopsis. Different members of the AtIPT gene family responded differently depending on the type of stress exposure. A high level of expression was observed in the case of OsIPT2 and OsIPT9 in all the developmental stages and tissues of rice, as compared to the other members. In the case of abiotic stresses, OsIPT5 showed significant up-regulation. Transcript abundance of OsIPT2, OsIPT5, OsIPT7-2 and OsIPT9 fluctuated after biotic stress, hormonal imbalance, chemical toxicity, and nutrient deficiency. These members of the OsIPT gene family might be the crucial stress modulators that were validated through semi-quantitative RT-PCR and their role could be explored further for the generation of abiotic stress tolerant plants.

Transcription factors WRKY11 and WRKY17 are involved in abiotic stress responses in Arabidopsis

Plant WRKY transcription factors play a vital role in abiotic stress tolerance and regulation of plant defense responses. This study examined AtWRKY11 and AtWRKY17 expression under ABA, salt, and osmotic stress at different developmental stages in Arabidopsis. We used reverse transcriptase PCR, quantitative real-time PCR, and promoter:GUS lines to analyze expression. Both genes were upregulated in response to abiotic stress. Next, we applied the same stressors to seedlings of T-DNA insertion wrky11 and 17 knock-out mutants (single and double). Under stress, the mutants exhibited slower germination and compromised root growth compared with the wild type. In most cases, double-mutant seedlings were more affected than single mutants. These results suggest that wrky11 and wrky17 are not strictly limited to plant defense responses but are also involved in conferring stress tolerance.

Expression Analysis of Sound Vibration-Regulated Genes by Touch Treatment in Arabidopsis.

Sound vibration (SV) is considered to be a mechanical stimulus which gives rise to various physiological and molecular changes in plants. Previously, we identified 17 SV-regulated genes (SRGs) which were up-regulated by SV treatments in Arabidopsis. Here, we analyzed the expression pattern of similar genes after an exposure of 500 Hertz at 80 decibels, for various time periods. Simultaneously, we confirmed the SV-mediated expression of these genes under lighted condition as many of them were reported to be dark-induced. For this, we designed an improved SV treatment chamber. Additionally, we checked the electrolyte leakage (EL), photosynthetic performance and expression of mechanosensitive (MS) ion channel genes after 5 days of SV treatment in the illuminated chamber. EL was higher, and the photosynthetic performance index was lower in the SV-treated plants compared to control. Seven out of the 13 MS ion channel genes were differentially expressed after the SV treatment. Simultaneously, we checked the touch-mediated expression pattern of 17 SRGs and 13 MS ion channel genes. The distinct expression pattern of 6 SRGs and 1 MS ion channel gene generate an idea that SV as a stimulus is different from touch. Developmental stage-specific expression profiling suggested that the majority of the SRGs were expressed spatiotemporally in different developmental stages of Arabidopsis, especially in imbibed seed, seedlings and leaves.

Reproductive organ and young tissues show constrained elemental composition in Arabidopsis thaliana.

The identification of stoichiometric homeostasis is crucial for understanding plant adaptive strategies under a changing environment. However, current knowledge of plant stoichiometric homeostasis has mainly been obtained from mature leaves, with little from other organs across different developmental stages. We conducted a greenhouse nitrogen (N) and phosphorus (P) addition experiment to evaluate the strength of stoichiometric homeostasis across different organs and developmental stages of Arabidopsis thaliana. Homeostatic regulation coefficients (H) for N (HN), P (HP) and N : P ratio (HNP) were highest in reproductive tissue, followed by stem and leaf at the same stage. All H parameters in the same organ decreased significantly over the developmental stages. Leaf HN, HP and HNP were highest at stage 1, followed by stages 2 and 3. Both stem and silique at stage 2 relative to stage 3 had higher HN, HP and HNP. These results suggested that reproductive tissue relative to other organs and young tissue relative to old tissue showed more constrained elemental composition in response to nutrient availabilities, and such trends were also evidenced by stoichiometric scaling relationships. Our findings highlight that stoichiometric homeostasis is tightly related to the ontogenesis of plant tissue. These results could have a strong implication for diagnosing relative availabilities of N and P in ecosystems, suggesting that the N and P stoichiometry of old tissues might be stronger indicators of nutrient status for plants, but further study is needed to test the generality across species with more distinguishable functional traits.

Mannan synthase activity in the CSLD family

Cellulose Synthase Like (CSL) proteins are a group of plant glycosyltransferases that are predicted to synthesize β-1,4-linked polysaccharide backbones. CSLC, CSLF and CSLH families have been confirmed to synthesize xyloglucan and mixed linkage β-glucan, while CSLA family proteins have been shown to synthesize mannans. The polysaccharide products of the five remaining CSL families have not been determined. Five CSLD genes have been identified in Arabidopsis thaliana and a role in cell wall biosynthesis has been demonstrated by reverse genetics. We have extended past research by producing a series of double and triple Arabidopsis mutants and gathered evidence that CSLD2, CSLD3 and CSLD5 are involved in mannan synthesis and that their products are necessary for the transition between early developmental stages in Arabidopsis. Moreover, our data revealed a complex interaction between the three glycosyltransferases and brought new evidence regarding the formation of non-cellulosic polysaccharides through multimeric complexes.

The microRNA156 and microRNA172 gene regulation cascades at post-germinative stages inArabidopsis

AbstractMicroRNAs (miRNAs) are involved in developmental programmes of plants, including seed germination and post-germination. Here, we provide evidence that two different miRNA pathways, miR156 and miR172, interact during the post-germination stages inArabidopsis. Mutant seedlings expressing miR156-resistantSQUAMOSA PROMOTER-BINDING PROTEIN-LIKE13(mSPL13), which has silent mutations in the miR156 complementary sequence, over-accumulatedSPL13mRNA and exhibited a delay in seedling development. Microarray analysis indicated thatSCHNARCHZAPFEN(SNZ), anAP2-like gene targeted by miR172, was down-regulated in these mutants. Quantitative reverse transcription-polymerase chain reaction (RT-PCR) and miRNA gel blot analyses showed that theMIR172genes were up-regulated inmSPL13mutants. These results suggest that the miRNA regulation cascades (miR156⊣SPL13 → miR172⊣SNZ) play a critical role during the post-germination developmental stages inArabidopsis.

Characterization of the Ubiquitin E2 Enzyme Variant Gene Family in Arabidopsis

AbstractUbiquitin E2 enzyme variant (UEV) proteins are similar to ubiquitin‐conjugating enzyme (E2) in both sequence and structure, but the lack of a catalytic cysteine residue renders them incapable of forming a thiol‐ester linkage with ubiquitin. While the functional roles of several UEVs have been defined in yeast and animal systems, Arabidopsis COP10, a photomorphogenesis repressor, is the only UEV characterized in plants. Phylogenetic analysis revealed that the eight Arabidopsis UEV genes belong to three subfamilies. The expression of those genes is supported by either the presence of ESTs or RT‐PCR analysis. We also characterized the other members of the COP10 subfamily, UEV2. Semi‐quantitative RT‐PCR analysis indicated that the UEV2 transcripts can be detected in most organs of Arabidopsis. Analysis of UEV2::GUS transgenic lines also showed its ubiquitous expression in nearly all the developmental stages of Arabidopsis. Transient expression analysis indicated that the sGFP‐UEV2 fusion protein can localize to both the cytoplasm and nucleus. A T‐DNA insertion mutant, uev2‐1, which abolished the transcription of UEV2, displays no visible phenotype. Further, the cop10‐4 uev2‐1 double mutant exhibits the same phenotype as the cop10‐4 mutant in darkness. UEV2 is therefore not functionally redundant with COP10.