The Arabidopsis thaliana SET-domain-containing protein ASHH1/SDG26 interacts with itself and with distinct histone lysine methyltransferases

H3K36 methyltransferase GhKMT3;1a and GhKMT3;2a promote flowering in upland cotton

BACKGROUND

The SET domain group (SDG) genes encode histone lysine methyltransferases, which regulate gene transcription by altering chromatin structure and play pivotal roles in plant flowering determination. However, few studies have investigated their role in the regulation of flowering in upland cotton.

RESULTS

A total of 86 SDG genes were identified through genome-wide analysis in upland cotton (Gossypium hirsutum). These genes were unevenly distributed across 25 chromosomes. Cluster analysis revealed that the 86 GhSDGs were divided into seven main branches. RNA-seq data and qRT‒PCR analysis revealed that lysine methyltransferase 3 (KMT3) genes were expressed at high levels in stamens, pistils and other floral organs. Using virus-induced gene silencing (VIGS), functional characterization of GhKMT3;1a and GhKMT3;2a revealed that, compared with those of the controls, the GhKMT3;1a- and GhKMT3;2a-silenced plants exhibited later budding and flowering and lower plant heightwere shorter. In addition, the expression of flowering-related genes (GhAP1, GhSOC1 and GhFT) significantly decreased and the expression level of GhSVP significantly increased in the GhKMT3;1a- and GhKMT3;2a-silenced plants compared with the control plants.

CONCLUSION

A total of 86 SDG genes were identified in upland cotton, among which GhKMT3;1a and GhKMT3;2a might regulate flowering by affecting the expression of GhAP1, GhSOC1, GhFT and GhSVP. These findings will provide genetic resources for advanced molecular breeding in the future.

SDG26 Is Involved in Trichome Control in Arabidopsis thaliana: Affecting Phytohormones and Adjusting Accumulation of H3K27me3 on Genes Related to Trichome Growth and Development

Plant trichomes formed by specialized epidermal cells play a role in protecting plants from biotic and abiotic stresses and can also influence the economic and ornamental value of plant products. Therefore, further studies on the molecular mechanisms of plant trichome growth and development are important for understanding trichome formation and agricultural production. SET Domain Group 26 (SDG26) is a histone lysine methyltransferase. Currently, the molecular mechanism by which SDG26 regulates the growth and development of Arabidopsis leaf trichomes is still unclear. We found that the mutant of Arabidopsis (sdg26) possessed more trichomes on its rosette leaves compared to the wild type (Col-0), and the trichome density per unit area of sdg26 is significantly higher than that of Col-0. The content of cytokinins and jasmonic acid was higher in sdg26 than in Col-0, while the content of salicylic acid was lower in sdg26 than in Col-0, which is conducive to trichome growth. By measuring the expression levels of trichome-related genes, we found that the expression of genes that positively regulate trichome growth and development were up-regulated, while the negatively regulated genes were down-regulated in sdg26. Through chromatin immunoprecipitation sequencing (ChIP-seq) analysis, we found that SDG26 can directly regulate the expression of genes related to trichome growth and development such as ZFP1, ZFP5, ZFP6, GL3, MYB23, MYC1, TT8, GL1, GIS2, IPT1, IPT3, and IPT5 by increasing the accumulation of H3K27me3 on these genes, which further affects the growth and development of trichomes. This study reveals the mechanism by which SDG26 affects the growth and development of trichomes through histone methylation. The current study provides a theoretical basis for studying the molecular mechanism of histone methylation in regulating leaf trichome growth and development and perhaps guiding the development of new crop varieties.

DnaJs, the critical drivers of Hsp70s: genome-wide screening, characterization and expression of DnaJ family genes in Sorghum bicolor

The DnaJ/Hsp40s, are important components in the chaperone machine, and play pivotal roles in plant growth, development and stress tolerance. Sorghum, the semi-arid crop, is the drought resilient, model C₄ crop. However, no reports of DnaJs have been available. Genome-wide analysis of Sorghum bicolor revealed 113 DnaJ/Hsp40 genes, classified into four groups; 8 genes in SbDnaJ-A class, 10 in SbDnaJ-B, 82 in SbDnaJ-C and 13 in SbDnaJ-D distributed unevenly on all the 10 chromosomes. Chromosomes 1 and 3 were found hot spots with 22 and 20 genes respectively. All genes displayed large number of introns, with an exception of 11 of the SbDnaJ-C which is devoid of introns. Out of 36 paralogous duplications, 7 tandem and 29 segmental duplications were noticed, indicating the major role of segmental duplications in the expansion. Analysis of digital data revealed tissue and stage-specific expressions. Transcriptional profiling of 12 selected genes representing all 4 classes revealed highly significant expression in leaf followed by root tissues. No expression was noticed in stems with an exception of SbDnaJ-C76. The SbDnaJ-A1, D1, and C subgroup genes displayed upregulation in roots, stems and leaves under cold, inferring the involvement of Hsp40s for cellular protection during cold stress. The results demonstrate that C76 and D1 are the candidate genes associated with multiple abiotic stresses. Present research furnishes valuable information about the role of sorghum DnaJs in abiotic stress response and establishes a foundation for understanding the molecular mechanisms associated with plant development and stress tolerance.

The function of histone lysine methylation related SET domain group proteins in plants

Histone methylation, which is mediated by the histone lysine (K) methyltransferases (HKMTases), is a mechanism associated with many pathways in eukaryotes. Most HKMTases have a conserved SET (Su(var) 3-9,E(z),Trithorax) domain, while the HKMTases with SET domains are called the SET domain group (SDG) proteins. In plants, only SDG proteins can work as HKMTases. In this review, we introduced the classification of SDG family proteins in plants and the structural characteristics of each subfamily, surmise the functions of SDG family members in plant growth and development processes, including pollen and female gametophyte development, flowering, plant morphology and the responses to stresses. This review will help researchers better understand the SDG proteins and histone methylation in plants and lay a basic foundation for further studies on SDG proteins.

Genome-wide analysis of the rice J-protein family: identification, genomic organization, and expression profiles under multiple stresses

J-proteins which function as molecular chaperone played critical roles in plant growth, development, and response to various environment stresses, but little was reported on this gene family in rice. Here, we identified 115 putative rice J-proteins and classified them into nine major clades (I–IX) according to their phylogenetic relationships. Gene-structure analysis revealed that each member of the same clade has same or similar exon–intron structure, and most rice J-protein genes of clade VII were intronless. Chromosomes mapping suggested that tandem duplication was occurred in evolution. Expression profile showed that the 61 rice J-protein genes were expressed in at least one tissue. The result implied that they could be involved in the process of rice growth and development. The RNA-sequencing data identified 96 differentially expressed genes, 59.38% (57/96), 67.71% (65/96), and 62.50% (60/96) genes were induced by heat stress, drought stress, and salt stress, respectively. The results indicated that J-protein genes could participated in rice response to different stresses. The findings in this study would provide a foundation for further analyzing the function of J-proteins in rice.

Down-regulation of PvTRX1h increases nodule number and affects auxin, starch, and metabolic fingerprints in the common bean (Phaseolus vulgaris L.)

The legume-rhizobium symbiotic relationship has been widely studied and characterized. However, little information is available about the role of histone lysine methyltransferases in the legume-rhizobium interaction and in the formation of nitrogen-fixing nodules in the common bean. Thus, this study aimed to gain a better understanding of the epigenetic control of nodulation in the common bean. Specifically, we studied the role of PvTRX1h, a histone lysine methyltransferase coding gene, in nodule development and auxin biosynthesis. Through a reverse genetics approach, we generated common bean composite plants to knock-down PvTRX1h expression. Here we found that the down-regulation of PvTRX1h increased the number of nodules per plant, but reduced the number of colony-forming units recovered from nodules. Genes coding for enzymes involved in the synthesis of the indole-3-acetic acid were up-regulated, as was the concentration of this hormone. In addition, PvTRX1h down-regulation altered starch accumulation as determined by the number of amyloplasts per nodule. Metabolic fingerprinting by direct liquid introduction-electrospray ionization-mass spectrometry (DLI-ESI-MS) revealed that the root nodules were globally affected by PvTRX1h down-regulation. Therefore, PvTRX1h likely acts through chromatin histone modifications that alter the auxin signaling network to determine bacterial colonization, nodule number, starch accumulation, hormone levels, and cell proliferation.

Regulation of Long Noncoding RNAs Responsive to Phytoplasma Infection in Paulownia tomentosa

Paulownia witches' broom caused by phytoplasma infection affects the production of Paulownia trees worldwide. Emerging evidence showed that long noncoding RNAs (lncRNA) play a protagonist role in regulating the expression of genes in plants. So far, the identification of lncRNAs has been limited to a few model plant species, and their roles in mediating responses to Paulownia tomentosa that free of phytoplasma infection are yet to be characterized. Here, whole-genome identification of lncRNAs, based on strand-specific RNA sequencing, from four Paulownia tomentosa samples, was performed and identified 3689 lncRNAs. These lncRNAs showed low conservation among plant species and some of them were miRNA precursors. Further analysis revealed that the 112 identified lncRNAs were related to phytoplasma infection. We predicted the target genes of these phytoplasma-responsive lncRNAs, and our analysis showed that 51 of the predicted target genes were alternatively spliced. Moreover, we found the expression of the lncRNAs plays vital roles in regulating the genes involved in the reactive oxygen species induced hypersensitive response and effector-triggered immunity in phytoplasma-infected Paulownia. This study indicated that diverse sets of lncRNAs were responsive to Paulownia witches' broom, and the results will provide a starting point to understand the functions and regulatory mechanisms of Paulownia lncRNAs in the future.

[Reciprocity between active transcription and histone methylation]

In the nucleus of eukaryotic cells, the chromatin states dictated by the different combinations of histone post-translational modifications, such as the methylation of lysine residues, are an integral part of the multitude of epigenomes involved in the fine tuning of all genome functions, and in particular transcription. Over the last decade, an increasing number of factors have been identified as regulators involved in the establishment, reading or erasure of histone methylations. Their characterization in model organisms such as Arabidopsis has thus unraveled their fundamental roles in the control and regulation of essential developmental processes such as the floral transition, cell differentiation, gametogenesis, and/or the response/adaptation of plants to environmental stresses. In this review, we will focus on the methylation of histones functioning as a mark of activate transcription and we will try to highlight, based on recent findings, the more or less direct links between this mark and gene expression. Thus, we will discuss the different mechanisms allowing the dynamics and the integration of the chromatin states resulting from the different histone methylations in connection with the transcriptional machinery of the RNA polymerase II.

The interaction between Turnip crinkle virus p38 and Cucumber mosaic virus 2b and its critical domains

Cross protection is a common phenomenon among closely related strain viruses in co-infected plants. However, unrelated viruses, Turnip crinkle virus (TCV) and Cucumber mosaic virus (CMV), also show an antagonistic effect in co-infected Arabidopsis plants. In many cases, viral suppressors of RNA silencing (VSRs) have important roles in the interactions between viruses in mixed infections. CMV 2b and TCV p38 are multifunctional proteins and both of them are well characterized VSRs and have important roles in operation synergistic interactions with other viruses. Here, we demonstrated antagonistic effects of TCV toward CMV and showed that RNA silencing-mediated resistance protein, RCY1 and TCV-interacting protein (TIP) of Arabidopsis plants did not affect this antagonism effect. We further showed that TCV p38 and CMV 2b could interact with each other in vivo but not in vitro. Further mutational analysis showed that C-terminal of 2b and middle domains of p38 had more important roles in the interaction between the two viruses.

Coupling of histone methylation and RNA processing by the nuclear mRNA cap-binding complex

In eukaryotes, genes are transcribed into pre-mRNAs that are subsequently processed into mature mRNAs by adding a 5'-cap and a 3'-polyA tail and splicing introns. Pre-mRNA processing involves their binding proteins and processing factors, whereas gene transcription often involves chromatin modifiers. It has been unclear how the factors involved in chromatin modifications and RNA processing function in concert to control mRNA production. Here, we show that in Arabidopsis thaliana, the evolutionarily conserved nuclear mRNA cap-binding complex (CBC) forms multi-protein complexes with a conserved histone 3 lysine 4 (H3K4) methyltransferase complex called COMPASS-like and a histone 3 lysine 36 (H3K36) methyltransferase to integrate active histone methylations with co-transcriptional mRNA processing and cap preservation, leading to a high level of mature mRNA production. We further show that CBC is required for H3K4 and H3K36 trimethylation, and the histone methyltransferases are required for CBC-mediated mRNA cap preservation and efficient pre-mRNA splicing at their target loci, suggesting that these factors are functionally interdependent. Our study reveals novel roles for histone methyltransferases in RNA-processing-related events and provides mechanistic insights into how the 'downstream' RNA CBC controls eukaryotic gene transcription.

Diversification and evolution of the SDG gene family in Brassica rapa after the whole genome triplication

Histone lysine methylation, controlled by the SET Domain Group (SDG) gene family, is part of the histone code that regulates chromatin function and epigenetic control of gene expression. Analyzing the SDG gene family in Brassica rapa for their gene structure, domain architecture, subcellular localization, rate of molecular evolution and gene expression pattern revealed common occurrences of subfunctionalization and neofunctionalization in BrSDGs. In comparison with Arabidopsis thaliana, the BrSDG gene family was found to be more divergent than AtSDGs, which might partly explain the rich variety of morphotypes in B. rapa. In addition, a new evolutionary pattern of the four main groups of SDGs was presented, in which the Trx group and the SUVR subgroup evolved faster than the E(z), Ash groups and the SUVH subgroup. These differences in evolutionary rate among the four main groups of SDGs are perhaps due to the complexity and variability of the regions that bind with biomacromolecules, which guide SDGs to their target loci.

The impact of Polycomb group (PcG) and Trithorax group (TrxG) epigenetic factors in plant plasticity

Current advances indicate that epigenetic mechanisms play important roles in the regulatory networks involved in plant developmental responses to environmental conditions. Hence, understanding the role of such components becomes crucial to understanding the mechanisms underlying the plasticity and variability of plant traits, and thus the ecology and evolution of plant development. We now know that important components of phenotypic variation may result from heritable and reversible epigenetic mechanisms without genetic alterations. The epigenetic factors Polycomb group (PcG) and Trithorax group (TrxG) are involved in developmental processes that respond to environmental signals, playing important roles in plant plasticity. In this review, we discuss current knowledge of TrxG and PcG functions in different developmental processes in response to internal and environmental cues and we also integrate the emerging evidence concerning their function in plant plasticity. Many such plastic responses rely on meristematic cell behavior, including stem cell niche maintenance, cellular reprogramming, flowering and dormancy as well as stress memory. This information will help to determine how to integrate the role of epigenetic regulation into models of gene regulatory networks, which have mostly included transcriptional interactions underlying various aspects of plant development and its plastic response to environmental conditions.

The trxG family histone methyltransferase SET DOMAIN GROUP 26 promotes flowering via a distinctive genetic pathway

Histone methylation is a major component in numerous processes such as determination of flowering time, which is fine-tuned by multiple genetic pathways that integrate both endogenous and environmental signals. Previous studies identified SET DOMAIN GROUP 26 (SDG26) as a histone methyltransferase involved in the activation of flowering, as loss of function of SDG26 caused a late-flowering phenotype in Arabidopsis thaliana. However, the SDG26 function and the underlying molecular mechanism remain largely unknown. In this study, we undertook a genetic analysis by combining the sdg26 mutant with mutants of other histone methylation enzymes, including the methyltransferase mutants Arabidopsis trithorax1 (atx1), sdg25 and curly leaf (clf), as well as the demethylase double mutant lsd1-like1 lsd1-like2 (ldl1 ldl2). We found that the early-flowering mutants sdg25, atx1 and clf interact antagonistically with the late-flowering mutant sdg26, whereas the late-flowering mutant ldl1 ldl2 interacts synergistically with sdg26. Based on microarray analysis, we observed weak overlaps in the genes that were differentially expressed between sdg26 and the other mutants. Our analyses of the chromatin of flowering genes revealed that the SDG26 protein binds at the key flowering integrator SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1/AGAMOUS-LIKE 20 (SOC1/AGL20), and is required for histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 36 trimethylation (H3K36me3) at this locus. Together, our results indicate that SDG26 promotes flowering time through a distinctive genetic pathway, and that loss of function of SDG26 causes a decrease in H3K4me3 and H3K36me3 at its target gene SOC1, leading to repression of this gene and the late-flowering phenotype.

Genome-wide identification, phylogenetic and co-expression analysis of OsSET gene family in rice

BACKGROUND

SET domain is responsible for the catalytic activity of histone lysine methyltransferases (HKMTs) during developmental process. Histone lysine methylation plays a crucial and diverse regulatory function in chromatin organization and genome function. Although several SET genes have been identified and characterized in plants, the understanding of OsSET gene family in rice is still very limited.

METHODOLOGY/PRINCIPAL FINDINGS

In this study, a systematic analysis was performed and revealed the presence of at least 43 SET genes in rice genome. Phylogenetic and structural analysis grouped SET proteins into five classes, and supposed that the domains out of SET domain were significant for the specific of histone lysine methylation, as well as the recognition of methylated histone lysine. Based on the global microarray, gene expression profile revealed that the transcripts of OsSET genes were accumulated differentially during vegetative and reproductive developmental stages and preferentially up or down-regulated in different tissues. Cis-elements identification, co-expression analysis and GO analysis of expression correlation of 12 OsSET genes suggested that OsSET genes might be involved in cell cycle regulation and feedback.

CONCLUSIONS/SIGNIFICANCE

This study will facilitate further studies on OsSET family and provide useful clues for functional validation of OsSETs.

Functional relevance of J-protein family of rice (Oryza sativa)

Protein folding and disaggregation are crucial processes for survival of cells under unfavorable conditions. A network of molecular chaperones supports these processes. Collaborative action of Hsp70 and Hsp100 proteins is an important component of this network. J-proteins/DnaJ members as co-chaperones assist Hsp70. As against 22 DnaJ sequences noted in yeast, rice genome contains 104 J-genes. Rice J-genes were systematically classified into type A (12 sequences), type B (9 sequences), and type C (83 sequences) classes and a scheme of nomenclature of these proteins is proposed. Transcript expression profiles revealed that J-proteins are possibly involved in basal cellular activities, developmental programs, and in stress. Ydj1 is the most abundant J-protein in yeast. Ydj1 deleted yeast cells are nonviable at 37 °C. Two rice ortholog proteins of yeast Ydj1 protein namely OsDjA4 and OsDjA5 successfully rescued the growth defect in mutant yeast. As Hsp70 and J-proteins work in conjunction, it emerges that rice J-proteins can partner with yeast Hsp70 proteins in functioning. It is thus shown that J-protein machine is highly conserved.