Characterization of the PRMT gene family in rice reveals conservation of arginine methylation

Type I arginine methyltransferases play crucial roles in development and pathogenesis of Phytophthora capsici

Phytophthora capsici, a pathogenic oomycete, poses a serious threat to global vegetable production. This study investigated the role of protein arginine methylation, a notable post-translational modification, in the epigenetic regulation of P. capsici. We identified and characterized five protein arginine methyltransferases (PRMTs) in P. capsici, with a focus on four putative type I PRMTs exhibiting similar functional domain. Deletion of PcPRMT3, a homolog of PRMT3, significantly affected mycelial growth, asexual spore development, pathogenicity, and stress responses in P. capsici. Transcriptome analyses indicated that absence of PcPRMT3 disrupted multiple biological pathways. The PcPRMT3 deletion mutant displayed heightened susceptibility to oxidative stress, correlated with the downregulation of genes involved in peroxidase and peroxisome activities. Additionally, PcPRMT3 acted as a negative regulator, modulating the transcription levels of specific elicitins, which in turn affects the defense response of host plant against P. capsici. Furthermore, PcPRMT3 was found to affect global arginine methylation levels in P. capsici, implying potential alterations in the functions of its substrate proteins.

OsPRMT6a-mediated arginine methylation of OsJAZ1 regulates jasmonate signaling and spikelet development in rice

Although both protein arginine methylation (PRMT) and jasmonate (JA) signaling are crucial for regulating plant development, the relationship between these processes in the control of spikelet development remains unclear. In this study, we used the CRISPR/Cas9 technology to generate two OsPRMT6a loss-of-function mutants that exhibit various abnormal spikelet structures. Interestingly, we found that OsPRMT6a can methylate arginine residues in JA signal repressors OsJAZ1 and OsJAZ7. We showed that arginine methylation of OsJAZ1 enhances the binding affinity of OsJAZ1 with the JA receptors OsCOI1a and OsCOI1b in the presence of JAs, thereby promoting the ubiquitination of OsJAZ1 by the SCFOsCOI1a/OsCOI1b complex and degradation via the 26S proteasome. This process ultimately releases OsMYC2, a core transcriptional regulator in the JA signaling pathway, to activate or repress JA-responsive genes, thereby maintaining normal plant (spikelet) development. However, in the osprmt6a-1 mutant, reduced arginine methylation of OsJAZ1 impaires the interaction between OsJAZ1 and OsCOI1a/OsCOI1b in the presence of JAs. As a result, OsJAZ1 proteins become more stable, repressing JA responses, thus causing the formation of abnormal spikelet structures. Moreover, we discovered that JA signaling reduces the OsPRMT6a mRNA level in an OsMYC2-dependent manner, thereby establishing a negative feedback loop to balance JA signaling. We further found that OsPRMT6a-mediated arginine methylation of OsJAZ1 likely serves as a switch to tune JA signaling to maintain normal spikelet development under harsh environmental conditions such as high temperatures. Collectively, our study establishes a direct molecular link between arginine methylation and JA signaling in rice.

Genome-wide identification and expression analysis of protein arginine methyltransferase and JmjC domain-containing family in apple

Histone methylation is an important type of histone modification that regulates gene expression in plants. In this study, we identified 14 arginine methylation-related genes (Protein Arginine Methyltransferase, MdPRMT) and 32 demethylation-related genes (JmjC Domain-Containing Family, MdJMJ) in apple. Furthermore, we investigated the phylogenetic relationship, chromosome distribution, gene structure, motif analysis, promoter sequence analysis, and expression patterns of MdPRMT and MdJMJ genes. Homology analysis showed a high degree of conservation and homology between PRMT and JMJ genes in Arabidopsis and apple. We identified the types of duplicated genes in the MdJMJ and MdPRMT gene families, found a large number of whole-genome duplicates (WGD) gene pairs and a small number of tandem duplicates (TD) pairs, transposed duplication (TRD) gene pairs as well as proximal duplicates (PD) pairs, and discussed the possible evolutionary pathways of the gene families from the perspective of duplicated genes. Homology analysis showed a high degree of conservation and homology between PRMT and JMJ genes in Arabidopsis and apple. In addition, the promoter regions of MdPRMT and MdJMJ contain numerous cis-acting elements involved in plant growth and development, hormone response, and stress responses. Based on the transcriptional profiles of MdPRMT and MdJMJ in different tissues and developmental stages, it was found that MdPRMT and MdJMJ may play multiple roles in apple growth and development, for example, MdJMJ21 may be involved in the regulation of apple endosperm formation. MdPRMT and MdJMJ exhibit different expression patterns in response to hormone signaling in apple, MdJMJ3, MdJMJ18, MdJMJ30, MdPRMT2, MdPRMT13, and MdPRMT14 may play roles in apple response to drought stress, while the expression of MdJMJ13, MdPRMT3, MdPRMT4, and MdPRMT6 is affected by cold stress. Our study provides a foundation for determining the functional roles of MdPRMT and MdJMJ genes in apple.

A review of the potential involvement of small RNAs in transgenerational abiotic stress memory in plants

Crop production is increasingly threatened by the escalating weather events and rising temperatures associated with global climate change. Plants have evolved adaptive mechanisms, including stress memory, to cope with abiotic stresses such as heat, drought, and salinity. Stress memory involves priming, where plants remember prior stress exposures, providing enhanced responses to subsequent stress events. Stress memory can manifest as somatic, intergenerational, or transgenerational memory, persisting for different durations. The chromatin, a central regulator of gene expression, undergoes modifications like DNA acetylation, methylation, and histone variations in response to abiotic stress. Histone modifications, such as H3K4me3 and acetylation, play crucial roles in regulating gene expression. Abiotic stresses like drought and salinity are significant challenges to crop production, leading to yield reductions. Plant responses to stress involve strategies like escape, avoidance, and tolerance, each influencing growth stages differently. Soil salinity affects plant growth by disrupting water potential, causing ion toxicity, and inhibiting nutrient uptake. Understanding plant responses to these stresses requires insights into histone-mediated modifications, chromatin remodeling, and the role of small RNAs in stress memory. Histone-mediated modifications, including acetylation and methylation, contribute to epigenetic stress memory, influencing plant adaptation to environmental stressors. Chromatin remodeling play a crucial role in abiotic stress responses, affecting the expression of stress-related genes. Small RNAs; miRNAs and siRNAs, participate in stress memory pathways by guiding DNA methylation and histone modifications. The interplay of these epigenetic mechanisms helps plants adapt to recurring stress events and enhance their resilience. In conclusion, unraveling the epigenetic mechanisms in plant responses to abiotic stresses provides valuable insights for developing resilient agricultural techniques. Understanding how plants utilize stress memory, histone modifications, chromatin remodeling, and small RNAs is crucial for designing strategies to mitigate the impact of climate change on crop production and global food security.

SISTER OF FCA physically associates with SKB1 to regulate flowering time in Arabidopsis thaliana

BACKGROUND

Proper flowering time is important for the growth and development of plants, and both too early and too late flowering impose strong negative influences on plant adaptation and seed yield. Thus, it is vitally important to study the mechanism underlying flowering time control in plants. In a previous study by the authors, genome-wide association analysis was used to screen the candidate gene SISTER OF FCA (SSF) that regulates FLOWERING LOCUS C (FLC), a central gene encoding a flowering suppressor in Arabidopsis thaliana.

RESULTS

SSF physically interacts with Protein arginine methyltransferase 5 (PRMT5, SKB1). Subcellular co-localization analysis showed that SSF and SKB1 interact in the nucleus. Genetically, SSF and SKB1 exist in the same regulatory pathway that controls FLC expression. Furthermore, RNA-sequencing analysis showed that both SSF and SKB1 regulate certain common pathways.

CONCLUSIONS

This study shows that PRMT5 interacts with SSF, thus controlling FLC expression and facilitating flowering time control.

Genome-wide identification and expression analysis reveal the role of histone methyltransferase and demethylase genes in heat stress response in potato (Solanum tuberosum L.)

BACKGROUND

Potato (Solanum tuberosum L.), the third most important non-cereal crop, is sensitive to high temperature. Histone modifications have been known to regulate various abiotic stress responses. However, the role of histone methyltransferases and demethylases remain unexplored in potato under heat stress.

METHODS

Potato genome database was used for genome-wide analysis of StPRMT and StHDMA gene families, which were further characterized by analyzing gene structure, conserved motif, domain organization, sub-cellular localization, promoter region and phylogenetic relationships. Additionally, expression profiling under high-temperature stress in leaf and stolon tissue of heat contrasting potato genotypes was done to study their role in response to high temperature stress.

RESULTS

The genome-wide analysis led to identification of nine StPRMT and eleven StHDMA genes. Structural analysis, including conserved motifs, exon/intron structure and phylogenetic relationships classified StPRMT and StHDMA gene families into two classes viz. Class I and Class II. A variety of cis-regulatory elements were explored in the promoter region associated with light, developmental, hormonal and stress responses. Prediction of sub-cellular localization of StPRMT proteins revealed their occurrence in nucleus and cytoplasm, whereas StHDMA proteins were observed in different sub-cellular compartments. Furthermore, expression profiling of StPRMT and StHDMA gene family members revealed genes responding to heat stress. Heat-inducible expression of StPRMT1, StPRMT3, StPRMT4 and StPRMT5 in leaf and stolon tissues of HS and HT cultivar indicated them as probable candidates for enhancing thermotolerance in potato. However, StHDMAs responded dynamically in leaf and stolon tissue of heat contrasting genotypes under high temperature.

CONCLUSION

The current study presents a detailed analysis of histone modifiers in potato and indicates their role as an important epigenetic regulators modulating heat tolerance.

GENERAL SIGNIFICANCE

Understanding epigenetic mechanisms underlying heat tolerance in potato will contribute towards breeding of thermotolerant potato varieties.

Genome-Wide Identification of Maize Protein Arginine Methyltransferase Genes and Functional Analysis of ZmPRMT1 Reveal Essential Roles in Arabidopsis Flowering Regulation and Abiotic Stress Tolerance

Histone methylation, as one of the important epigenetic regulatory mechanisms, plays a significant role in growth and developmental processes and stress responses of plants, via altering the methylation status or ratio of arginine and lysine residues of histone tails, which can affect the regulation of gene expression. Protein arginine methyltransferases (PRMTs) have been revealed to be responsible for histone methylation of specific arginine residues in plants, which is important for maintaining pleiotropic development and adaptation to abiotic stresses in plants. Here, for the first time, a total of eight PRMT genes in maize have been identified and characterized in this study, named as ZmPRMT1-8. According to comparative analyses of phylogenetic relationship and structural characteristics among PRMT gene family members from several representative species, all maize 8 PRMT proteins were categorized into three distinct subfamilies. Further, schematic structure and chromosome location analyses displayed evolutionarily conserved structure features and an unevenly distribution on maize chromosomes of ZmPRMT genes, respectively. The expression patterns of ZmPRMT genes in different tissues and under various abiotic stresses (heat, drought, and salt) were determined. The expression patterns of ZmPRMT genes indicated that they play a role in regulating growth and development and responses to abiotic stress. Eventually, to verify the biological roles of ZmPRMT genes, the transgenic Arabidopsis plants overexpressing ZmPRMT1 gene was constructed as a typical representative. The results demonstrated that overexpression of ZmPRMT1 can promote earlier flowering time and confer enhanced heat tolerance in transgenic Arabidopsis. Taken together, our results are the first to report the roles of ZmPRMT1 gene in regulating flowering time and resisting heat stress response in plants and will provide a vital theoretical basis for further unraveling the functional roles and epigenetic regulatory mechanism of ZmPRMT genes in maize growth, development and responses to abiotic stresses.

Dwarf and High Tillering1 represses rice tillering through mediating the splicing of D14 pre-mRNA

Strigolactones (SLs) constitute a class of plant hormones that regulate many aspects of plant development, including repressing tillering in rice (Oryza sativa). However, how SL pathways are regulated is still poorly understood. Here, we describe a rice mutant dwarf and high tillering1 (dht1), which exhibits pleiotropic phenotypes (such as dwarfism and increased tiller numbers) similar to those of mutants defective in SL signaling. We show that DHT1 encodes a monocotyledon-specific hnRNP-like protein that acts as a previously unrecognized intron splicing factor for many precursor mRNAs (pre-mRNAs), including for the SL receptor gene D14. We find that the dht1 (DHT1I232F) mutant protein is impaired in its stability and RNA binding activity, causing defective splicing of D14 pre-mRNA and reduced D14 expression, and consequently leading to the SL signaling-defective phenotypes. Overall, our findings deepen our understanding of the functional diversification of hnRNP-like proteins and establish a connection between posttranscriptional splicing and SL signaling in the regulation of plant development.

Genome-Wide Identification and Spatial Expression Analysis of Histone Modification Gene Families in the Rubber Dandelion Taraxacum kok-saghyz

Taraxacum kok-saghyz (Tks), also known as the Russian dandelion, is a recognized alternative source of natural rubber quite comparable, for quality and use, to the one obtained from the so-called rubber tree, Hevea brasiliensis. In addition to that, Tks roots produce several other compounds, including inulin, whose use in pharmaceutical and dietary products is quite extensive. Histone-modifying genes (HMGs) catalyze a series of post-translational modifications that affect chromatin organization and conformation, which, in turn, regulate many downstream processes, including gene expression. In this study, we present the first analysis of HMGs in Tks. Altogether, we identified 154 putative Tks homologs: 60 HMTs, 34 HDMs, 42 HATs, and 18 HDACs. Interestingly, whilst most of the classes showed similar numbers in other plant species, including M. truncatula and A. thaliana, HATs and HMT-PRMTs were indeed more abundant in Tks. Composition and structure analysis of Tks HMG proteins showed, for some classes, the presence of novel domains, suggesting a divergence from the canonical HMG model. The analysis of publicly available transcriptome datasets, combined with spatial expression of different developmental tissues, allowed us to identify several HMGs with a putative role in metabolite biosynthesis. Overall, our work describes HMG genomic organization and sets the premises for the functional characterization of epigenetic modifications in rubber-producing plants.

Comprehensive molecular evaluation of the histone methyltransferase gene family and their important roles in two-line hybrid wheat

BACKGROUND

Histone methylation usually plays important roles in plant development through post-translational regulation and may provide a new visual field for heterosis. The histone methyltransferase gene family has been identified in various plants, but its members and functions in hybrid wheat related in heterosis is poorly studied.

RESULTS

In this study, 175 histone methyltransferase (HMT) genes were identified in wheat, including 152 histone lysine methyltransferase (HKMT) genes and 23 protein arginine methyltransferase (PRMT) genes. Gene structure analysis, physicochemical properties and subcellular localization predictions of the proteins, exhibited the adequate complexity of this gene family. As an allohexaploid species, the number of the genes (seven HKMTs orthologous groups and four PRMTs orthologous groups) in wheat were about three times than those in diploids and showed certain degrees of conservation, while only a small number of subfamilies such as ASH-like and Su-(var) subfamilies have expanded their members. Transcriptome analysis showed that HMT genes were mainly expressed in the reproductive organs. Expression analysis showed that some TaHMT genes with different trends in various hybrid combinations may be regulated by lncRNAs with similar expression trends. Pearson correlation analysis of the expression of TaHMT genes and two yield traits indicated that four DEGs may participate in the yield heterosis of two-line hybrid wheat. ChIP-qPCR results showed that the histone modifications (H3K4me3, H3K36me3 and H3K9ac) enriched in promoter regions of three TaCCA1 genes which are homologous to Arabidopsis heterosis-related CCA1/LHY genes. The higher expression levels of TaCCA1 in F₁ than its parents are positive with these histone modifications. These results showed that histone modifications may play important roles in wheat heterosis.

CONCLUSIONS

Our study identified characteristics of the histone methyltransferase gene family and enhances the understanding of the evolution and function of these members in allohexaploid wheat. The causes of heterosis of two-line hybrid wheat were partially explained from the perspective of histone modifications.

Genome-wide identification of chromatin regulators in Sorghum bicolor

Chromatin regulators play important roles in plant development and stress response. In this study, we identified totally 231 chromatin regulators including 63 histones, 29 histone chaperones, 101 histone modification enzymes, and 38 chromatin remodeling factors from Sorghum bicolor (L.) Moench. Most of these chromatin regulators are homologous to their counterparts in Arabidopsis or rice. However, sorghum genome evolves a few novel histone variants specific to some grass species and a sorghum-unique chromatin remodeling factor that contain the domains belonging to the elongation factor EF-Tu and the histone chaperone SPT16. Finally, we performed co-expression analysis for the chromatin regulator-encoding genes by clustering the expression patterns of these genes. Our results provide useful information for the future studies on the mechanism of epigenetic regulation in sorghum and its roles in development and stress response.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03181-8.

Protein arginine methyltransferases in protozoan parasites

Arginine methylation is a post-translational modification involved in gene transcription, signalling pathways, DNA repair, RNA metabolism and splicing, among others, mechanisms that in protozoa parasites may be involved in pathogenicity-related events. This modification is performed by protein arginine methyltransferases (PRMTs), which according to their products are divided into three main types: type I yields monomethylarginine (MMA) and asymmetric dimethylarginine; type II produces MMA and symmetric dimethylarginine; whereas type III catalyses MMA only. Nine PRMTs (PRMT1 to PRMT9) have been characterized in humans, whereas in protozoa parasites, except for Giardia intestinalis, three to eight PRMTs have been identified, where in each group there are at least two enzymes belonging to type I, the majority with higher similarity to human PRMT1, and one of type II, related to human PRMT5. However, the information on the role of most of these enzymes in the parasites biology is limited so far. Here, current knowledge of PRMTs in protozoan parasites is reviewed; these enzymes participate in the cell growth, stress response, stage transitions and virulence of these microorganisms. Thus, PRMTs are attractive targets for developing new therapeutic strategies against these pathogens.

Genome-Wide Identification of Histone Modification Gene Families in the Model Legume Medicago truncatula and Their Expression Analysis in Nodules

Histone methylation and acetylation are key processes in the epigenetic regulation of plant growth, development, and responses to environmental stimuli. The genes encoding for the enzymes that are responsible for these chromatin post-translational modifications, referred to as histone modification genes (HMGs), have been poorly investigated in Leguminosae species, despite their importance for establishment and activity of nitrogen-fixing nodules. In silico analysis of Medicago truncatula HMGs identified 81 histone methyltransferases, 46 histone demethylases, 64 histone acetyltransferases, and 15 histone deacetylases. MtHMGs were analyzed for their structure and domain composition, and some combinations that were not yet reported in other plant species were identified. Genes have been retrieved from M. truncatula A17 and R108 genotypes as well as M. sativa CADL and Zhongmu No.1; the gene number and distribution were compared with Arabidopsis thaliana. Furthermore, by analyzing the expression data that were obtained at various developmental stages and in different zones of nitrogen-fixing nodules, we identified MtHMG loci that could be involved in nodule development and function. This work sets a reference for HMG genomic organization in legumes which will be useful for functional investigation that is aimed at elucidating HMGs involvement in nodule development and symbiotic nitrogen fixation.

Not all Is SET for Methylation: Evolution of Eukaryotic Protein Methyltransferases

Dynamic posttranslational modifications to canonical histones that constitute the nucleosome (H2A, H2B, H3, and H4) control all aspects of enzymatic transactions with DNA. Histone methylation has been studied heavily for the past 20 years, and our mechanistic understanding of the control and function of individual methylation events on specific histone arginine and lysine residues has been greatly improved over the past decade, driven by excellent new tools and methods. Here, we will summarize what is known about the distribution and some of the functions of protein methyltransferases from all major eukaryotic supergroups. The main conclusion is that protein, and specifically histone, methylation is an ancient process. Many taxa in all supergroups have lost some subfamilies of both protein arginine methyltransferases (PRMT) and the heavily studied SET domain lysine methyltransferases (KMT). Over time, novel subfamilies, especially of SET domain proteins, arose. We use the interactions between H3K27 and H3K36 methylation as one example for the complex circuitry of histone modifications that make up the "histone code," and we discuss one recent example (Paramecium Ezl1) for how extant enzymes that may resemble more ancient SET domain KMTs are able to modify two lysine residues that have divergent functions in plants, fungi, and animals. Complexity of SET domain KMT function in the well-studied plant and animal lineages arose not only by gene duplication but also acquisition of novel DNA- and histone-binding domains in certain subfamilies.

Molecular cloning and in-depth bioinformatics analysis of type II ribosome-inactivating protein isolated from Sambucus ebulus

Plant ribosome-inactivating proteins (RIPs) are N-glycosidases which inhibit protein synthesis through depurination of the ribosomal RNA sequence. Type II RIPs are heterodimer proteins which can bind to cell surfaces. The cytotoxicity of these RIPs is different. Sambucus spp. are a rich source of RIP proteins with different properties. In the present study, a type II RIP was isolated from S. ebulus plant that grows widely in the north of Iran, and different bioinformatics tools were used for the evaluation of physicochemical, functional and 3D protein characteristics. The results showed significant differences among isolated RIP and other Sambucus RIP proteins. The study of these differences can not only expand our insight into the functioning mechanisms of plant RIPs but also provide information about a novel RIP protein with potential biological applications.

Global Proteomic Analysis Reveals Widespread Lysine Succinylation in Rice Seedlings

Lysine succinylation (Ksu) is a dynamic and reversible post-translational modification that plays an important role in many biological processes. Although recent research has analyzed Ksu plant proteomes, little is known about the scope and cellular distribution of Ksu in rice seedlings. Here, we report high-quality proteome-scale Ksu data for rice seedlings. A total of 710 Ksu sites in 346 proteins with diverse biological functions and subcellular localizations were identified in rice samples. About 54% of the sites were predicted to be localized in the chloroplast. Six putative succinylation motifs were detected. Comparative analysis with succinylation data revealed that arginine (R), located downstream of Ksu sites, is the most conserved amino acid surrounding the succinylated lysine. KEGG pathway category enrichment analysis indicated that carbon metabolism, tricarboxylic acid cycle (TCA) cycle, oxidative phosphorylation, photosynthesis, and glyoxylate and dicarboxylate metabolism pathways were significantly enriched. Additionally, we compared published Ksu data from rice embryos with our data from rice seedlings and found conserved Ksu sites between the two rice tissues. Our in-depth survey of Ksu in rice seedlings provides the foundation for further understanding the biological function of lysine-succinylated proteins in rice growth and development.

Histone modifications and their regulatory roles in plant development and environmental memory

Plants grow in dynamic environments where they receive diverse environmental signals. Swift and precise control of gene expression is essential for plants to align their development and metabolism with fluctuating surroundings. Modifications on histones serve as "histone code" to specify chromatin and gene activities. Different modifications execute distinct functions on the chromatin, promoting either active transcription or gene silencing. Histone writers, erasers, and readers mediate the regulation of histone modifications by catalyzing, removing, and recognizing modifications, respectively. Growing evidence indicates the important function of histone modifications in plant development and environmental responses. Histone modifications also serve as environmental memory for plants to adapt to environmental changes. Here we review recent progress on the regulation of histone modifications in plants, the impact of histone modifications on environment-controlled developmental transitions including germination and flowering, and the role of histone modifications in environmental memory.

Protein Arginine Methyltransferase Expression Affects Ectomycorrhizal Symbiosis and the Regulation of Hormone Signaling Pathways

The genomes of all eukaryotic organisms, from small unicellular yeasts to humans, include members of the protein arginine methyltransferase (PRMT) family. These enzymes affect gene transcription, cellular signaling, and function through the posttranslational methylation of arginine residues. Mis-regulation of PRMTs results in serious developmental defects, disease, or death, illustrating the importance of these enzymes to cellular processes. Plant genomes encode almost the full complement of PRMTs found in other higher organisms, plus an additional PRMT found uniquely in plants, PRMT10. Here, we investigate the role of these highly conserved PRMTs in a process that is unique to perennial plants-the development of symbiosis with ectomycorrhizal fungi. We show that PRMT expression and arginine methylation is altered in the roots of the model tree Eucalyptus grandis by the presence of its ectomycorrhizal fungal symbiont Pisolithus albus. Further, using transgenic modifications, we demonstrate that E. grandis-encoded PRMT1 and PRMT10 have important but opposing effects in promoting this symbiosis. In particular, the plant-specific EgPRMT10 has a potential role in the expression of plant hormone pathways during the colonization process and its overexpression reduces fungal colonization success.

Protein arginine methyltransferases interact with intraflagellar transport particles and change location during flagellar growth and resorption

Protein arginine methyl transferases are located at specific sites in the flagellum. They change location during changes in flagellar dynamics (i.e., resorption and regeneration) via interaction with intraflagellar transport trains.

Changes in protein by posttranslational modifications comprise an important mechanism for the control of many cellular processes. Several flagellar proteins are methylated on arginine residues during flagellar resorption; however, the function is not understood. To learn more about the role of protein methylation during flagellar dynamics, we focused on protein arginine methyltransferases (PRMTs) 1, 3, 5, and 10. These PRMTs localize to the tip of flagella and in a punctate pattern along the length, very similar, but not identical, to that of intraflagellar transport (IFT) components. In addition, we found that PRMT 1 and 3 are also highly enriched at the base of the flagella, and the basal localization of these PRMTs changes during flagellar regeneration and resorption. Proteins with methyl arginine residues are also enriched at the tip and base of flagella, and their localization also changes during flagellar assembly and disassembly. PRMTs are lost from the flagella of fla10-1 cells, which carry a temperature-sensitive mutation in the anterograde motor for IFT. The data define the distribution of specific PRMTs and their target proteins in flagella and demonstrate that PRMTs are cargo for translocation within flagella by the process of IFT.

Root morphogenic pathways in Eucalyptus grandis are modified by the activity of protein arginine methyltransferases

BACKGROUND

Methylation of proteins at arginine residues, catalysed by members of the protein arginine methyltransferase (PRMT) family, is crucial for the regulation of gene transcription and for protein function in eukaryotic organisms. Inhibition of the activity of PRMTs in annual model plants has demonstrated wide-ranging involvement of PRMTs in key plant developmental processes, however, PRMTs have not been characterised or studied in long-lived tree species.

RESULTS

Taking advantage of the recently available genome for Eucalyptus grandis, we demonstrate that most of the major plant PRMTs are conserved in E. grandis as compared to annual plants and that they are expressed in all major plant tissues. Proteomic and transcriptomic analysis in roots suggest that the PRMTs of E. grandis control a number of regulatory proteins and genes related to signalling during cellular/root growth and morphogenesis. We demonstrate here, using chemical inhibition of methylation and transgenic approaches, that plant type I PRMTs are necessary for normal root growth and branching in E. grandis. We further show that EgPRMT1 has a key role in root hair initiation and elongation and is involved in the methylation of β-tubulin, a key protein in cytoskeleton formation.

CONCLUSIONS

Together, our data demonstrate that PRMTs encoded by E. grandis methylate a number of key proteins and alter the transcription of a variety of genes involved in developmental processes. Appropriate levels of expression of type I PRMTs are necessary for the proper growth and development of E. grandis roots.

Identification and expression analysis of rice histone genes

Histones, acting as the core of nucleosome, are the chief protein component of chromatin. They play an important role in gene regulation by covalent modification at several sites and histone variants replacement. Five major families of histones exist: H1, H2A, H2B, H3 and H4. The protein sequences within each family appear to be highly conserved. In this paper, we identified 60 histone proteins in rice (Oryza sativa) including 14 H2A, 15 H2B, 16 H3, 11 H4 and 4 H1. Sequence analysis indicates that histone protein sequences in plant are more variable than in animal. Interestingly, we found a rice-specific H4 variant which showed several amino acid substitutions with canonical protein and was expressed in different tissues in a low level. Expression analysis indicates that a subset of histone genes were expressed in a similar pattern and many of them responded to stress conditions. Specifically, we found that two H2A.Z genes were down-regulated by stress in leaves but not in roots suggesting that they might be involved in stress response.

Correlations between predicted protein disorder and post-translational modifications in plants

MOTIVATION

Protein structural research in plants lags behind that in animal and bacterial species. This lag concerns both the structural analysis of individual proteins and the proteome-wide characterization of structure-related properties. Until now, no systematic study concerning the relationships between protein disorder and multiple post-translational modifications (PTMs) in plants has been presented.

RESULTS

In this work, we calculated the global degree of intrinsic disorder in the complete proteomes of eight typical monocotyledonous and dicotyledonous plant species. We further predicted multiple sites for phosphorylation, glycosylation, acetylation and methylation and examined the correlations of protein disorder with the presence of the predicted PTM sites. It was found that phosphorylation, acetylation and O-glycosylation displayed a clear preference for occurrence in disordered regions of plant proteins. In contrast, methylation tended to avoid disordered sequence, whereas N-glycosylation did not show a universal structural preference in monocotyledonous and dicotyledonous plants. In addition, the analysis performed revealed significant differences between the integral characteristics of monocot and dicot proteomes. They included elevated disorder degree, increased rate of O-glycosylation and R-methylation, decreased rate of N-glycosylation, K-acetylation and K-methylation in monocotyledonous plant species, as compared with dicotyledonous species. Altogether, our study provides the most compelling evidence so far for the connection between protein disorder and multiple PTMs in plants.

CONTACT

tokmak@phoenix.kobe-u.ac.jp or tetsuya.sakurai@riken.jp Supplementary information: Supplementary data are available at Bioinformatics online.

An RNA-seq transcriptome analysis of histone modifiers and RNA silencing genes in soybean during floral initiation process

Epigenetics has been recognised to play vital roles in many plant developmental processes, including floral initiation through the epigenetic regulation of gene expression. The histone modifying proteins that mediate these modifications involve the SET domain-containing histone methyltransferases, JmjC domain-containing demethylase, acetylases and deacetylases. In addition, RNA interference (RNAi)-associated genes are also involved in epigenetic regulation via RNA-directed DNA methylation and post-transcriptional gene silencing. Soybean, a major crop legume, requires a short day to induce flowering. How histone modifications regulate the plant response to external cues that initiate flowering is still largely unknown. Here, we used RNA-seq to address the dynamics of transcripts that are potentially involved in the epigenetic programming and RNAi mediated gene silencing during the floral initiation of soybean. Soybean is a paleopolyploid that has been subjected to at least two rounds of whole genome duplication events. We report that the expanded genomic repertoire of histone modifiers and RNA silencing genes in soybean includes 14 histone acetyltransferases, 24 histone deacetylases, 47 histone methyltransferases, 15 protein arginine methyltransferases, 24 JmjC domain-containing demethylases and 47 RNAi-associated genes. To investigate the role of these histone modifiers and RNA silencing genes during floral initiation, we compared the transcriptional dynamics of the leaf and shoot apical meristem at different time points after a short-day treatment. Our data reveal that the extensive activation of genes that are usually involved in the epigenetic programming and RNAi gene silencing in the soybean shoot apical meristem are reprogrammed for floral development following an exposure to inductive conditions.

Plant PRMTs broaden the scope of arginine methylation

Post-translational methylation at arginine residues is one of the most important covalent modifications of proteins, involved in a myriad of essential cellular processes in eukaryotes, such as transcriptional regulation, RNA processing, signal transduction, and DNA repair. Methylation at arginine residues is catalyzed by a family of enzymes called protein arginine methyltransferases (PRMTs). PRMTs have been extensively studied in various taxa and there is a growing tendency to unveil their functional importance in plants. Recent studies in plants revealed that this evolutionarily conserved family of enzymes regulates essential traits including vegetative growth, flowering time, circadian cycle, and response to high medium salinity and ABA. In this review, we highlight recent advances in the field of post-translational arginine methylation with special emphasis on the roles and future prospects of this modification in plants.