Diversity, evolution and expression profiles of histone acetyltransferases and deacetylases in oomycetes

The effect of nitrosative stress on histone H3 and H4 acetylation in Phytophthora infestans life cycle

The oomycete Phytophthora infestans is one of the most destructive phytopathogens globally. It has a proven ability to adapt to changing environments rapidly; however, molecular mechanisms responsible for host invasion and adaptation to new environmental conditions still need to be explored. The study aims to understand the epigenetic mechanisms exploited by P. infestans in response to nitrosative stress conditions created by the (micro)environment and the host plant. To characterize reactive nitrogen species (RNS)-dependent acetylation profiles in avirulent/virulent (avr/vr) P. infestans, a transient gene expression, ChIP and immunoblot analyses, and nitric oxide (NO) emission by chemiluminescence were used in combination with the pharmacological approach. Nitrosative stress increased total H3/H4 acetylation and some histone acetylation marks, mainly in sporulating hyphae of diverse (avr/vr) isolates and during potato colonization. These results correlated with transcriptional up-regulation of acetyltransferases PifHAC3 and PifHAM1, catalyzing H3K56 and H4K16 acetylation, respectively. NO or peroxynitrite-mediated changes were also associated with H3K56 and H4K16 mark deposition on the critical pathogenicity-related gene promoters (CesA1, CesA2, CesA3, sPLD-like1, Hmp1, and Avr3a) elevating their expression. Our study highlights RNS-dependent transcriptional reprogramming via histone acetylation of essential gene expression in the sporulating and biotrophic phases of plant colonization by P. infestans as a tool promoting its evolutionary plasticity.

Histone (de)acetylation in epigenetic regulation of Phytophthora pathobiology

Phytophthora species are oomycetes that have evolved a broad spectrum of biological processes and improved strategies to cope with host and environmental challenges. A growing body of evidence indicates that the high pathogen plasticity is based on epigenetic regulation of gene expression linked to Phytophthora's rapid adjustment to endogenous cues and various stresses. As 5mC DNA methylation has not yet been identified in Phytophthora, the reversible processes of acetylation/deacetylation of histone proteins seem to play a pivotal role in the epigenetic control of gene expression in oomycetes. To explore this issue, we review the structure, diversity, and phylogeny of histone acetyltransferases (HATs) and histone deacetylases (HDACs) in six plant-damaging Phytophthora species: P. capsici, P. cinnamomi, P. infestans, P. parasitica, P. ramorum, and P. sojae. To further integrate and improve our understanding of the phylogenetic classification, evolutionary relationship, and functional characteristics, we supplement this review with a comprehensive view of HATs and HDACs using recent genome- and proteome-level databases. Finally, the potential functional role of transcriptional reprogramming mediated by epigenetic changes during Phytophthora species saprophytic and parasitic phases under nitro-oxidative stress is also briefly discussed.

HDAC1: An Essential and Conserved Member of the Diverse Zn2+-Dependent HDAC Family Driven by Divergent Selection Pressure

Zn2+-dependent histone deacetylases (HDACs) are enzymes that regulate gene expression by removing acetyl groups from histone proteins. These enzymes are essential in all living systems, playing key roles in cancer treatment and as potential pesticide targets. Previous phylogenetic analyses of HDAC in certain species have been published. However, their classification and evolutionary origins across biological kingdoms remain unclear, which limits our understanding of them. In this study, we collected the HDAC sequences from 1451 organisms and performed analyses. The HDACs are found to diverge into three classes and seven subclasses under divergent selection pressure. Most subclasses show species specificity, indicating that HDACs have evolved with high plasticity and diversification to adapt to different environmental conditions in different species. In contrast, HDAC1 and HDAC3, belonging to the oldest class, are conserved and crucial in major kingdoms of life, especially HDAC1. These findings lay the groundwork for the future application of HDACs.

The catalase-peroxidase PiCP1 plays a critical role in abiotic stress resistance, pathogenicity and asexual structure development in Phytophthora infestans

Catalase-peroxidase is a heme oxidoreductase widely distributed in bacteria and lower eukaryotes. In this study, we identified a catalase-peroxidase PiCP1 (PITG_05579) in Phytophthora infestans. PiCP1 had catalase/peroxidase and secretion activities and was highly expressed in sporangia and upregulated in response to oxidative and heat stresses. Compared with wild type, PiCP1-silenced transformants (STs) had decreased catalase activity, reduced oxidant stress resistance and damped cell wall integrity. In contrast, PiCP1-overexpression transformants (OTs) demonstrated increased tolerance to abiotic stresses and induced the upregulation of PR genes in the host salicylic acid pathway. The high concentration of PiCP1 can also induced callose deposition in plant tissue. Importantly, both STs and OTs have severely reduced sporangia formation and zoospore releasing rate, but the sporangia germination rate and type varied depending on environmental conditions. Comparative sequence analyses show that catalase-peroxidases are broadly distributed and highly conserved among soil-borne plant parasitic oomycetes, but not in freshwater-inhabiting or strictly plants-inhabiting oomycetes. In addition, we found that silencing PiCP1 downregulated the expression of PiCAT2. These results revealed the important roles of PiCP1 in abiotic stress resistance, pathogenicity and in regulating asexual structure development in response to environmental change. Our findings provide new insights into catalase-peroxidase functions in eukaryotic pathogens.

Epigenetic insight into regulatory role of chromatin covalent modifications in lifecycle and virulence of Phytophthora

The Oomycota phylum includes fungi-like filamentous microorganisms classified as plant pathogens. The most destructive genus within oomycetes is Phytophthora, which causes diseases in plants of economic importance in agriculture, forestry and ornamental. Phytophthora species are widespread worldwide and some of them enable adaptation to different hosts and environmental changes. The development of sexual and asexual reproductive structures and the secretion of proteins to control plant immunity are critical for the adaptative lifestyle. However, molecular mechanisms underlying the adaptation of Phytophthora to different hosts and environmental changes are poorly understood. In the last decade, the role of epigenetics has gained attention, and important evidence has demonstrated the potential role of chromatin covalent modifications, such as DNA methylation and histone acetylation/methylation, in the regulation of gene expression during Phytophthora development and plant infection. Here, we review for the first time the evidence of the potential role of chromatin covalent modifications in the lifecycle of the phytopathogenic genus Phytophthora, including virulence, and host and environment adaptation processes.

Comparative Transcriptome Analysis Revealed Genes Regulated by Histone Acetylation and Genes Related to Sex Hormone Biosynthesis in Phytophthora infestans

Late blight caused by Phytophthora infestans, is one of the most devastating diseases of potato, and was responsible for the death of millions of people during the Irish Potato Famine in the nineteenth century. Phytophthora infestans is a heterothallic oomycete that typically requires two compatible types (mating types), A1 and A2, to complete sexual reproduction (i.e., oospore production). Oospores have critical effects on disease epidemiology because they serve as the primary inoculum in subsequent growing seasons. The sexual reproduction of Phytophthora species is regulated by α hormones. In previous studies, we proved that transformants in which selected histone deacetylase (HDAC) genes are silenced exhibit abnormal hormone production. In the current study, we compared the transcriptomes of HDAC-silenced and wild-type strains to explore the genes regulated by HDAC and the genes involved in sex hormone biosynthesis in Phytophthora species. A total of 14,423 transcripts of unigenes were identified in the wild-type strain, the HDAC family-silenced transformant (HDST), and the HDAC7-silenced transformant (H7ST). After comparing the intergroup gene expression levels, 1,612 unigenes were identified as differentially expressed among these strains. The expression levels of 16 differentially expressed genes (DEGs) were validated by quantitative real-time PCR. The functional annotation of the DEGs by gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that HDACs affect the expression of genes related to metabolic and biosynthetic processes, RNA processing, translation, ribosome biogenesis, cellular structural constituents, RNA binding, and protein binding. Moreover, HDAC7 specifically influences the transcription of genes associated with transport, methylation, mitochondria, organelle inner membranes, receptors and transporters, and hydrolase activities. We also identified 18 candidate genes related to α hormones biosynthesis, including a gene encoding the NF-Y transcription factor (PITG_10861). The overexpression of PITG_10861 increased the production of hormone α2. The results of this study revealed P. infestans genes affected by histone acetylation. The data presented herein provide useful inputs for future research on the epigenetic mechanisms and mating behaviors of Phytophthora species.

A proper PiCAT2 level is critical for sporulation, sporangium function, and pathogenicity of Phytophthora infestans

Catalase is present in prokaryotic and eukaryotic organisms and is important for the protective effects of the antioxidant system against free radicals. Many studies have confirmed that catalase is required for the growth, development, and pathogenesis of bacteria, plants, animals, and fungi. However, there has been relatively little research on the catalases in oomycetes, which form an important group of fungus-like eukaryotes that produce zoosporangia. In this study, we detected two Phytophthora infestans genes encoding catalases, but only PiCAT2 exhibited catalase activity in the sporulation stage and was highly produced during asexual reproduction and in the late infection stage. Compared with the wild-type strain, the PiCAT2-silenced P. infestans transformants were more sensitive to abiotic stress, were less pathogenic, and had a lower colony expansion rate and lower PiMPK7, PiVPS1, and PiGPG1 expression levels. In contrast, the PiCAT2-overexpressed transformants were slightly less sensitive to abiotic stress. Interestingly, increasing and decreasing PiCAT2 expression from the normal level inhibited sporulation, germination, and infectivity, and down-regulated PiCdc14 expression, but up-regulated PiSDA1 expression. These results suggest that PiCAT2 is required for P. infestans mycelial growth, asexual reproduction, abiotic stress tolerance, and pathogenicity. However, a proper PiCAT2 level is critical for the formation and normal function of sporangia. Furthermore, PiCAT2 affects P. infestans sporangial formation and function, pathogenicity, and abiotic stress tolerance by regulating the expression of cell cycle-related genes (PiCdc14 and PiSDA1) and MAPK pathway genes. Our findings provide new insights into catalase functions in eukaryotic pathogens.

Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes

Background

Reversible protein acetylation occurring on Lys-N^e has emerged as a key regulatory post-translational modification in eukaryotes. It is mediated by two groups of enzymes: lysine acetyltransferases (KATs) and lysine deacetylases (KDACs) that catalyze the addition and removal of acetyl groups from target proteins. Estimates indicate that protein acetylation is second to protein phosphorylation in abundance, with thousands of acetylated sites now identified in different subcellular compartments. Considering the important regulatory role of protein phosphorylation, elucidating the diversity of KATs and KDACs across photosynthetic eukaryotes is essential in furthering our understanding of the impact of reversible protein acetylation on plant cell processes.

Results

We report a genome-scale analysis of lysine acetyltransferase (KAT)- and lysine deacetylase (KDAC)-families from 53 photosynthetic eukaryotes. KAT and KDAC orthologs were identified in sequenced genomes ranging from glaucophytes and algae to land plants and then analyzed for evolutionary relationships. Based on consensus molecular phylogenetic and subcellular localization data we found new sub-classes of enzymes in established KAT- and KDAC-families. Specifically, we identified a non-photosynthetic origin of the HD-tuin family KDACs, a new monocot-specific Class I HDA-family sub-class, and a phylogenetically distinct Class II algal/heterokont sub-class which maintains an ankyrin domain not conserved in land plant Class II KDACs. Protein structure analysis showed that HDA- and SRT-KDACs exist as bare catalytic subunits with highly conserved median protein length, while all KATs maintained auxiliary domains, with CBP- and TAF_II250-KATs displaying protein domain gain and loss over the course of photosynthetic eukaryote evolution in addition to variable protein length. Lastly, promoter element enrichment analyses across species revealed conserved cis-regulatory sequences that support KAT and KDAC involvement in the regulation of plant development, cold/drought stress response, as well as cellular processes such as the circadian clock.

Conclusions

Our results reveal new evolutionary, structural, and biological insights into the KAT- and KDAC-families of photosynthetic eukaryotes, including evolutionary parallels to protein kinases and protein phosphatases. Further, we provide a comprehensive annotation framework through our extensive phylogenetic analysis, from which future research investigating aspects of protein acetylation in plants can use to position new findings in a broader context.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3894-0) contains supplementary material, which is available to authorized users.