Chlamydial SET domain protein functions as a histone methyltransferase

Murata, Masayuki; Azuma, Yoshinao; Miura, Kazumasa; Rahman, Matiur; Matsutani, Minenosuke; Aoyama, Masahiro; Suzuki, Harumi; Sugi, Kazuro; Shirai, Mutsunori

doi:10.1099/mic.0.29213-0

Cited by 50 publications

(50 citation statements)

References 41 publications

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“…Evidence for this hypothesis emerged from studies of chlamydial SET proteins. A SET domain protein (cpnSET) from Chlamydophila pneumoniae, which causes acute respiratory diseases in humans, was first shown to methylate the chlamydial histone-like proteins HC1/HC2 (Murata et al 2007). Its homolog nuclear effector (NUE) from Chlamydia trachomatis was subsequently identified as a T3SS effector that enters the nucleus of infected cells, where it associates with chromatin ( Fig.…”

Section: Histone-modifying Bacterial Enzymesmentioning

confidence: 99%

Epigenetics and Bacterial Infections

Bierne¹,

Hamon²,

Cossart³

2012

Cold Spring Harbor Perspectives in Medicine

313

230

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Epigenetic mechanisms regulate expression of the genome to generate various cell types during development or orchestrate cellular responses to external stimuli. Recent studies highlight that bacteria can affect the chromatin structure and transcriptional program of host cells by influencing diverse epigenetic factors (i.e., histone modifications, DNA methylation, chromatin-associated complexes, noncoding RNAs, and RNA splicing factors). In this article, we first review the molecular bases of the epigenetic language and then describe the current state of research regarding how bacteria can alter epigenetic marks and machineries. Bacterial-induced epigenetic deregulations may affect host cell function either to promote host defense or to allow pathogen persistence. Thus, pathogenic bacteria can be considered as potential epimutagens able to reshape the epigenome. Their effects might generate specific, long-lasting imprints on host cells, leading to a memory of infection that influences immunity and might be at the origin of unexplained diseases.

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Section: Histone-modifying Bacterial Enzymesmentioning

confidence: 99%

Epigenetics and Bacterial Infections

Bierne¹,

Hamon²,

Cossart³

2012

Cold Spring Harbor Perspectives in Medicine

313

230

View full text Add to dashboard Cite

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“…On the other hand, phylogenetic analysis have shown that bacterial SET domain genes have undergone an evolution of their own, unrelated to the evolution of the eukaryotic SET domain genes (Alvarez-Venegas et al, 2007; Murata et al, 2007). This can be substantiated, for example, by performing a BLASTP search at NCBI, with any SET-domain.…”

Section: Bacterial Set Domainmentioning

confidence: 99%

Bacterial SET domain proteins and their role in eukaryotic chromatin modification

Álvarez-Venegas

2014

Front. Genet.

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It has been shown by many researchers that SET-domain containing proteins modify chromatin structure and, as expected, genes coding for SET-domain containing proteins have been found in all eukaryotic genomes sequenced to date. However, during the last years, a great number of bacterial genomes have been sequenced and an important number of putative genes involved in histone post-translational modifications (histone PTMs) have been identified in many bacterial genomes. Here, I aim at presenting an overview of SET domain genes that have been identified in numbers of bacterial genomes based on similarity to SET domains of eukaryotic histone methyltransferases. I will argue in favor of the hypothesis that SET domain genes found in extant bacteria are of bacterial origin. Then, I will focus on the available information on pathogen and symbiont SET-domain containing proteins and their targets in eukaryotic organisms, and how such histone methyltransferases allow a pathogen to inhibit transcriptional activation of host defense genes.

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“…An exception are the homologs of the nonhistone-fold protein histone H1 in Chlamydiae [64,119] likely acquired by lateral transfer from a eukaryotic host. HU and its homologs are phylogenetically the most widespread ChAPs in Eubacteria.…”

Section: The Architecture Of Chromatinmentioning

confidence: 99%

Innovation in gene regulation: The case of chromatin computation

Prohaska

Stadler

Krakauer

2010

Journal of Theoretical Biology

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Chromatin regulation is understood to be one of the fundamental modes of gene regulation in eukaryotic cells. We argue that the basic proteins that determine the chromatin architecture constitute an evolutionary ancient layer of transcriptional regulation common to all three domains of life. We explore phylogenetically, sources of innovation in chromatin regulation, focusing on protein domains related to chromatin structure and function, demonstrating a step-wise increase of complexity in chromatin regulation. Building upon the highly conserved use of variants of chromosomal architectural proteins to distinguish chromosomal states, Eukarya secondarily acquired mechanisms for "writing" chemical modifications onto chromatin that constitute persistent signals. The acquisition of reader domains enabled decoding of these complex, signal combinations and a decoupling of the signal from immediate biochemical effects. We show how the coupling of reading and writing, which is most prevalent in crown-group Eukarya, could have converted chromatin into a powerful computational device capable of storing and processing more information than pure cis-regulatory networks.Key words: Chromatin, gene regulation, evolution Summary of Findings and Evolutionary HypothesisGene regulation in extant organisms is a complex adaptive system making use of a diversity of mechanisms to ensure that proteins and complementary macromolecular components are produced and maintained at functional levels in variable environments.In this contribution we focus on one key regulatory subsystem of the cell: chromatin regulation. We argue that chromatin functioned as general regulator of transcription in the primordial nucleus, and that a series of key molecular innovations has significantly expanded the regulatory scope of the cell. In this section we summarize the key empirical results of the paper. Sections 2 through 6 provide the empirical support for these claims. In section 7, we formulate an evolutionary Email addresses: sonja@bioinf.uni-leipzig.de (Sonja J. Prohaska), studla@bioinf.uni-leipzig.de (Peter F. Stadler), krakauer@santafe.edu (David C. Krakauer) hypothesis that seeks to explain our findings in terms of the evolution of proto-genetic regulation. We then interpret this evolutionary sequence in terms of increasing computational power by locating key stages of the evolutionary sequence within a formal model of computation. Since sections 2-6 are primarily concerned with presenting evidence, those interested in the conceptual development of the argument can focus on sections 7 and 8.Two variants of Chromosomal Architectural Proteins (ChAPs) are sufficient to define binary genomic, and potentially phenotypic, states. We show how extensions to this binary system lead to potential distinctions among an increasing number of genomic states, culminating in forms of control localized to specific sites in the genome, as illustrated for example by extant mammalian histone variants capable of differential expression and/or localization to r...

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Chlamydial SET domain protein functions as a histone methyltransferase

Cited by 50 publications

References 41 publications

Epigenetics and Bacterial Infections

Epigenetics and Bacterial Infections

Bacterial SET domain proteins and their role in eukaryotic chromatin modification

Innovation in gene regulation: The case of chromatin computation

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