Regulatory (pan-)genome of an obligate intracellular pathogen in the PVC superphylum

Barsy, Marie de; Frandi, Antonio; Panis, Gaël; Théraulaz, Laurence; Pillonel, Trestan; Greub, Gilbert; Viollier, Patrick H.

doi:10.1038/ismej.2016.23

Cited by 16 publications

(16 citation statements)

References 98 publications

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“…All described Chlamydiae exhibit a similar biphasic developmental cycle, including the most deeply branching clades (Abdelrahman and Belland, 2005 ; Steigen et al, 2013 ; Seth-Smith et al, 2017 ). The transcription factor Euo targets more than 100 promoters in W. chondrophila , and may be a key player in cell cycle regulation (Domman and Horn, 2015 ; de Barsy et al, 2016 ). It is conserved throughout the whole phylum, including S. epinepheli and “ Ca .…”

Section: Resultsmentioning

confidence: 99%

Environmental Metagenomic Assemblies Reveal Seven New Highly Divergent Chlamydial Lineages and Hallmarks of a Conserved Intracellular Lifestyle

2018

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The Chlamydiae phylum exclusively encompasses bacteria sharing a similar obligate intracellular life cycle. Existing 16S rDNA data support a high diversity within the phylum, however genomic data remain scarce owing to the difficulty in isolating strains using culture systems with eukaryotic cells. Yet, Chlamydiae genome data extracted from large scale metagenomic studies might help fill this gap. This work compares 33 cultured and 27 environmental, uncultured chlamydial genomes, in order to clarify the phylogenetic relatedness of the new chlamydial clades and to investigate the genetic diversity of the Chlamydiae phylum. The analysis of published chlamydial genomes from metagenomics bins and single cell sequencing allowed the identification of seven new deeply branching chlamydial clades sharing genetic hallmarks of parasitic Chlamydiae. Comparative genomics suggests important biological differences between those clades, including loss of many proteins involved in cell division in the genus Similichlamydia, and loss of respiratory chain and tricarboxylic acid cycle in several species. Comparative analyses of chlamydial genomes with two proteobacterial orders, the Rhizobiales and the Rickettsiales showed that genomes of different Rhizobiales families are much more similar than genomes of different Rickettsiales families. On the other hand, the chlamydial 16S rRNAs exhibit a higher sequence conservation than their Rickettsiales counterparts, while chlamydial proteins exhibit increased sequence divergence. Studying the diversity and genome plasticity of the entire Chlamydiae phylum is of major interest to better understand the emergence and evolution of this ubiquitous and ancient clade of obligate intracellular bacteria.

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Section: Resultsmentioning

confidence: 99%

Environmental Metagenomic Assemblies Reveal Seven New Highly Divergent Chlamydial Lineages and Hallmarks of a Conserved Intracellular Lifestyle

2018

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“…Global detection of YtgR repression by chromatin immunoprecipitation (ChIP) sequencing or targeted analysis of specific promoters will be necessary to delineate the contribution of YtgR activity to that of the detected iron-responsive regulon. Recent work to define targets of known transcription factors in Waddlia chondophila discovered binding sites of YtgC by ChIP sequencing ( 68 ). Interestingly, the level of the most frequent target, hrcA , was also increased during iron starvation in our study, indicating that it may also be a target of YtgC in C. trachomatis .…”

Section: Discussionmentioning

confidence: 99%

Genomewide Transcriptional Responses of Iron-Starved Chlamydia trachomatis Reveal Prioritization of Metabolic Precursor Synthesis over Protein Translation

2018

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By utilizing an experimental approach that monitors the immediate global response of Chlamydia trachomatis to iron starvation, clues to long-standing issues in Chlamydia biology are revealed, including how Chlamydia adapts to this stress. We determined that this pathogen initiates a transcriptional program that prioritizes replenishment of nutrient stores over replication, possibly in preparation for rapid growth once optimal iron levels are restored. Transcription of genes for biosynthesis of metabolic precursors was generally upregulated, while those involved in multiple steps of translation were downregulated. We also observed an increase in transcription of genes involved in DNA repair and neutralizing oxidative stress, indicating that Chlamydia employs an “all-or-nothing” strategy. Its small genome limits its ability to tailor a specific response to a particular stress. Therefore, the “all-or-nothing” strategy may be the most efficient way of surviving within the host, where the pathogen likely encounters multiple simultaneous immunological and nutritional insults.

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“…ChIP was performed as described in ( 37 ) with modifications. 10 ml (for ChIP-qPCR) or 100 ml (for ChIP-seq) cultures were grown in LB medium supplemented with 0.02% arabinose unless stated otherwise.…”

Section: Methodsmentioning

confidence: 99%

QstR-dependent regulation of natural competence and type VI secretion in Vibrio cholerae

Jaskólska

Stutzmann

Stoudmann

et al. 2018

Nucleic Acids Research

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During growth on chitinous surfaces in its natural aquatic environment Vibrio cholerae develops natural competence for transformation and kills neighboring non-immune bacteria using a type VI secretion system (T6SS). Activation of these two phenotypes requires the chitin-induced regulator TfoX, but also integrates signals from quorum sensing via the intermediate regulator QstR, which belongs to the LuxR-type family of regulators. Here, we define the QstR regulon using RNA sequencing. Moreover, by mapping QstR binding sites using chromatin immunoprecipitation coupled with deep sequencing we demonstrate that QstR is a transcription factor that binds upstream of the up- and down-regulated genes. Like other LuxR-type family transcriptional regulators we show that QstR function is dependent on dimerization. However, in contrast to the well-studied LuxR-type biofilm regulator VpsT of V. cholerae, which requires the second messenger c-di-GMP, we show that QstR dimerization and function is c-di-GMP independent. Surprisingly, although ComEA, which is a periplasmic DNA-binding protein essential for transformation, is produced in a QstR-dependent manner, QstR-binding was not detected upstream of comEA suggesting the existence of a further regulatory pathway. Overall, these results provide detailed insights into the function of a key regulator of natural competence and type VI secretion in V. cholerae.

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Regulatory (pan-)genome of an obligate intracellular pathogen in the PVC superphylum

Cited by 16 publications

References 98 publications

Environmental Metagenomic Assemblies Reveal Seven New Highly Divergent Chlamydial Lineages and Hallmarks of a Conserved Intracellular Lifestyle

Environmental Metagenomic Assemblies Reveal Seven New Highly Divergent Chlamydial Lineages and Hallmarks of a Conserved Intracellular Lifestyle

Genomewide Transcriptional Responses of Iron-Starved Chlamydia trachomatis Reveal Prioritization of Metabolic Precursor Synthesis over Protein Translation

QstR-dependent regulation of natural competence and type VI secretion in Vibrio cholerae

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