Revealing of Mycobacterium marinum Transcriptome by RNA-seq

Wang, Sen; Dong, Xinran; Zhu, Yaping; Wang, Chuan; Sun, Gang; Luò, Tāo; Tian, Weidong; Zheng, Huajun; Gao, Qian

doi:10.1371/journal.pone.0075828

Cited by 17 publications

(23 citation statements)

References 39 publications

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“…A similar method has also been used to study the transcriptome of Mycobacterium marinum [20]. In this study, we report an operon map of M. tuberculosis during both exponential and stationary phases of growth and validate the REMap predictions through comparisons to previously published operons as well as confirmation of newly predicted operons.…”

Section: Introductionsupporting

confidence: 66%

REMap: Operon map of M. tuberculosis based on RNA sequence data

et al. 2016

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A map of the transcriptional organization of genes of an organism is a basic tool that is necessary to understand and facilitate a more accurate genetic manipulation of the organism. Operon maps are largely generated by computational prediction programs that rely on gene conservation and genome architecture and may not be physiologically relevant. With the widespread use of RNA sequencing (RNAseq), the prediction of operons based on actual transcriptome sequencing rather than computational genomics alone is much needed. Here, we report a validated operon map of Mycobacterium tuberculosis, developed using RNAseq data from both the exponential and stationary phases of growth. At least 58.4% of M. tuberculosis genes are organized into 749 operons. Our prediction algorithm, REMap (RNA Expression Mapping of operons), considers the many cases of transcription coverage of intergenic regions, and avoids dependencies on functional annotation and arbitrary assumptions about gene structure. As a result, we demonstrate that REMap is able to more accurately predict operons, especially those that contain long intergenic regions or functionally unrelated genes, than previous operon prediction programs. The REMap algorithm is publicly available as a user-friendly tool that can be readily modified to predict operons in other bacteria.

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Section: Introductionsupporting

confidence: 66%

REMap: Operon map of M. tuberculosis based on RNA sequence data

et al. 2016

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“…The transcriptome of the M . marinum M strain has recently been published [ 23 ]. We therefore extracted the σ-factor mRNA data for exponentially and stationary growing cells and included these in our analysis.…”

Section: Resultsmentioning

confidence: 99%

“…The small difference in σ-factor mRNA levels in the M-strain data (exponential vs . stationary phase cells; S3 Fig panels F and G, and S4 Fig ) might be due to the way this strain was cultivated [ 23 ].…”

Section: Resultsmentioning

confidence: 99%

Comparative Sigma Factor-mRNA Levels in Mycobacterium marinum under Stress Conditions and during Host Infection

et al. 2015

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We have used RNASeq and qRT-PCR to study mRNA levels for all σ-factors in different Mycobacterium marinum strains under various growth and stress conditions. We also studied their levels in M. marinum from infected fish and mosquito larvae. The annotated σ-factors were expressed and transcripts varied in relation to growth and stress conditions. Some were highly abundant such as sigA, sigB, sigC, sigD, sigE and sigH while others were not. The σ-factor mRNA profiles were similar after heat stress, during infection of fish and mosquito larvae. The similarity also applies to some of the known heat shock genes such as the α-crystallin gene. Therefore, it seems probable that the physiological state of M. marinum is similar when exposed to these different conditions. Moreover, the mosquito larvae data suggest that this is the state that the fish encounter when infected, at least with respect to σ-factor mRNA levels. Comparative genomic analysis of σ-factor gene localizations in three M. marinum strains and Mycobacterium tuberculosis H37Rv revealed chromosomal rearrangements that changed the localization of especially sigA, sigB, sigD, sigE, sigF and sigJ after the divergence of these two species. This may explain the variation in species-specific expression upon exposure to different growth conditions.

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“…RNA-seq has also been used to study the transcriptomic response in other phylogenetically related bacteria, such as Legionella pneumophila [20,21]. Mycobacterium marinum [22], which is another pathogen causing disease in fish, show a similar mechanism of persistency like P . salmonis .…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis of the Intracellular Facultative Pathogen Piscirickettsia salmonis: Expression of Putative Groups of Genes Associated with Virulence and Iron Metabolism

Machuca

Martı́nez

2016

PLoS ONE

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The intracellular facultative bacteria Piscirickettsia salmonis is one of the most important pathogens of the Chilean aquaculture. However, there is a lack of information regarding the whole genomic transcriptional response according to different extracellular environments. We used next generation sequencing (NGS) of RNA (RNA-seq) to study the whole transcriptome of an isolate of P. salmonis (FAVET-INBIOGEN) using a cell line culture and a modified cell-free liquid medium, with or without iron supplementation. This was done in order to obtain information about the factors there are involved in virulence and iron acquisition. First, the isolate was grown in the Sf21 cell line; then, the bacteria were cultured into a cell-free liquid medium supplemented or not with iron. We identified in the transcriptome, genes associated with type IV secretion systems, genes related to flagellar structure assembly, several proteases and sigma factors, and genes related to the development of drug resistance. Additionally, we identified for the first time several iron-metabolism associated genes including at least two iron uptake pathways (ferrous iron and ferric iron uptake) that are actually expressed in the different conditions analyzed. We further describe putative genes that are related with the use and storage of iron in the bacteria, which have not been previously described. Several sets of genes related to virulence were expressed in both the cell line and cell-free culture media (for example those related to flagellar structure; such as basal body, MS-ring, C-ring, proximal and distal rod, and filament), which may play roles in other basic processes rather than been restricted to virulence.

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Revealing of Mycobacterium marinum Transcriptome by RNA-seq

Cited by 17 publications

References 39 publications

REMap: Operon map of M. tuberculosis based on RNA sequence data

REMap: Operon map of M. tuberculosis based on RNA sequence data

Comparative Sigma Factor-mRNA Levels in Mycobacterium marinum under Stress Conditions and during Host Infection

Transcriptome Analysis of the Intracellular Facultative Pathogen Piscirickettsia salmonis: Expression of Putative Groups of Genes Associated with Virulence and Iron Metabolism

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