Gene and Protein Expression in Response to Different Growth Temperatures and Oxygen Availability in Burkholderia thailandensis

Peano, Clelia; Chiaramonte, Fabrizio; Motta, Sara; Pietrelli, Alessandro; Jaillon, Sébastien; Rossi, Elio; Consolandi, Clarissa; Champion, Olivia L.; Michell, Stephen L.; Freddi, Luca; Falciola, L.; Basilico, Fabrizio; Garlanda, Cecília; Mauri, Pierluigi; Bellis, Gianluca De; Landini, Paolo

doi:10.1371/journal.pone.0093009

Cited by 20 publications

(21 citation statements)

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“…To generate a high-quality mapping for each sample, we applied quality filters by excluding those reads with more than four mismatches or those with mapping quality score (MAPQ) less than 15. Read counts for gene relative abundance, differential expression analysis and statistical analysis were calculated as previously described [42, 43]. …”

Section: Methodsmentioning

confidence: 99%

Genomic and transcriptomic comparison between Staphylococcus aureus strains associated with high and low within herd prevalence of intra-mammary infection

et al. 2017

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Background Staphylococcus aureus (Staph. aureus) is one of the major pathogens causing mastitis in dairy ruminants worldwide. The chronic nature of Staph. aureus infection enhances the contagiousness risk and diffusion in herds. In order to identify the factors involved in intra-mammary infection (IMI) and diffusion in dairy cows, we investigated the molecular characteristics of two groups of Staph. aureus strains belonging to ST8 and ST398, differing in clinical properties, through comparison of whole genome and whole transcriptome sequencing.ResultsThe two groups of strains, one originated from high IMI prevalence herds and the other from low IMI prevalence herds, present a peculiar set of genes and polymorphisms related to phenotypic features, such as bacterial invasion of mammary epithelial cells and host adaptation. Transcriptomic analysis supports the high propensity of ST8 strain to chronicity of infection and to a higher potential cytotoxicity.ConclusionsOur data are consistent with the invasiveness and host adaptation feature for the strains GTB/ST8 associated to high within-herd prevalence of mastitis. Variation in genes coding for surface exposed proteins and those associated to virulence and defence could constitute good targets for further research.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-017-0931-8) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Genomic and transcriptomic comparison between Staphylococcus aureus strains associated with high and low within herd prevalence of intra-mammary infection

et al. 2017

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“…Temperature changes also regulates flagellar production both in B. pseudomallei and in B. thailandensis : in the latter species, flagellar motility is strongly affected at 37 vs 28°C, due to negative regulation of the flagellar operon at the mRNA stability level at the host temperature (Peano et al . ). Negative regulation of flagellar expression at host temperature has also been reported in Listeria monocytogenes , another opportunistic pathogen (Kamp and Higgins ).…”

Section: Role Of Motility and Biofilm Determinants In Pathogenicity Omentioning

confidence: 97%

Biofilm and motility in response to environmental and host-related signals in Gram negative opportunistic pathogens

2018

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Most bacteria can switch between a planktonic, sometimes motile, form and a biofilm mode, in which bacterial cells can aggregate and attach to a solid surface. The transition between these two forms represents an example of bacterial adaptation to environmental signals and stresses. In 'environmental pathogens', namely, environmental bacteria that are also able to cause disease in animals and humans, signals associated either with the host or with the external environment, such as temperature, oxygen availability, nutrient concentrations etc., play a major role in triggering the switch between the motile and the biofilm mode, via complex regulatory mechanisms that control flagellar synthesis and motility, and production of adhesion factors. In this review article, we present examples of how environmental signals can impact biofilm formation and cell motility in the Gram negative bacteria Pseudomonas aeruginosa, Escherichia coli and in the Burkholderia genus, and how the switch between motile and biofilm mode can be an essential part of a more general process of adaptation either to the host or to the external environment.

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“…(29). ( A ) Gene Expression Data are obtained from an RNA-seq experiment in which Burkholderia thailandensis (E264 strain) response to growth in oxygen limiting condition was analyzed: i.e.…”

Section: Web Server Descriptionmentioning

confidence: 99%

WoPPER: Web server for Position Related data analysis of gene Expression in Prokaryotes

Puccio

Grillo

Licciulli

et al. 2017

Nucleic Acids Research

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The structural and conformational organization of chromosomes is crucial for gene expression regulation in eukaryotes and prokaryotes as well. Up to date, gene expression data generated using either microarray or RNA-sequencing are available for many bacterial genomes. However, differential gene expression is usually investigated with methods considering each gene independently, thus not taking into account the physical localization of genes along a bacterial chromosome. Here, we present WoPPER, a web tool integrating gene expression and genomic annotations to identify differentially expressed chromosomal regions in bacteria. RNA-sequencing or microarray-based gene expression data are provided as input, along with gene annotations. The user can select genomic annotations from an internal database including 2780 bacterial strains, or provide custom genomic annotations. The analysis produces as output the lists of positionally related genes showing a coordinated trend of differential expression. Graphical representations, including a circular plot of the analyzed chromosome, allow intuitive browsing of the results. The analysis procedure is based on our previously published R-package PREDA. The release of this tool is timely and relevant for the scientific community, as WoPPER will fill an existing gap in prokaryotic gene expression data analysis and visualization tools. WoPPER is open to all users and can be reached at the following URL: https://WoPPER.ba.itb.cnr.it

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Gene and Protein Expression in Response to Different Growth Temperatures and Oxygen Availability in Burkholderia thailandensis

Cited by 20 publications

References 55 publications

Genomic and transcriptomic comparison between Staphylococcus aureus strains associated with high and low within herd prevalence of intra-mammary infection

Genomic and transcriptomic comparison between Staphylococcus aureus strains associated with high and low within herd prevalence of intra-mammary infection

Biofilm and motility in response to environmental and host-related signals in Gram negative opportunistic pathogens

WoPPER: Web server for Position Related data analysis of gene Expression in Prokaryotes

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