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Comparative RNA-Seq based dissection of the regulatory networks and environmental stimuli underlying Vibrio parahaemolyticus gene expression during infection.

Livny J, Zhou X, Mandlik A, Hubbard T, Davis BM, Waldor MK - Nucleic Acids Res. (2014)

Bottom Line: Vibrio parahaemolyticus is the leading worldwide cause of seafood-associated gastroenteritis, yet little is known regarding its intraintestinal gene expression or physiology.Our analyses also suggest that V. parahaemolyticus has access to glucose or other preferred carbon sources in vivo, but that iron is inconsistently available.The V. parahaemolyticus transcriptional response to in vivo growth is far more widespread than and largely distinct from that of V. cholerae, likely due to the distinct ways in which these diarrheal pathogens interact with and modulate the environment in the small intestine.

View Article: PubMed Central - PubMed

Affiliation: The Broad Institute, Cambridge, MA, USA Division of Infectious Diseases, Department of Microbiology and Immunobiology, Brigham & Women's Hospital, Harvard Medical School and HHMI, 181 Longwood Ave., Boston, MA, USA livny@broadinstitute.org.

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MA plots of relative transcript abundance in cecal fluid versus LB. The log2 of the ratio of abundances of each transcript between the two conditions (M) is plotted against the average log2 of abundance of that transcript in both conditions (A). Members of GO groups that are significantly overrepresented among up- and down-regulated V. parahaemolyticus genes are highlighted. Transcriptome data is plotted for V. parahaemolyticus (left) and V. cholerae (right).
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Figure 2: MA plots of relative transcript abundance in cecal fluid versus LB. The log2 of the ratio of abundances of each transcript between the two conditions (M) is plotted against the average log2 of abundance of that transcript in both conditions (A). Members of GO groups that are significantly overrepresented among up- and down-regulated V. parahaemolyticus genes are highlighted. Transcriptome data is plotted for V. parahaemolyticus (left) and V. cholerae (right).

Mentions: To gain additional insight into V. parahaemolyticus physiology in vivo, we grouped the differentially expressed genes based on their GO annotations. This analysis revealed that several GO categories are significantly enriched (>2-fold, P < 1 × 10−3) among V. parahaemolyticus genes down-regulated in CF compared to LB, including those involved in branched-chain aliphatic amino acid transport, histidine catabolism and the trichloroacetic acid cycle (Figure 2A; Supplementary Table S3). We did not detect differential expression of these pathways in our previous RNA-Seq based investigation of the V. cholerae transcriptome during infection of infant rabbits ((24), Figure 2 and see below), suggesting that the metabolic requirements for in vivo growth may differ between these pathogens. Among upregulated genes, overrepresented GOs include protein secretion, transport activity, maltose and phosphate transport and pathogenesis (Figure 2; Supplementary Table S3). It should be noted though that assignments to the ‘pathogenesis’ category are based primarily on homology, rather than experimental evidence in V. parahaemolyticus; in fact, T3SS1 genes are classified within pathogenesis, whereas T3SS2 genes are not associated with any GO group. Many V. cholerae virulence genes (e.g. the components of the critical colonization factor TCP) are also not associated with the GO pathogenesis category. However, classification of genes associated with more conserved functions is likely more reliable, and thus supports the idea that V. parahaemolyticus and V. cholerae rely on distinct metabolic processes to grow in the small intestine.


Comparative RNA-Seq based dissection of the regulatory networks and environmental stimuli underlying Vibrio parahaemolyticus gene expression during infection.

Livny J, Zhou X, Mandlik A, Hubbard T, Davis BM, Waldor MK - Nucleic Acids Res. (2014)

MA plots of relative transcript abundance in cecal fluid versus LB. The log2 of the ratio of abundances of each transcript between the two conditions (M) is plotted against the average log2 of abundance of that transcript in both conditions (A). Members of GO groups that are significantly overrepresented among up- and down-regulated V. parahaemolyticus genes are highlighted. Transcriptome data is plotted for V. parahaemolyticus (left) and V. cholerae (right).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231756&req=5

Figure 2: MA plots of relative transcript abundance in cecal fluid versus LB. The log2 of the ratio of abundances of each transcript between the two conditions (M) is plotted against the average log2 of abundance of that transcript in both conditions (A). Members of GO groups that are significantly overrepresented among up- and down-regulated V. parahaemolyticus genes are highlighted. Transcriptome data is plotted for V. parahaemolyticus (left) and V. cholerae (right).
Mentions: To gain additional insight into V. parahaemolyticus physiology in vivo, we grouped the differentially expressed genes based on their GO annotations. This analysis revealed that several GO categories are significantly enriched (>2-fold, P < 1 × 10−3) among V. parahaemolyticus genes down-regulated in CF compared to LB, including those involved in branched-chain aliphatic amino acid transport, histidine catabolism and the trichloroacetic acid cycle (Figure 2A; Supplementary Table S3). We did not detect differential expression of these pathways in our previous RNA-Seq based investigation of the V. cholerae transcriptome during infection of infant rabbits ((24), Figure 2 and see below), suggesting that the metabolic requirements for in vivo growth may differ between these pathogens. Among upregulated genes, overrepresented GOs include protein secretion, transport activity, maltose and phosphate transport and pathogenesis (Figure 2; Supplementary Table S3). It should be noted though that assignments to the ‘pathogenesis’ category are based primarily on homology, rather than experimental evidence in V. parahaemolyticus; in fact, T3SS1 genes are classified within pathogenesis, whereas T3SS2 genes are not associated with any GO group. Many V. cholerae virulence genes (e.g. the components of the critical colonization factor TCP) are also not associated with the GO pathogenesis category. However, classification of genes associated with more conserved functions is likely more reliable, and thus supports the idea that V. parahaemolyticus and V. cholerae rely on distinct metabolic processes to grow in the small intestine.

Bottom Line: Vibrio parahaemolyticus is the leading worldwide cause of seafood-associated gastroenteritis, yet little is known regarding its intraintestinal gene expression or physiology.Our analyses also suggest that V. parahaemolyticus has access to glucose or other preferred carbon sources in vivo, but that iron is inconsistently available.The V. parahaemolyticus transcriptional response to in vivo growth is far more widespread than and largely distinct from that of V. cholerae, likely due to the distinct ways in which these diarrheal pathogens interact with and modulate the environment in the small intestine.

View Article: PubMed Central - PubMed

Affiliation: The Broad Institute, Cambridge, MA, USA Division of Infectious Diseases, Department of Microbiology and Immunobiology, Brigham & Women's Hospital, Harvard Medical School and HHMI, 181 Longwood Ave., Boston, MA, USA livny@broadinstitute.org.

Show MeSH
Related in: MedlinePlus