RNA-seq analysis identifies new genes regulated by the histone-like nucleoid structuring protein (H-NS) affecting Vibrio cholerae virulence, stress response and chemotaxis.

Hongxia Wang,Jorge A Benitez,Anisia J Silva,Julio C Ayala

doi:10.1371/journal.pone.0118295

Abstract

The histone-like nucleoid structuring protein (H-NS) functions as a transcriptional silencer by binding to AT-rich sequences at bacterial promoters. However, H-NS repression can be counteracted by other transcription factors in response to environmental changes. The identification of potential toxic factors, the expression of which is prevented by H-NS could facilitate the discovery of new regulatory proteins that may contribute to the emergence of new pathogenic variants by anti-silencing. Vibrio cholerae hns mutants of the El Tor biotype exhibit altered virulence, motility and environmental stress response phenotypes compared to wild type. We used an RNA-seq analysis approach to determine the basis of the above hns phenotypes and identify new targets of H-NS transcriptional silencing. H-NS affected the expression of 18% of all predicted genes in a growth phase-dependent manner. Loss of H-NS resulted in diminished expression of numerous genes encoding methyl-accepting chemotaxis proteins as well as chemotaxis toward the attractants glycine and serine. Deletion of hns also induced an endogenous envelope stress response resulting in elevated expression of rpoE encoding the extracytoplamic sigma factor E (σE). The RNA-seq analysis identified new genes directly repressed by H-NS that can affect virulence and biofilm development in the El Tor biotype cholera bacterium. We show that H-NS and the quorum sensing regulator HapR silence the transcription of the vieSAB three-component regulatory system in El Tor biotype V. cholerae. We also demonstrate that H-NS directly represses the transcription of hlyA (hemolysin), rtxCA (the repeat in toxin or RTX), rtxBDE (RTX transport) and the biosynthesis of indole. Of these genes, H-NS occupancy at the hlyA promoter was diminished by overexpression of the transcription activator HlyU. We discuss the role of H-NS transcriptional silencing in phenotypic differences exhibited by V. cholerae biotypes.

Highlights

Cholera is an acute water-borne diarrheal disease caused by Vibrio cholerae of serogroups O1 and O139
The raw and processed datasets have been deposited in the Gene Expression Omnibus (GEO) repository and assigned accession number GSE62785
Genes known to be transcriptionally silenced by histone-like nucleoid structuring protein (H-NS) such as ctxAB, the tcpA-F cluster, tcpPH, toxT [23, 24, 28, 50] and vps genes required for biofilm matrix exopolysaccharide [32] were identified in the dataset

Summary

Introduction

Cholera is an acute water-borne diarrheal disease caused by Vibrio cholerae of serogroups O1 and O139. V. cholerae O1 can be divided in two biotypes, classical and El Tor [1], which differ in the expression and regulation of major virulence factors [1,2,3]. One major difference is that El Tor biotype strains require special conditions for the in vitro expression of cholera toxin (CT) and the toxin co-regulated pilus (TCP), required for intestinal colonization [4]. Vibrios are subject to numerous physical, chemical and biological stresses which include nutrient limitation, extreme temperatures, oxidative stress, bacteriophage infection and protozoan grazing [5,6,7,8]. Transitions between the aquatic environment and the human small intestine require the regulation, integration and fine tuning of numerous cellular processes, such as virulence gene expression, motility and biofilm development. The formation of biofilm communities is critical for V. cholerae survival and persistence in nature as well as in disease transmission [5, 9,10,11]

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