The nucleoid occlusion protein SlmA is a direct transcriptional activator of chitobiose utilization in Vibrio cholerae

Abstract

Chitin utilization by the cholera pathogen Vibrio cholerae is required for its persistence and evolution via horizontal gene transfer in the marine environment. Genes involved in the uptake and catabolism of the chitin disaccharide chitobiose are encoded by the chb operon. The orphan sensor kinase ChiS is critical for regulation of this locus, however, the mechanisms downstream of ChiS activation that result in expression of the chb operon are poorly understood. Using an unbiased transposon mutant screen, we uncover that the nucleoid occlusion protein SlmA is a regulator of the chb operon. SlmA has not previously been implicated in gene regulation. Also, SlmA is a member of the TetR family of proteins, which are generally transcriptional repressors. In vitro, we find that SlmA binds directly to the chb operon promoter, and in vivo, we show that this interaction is required for transcriptional activation of this locus and for chitobiose utilization. Using point mutations that disrupt distinct functions of SlmA, we find that DNA-binding, but not nucleoid occlusion, is critical for transcriptional activation. This study identifies a novel role for SlmA as a transcriptional regulator in V. cholerae in addition to its established role as a cell division licensing factor.

TetR-family transcription factors in Gram-negative bacteria: conservation, variation and implications for efflux-mediated antimicrobial resistance

“…A biological role was assigned from the literature if experimental evidence was provided (e.g. binding assays to show TFTR binding to promoter)TFTRCore/Accessory (%)PathwayGene(s) or process regulated (organism)LigandsReferencesAcrR Core** Multidrug efflux (RND) Multidrug efflux (ABC) Multidrug efflux (MFS) Motility acrAB (Enterobacteriales) flhDC Rhodamine 6 g Proflavin Ethidium bromide Ciprofloxacin[19][20][21]EnvR Core** Multidrug efflux (RND) Multidrug efflux (RND) acrAB (Enterobacteriales) acrEF (Enterobacteriales)No data available[9]NemR Core** Bleach survival nemAB Choline[22]SlmA Core* Cell division Chitin catabolismFtsZ ring formation(Enterobacteriales) chb operon ( V. cholera )Target DNA sequences FtsZ protein[23][24][25]YbiH Core* Multidrug efflux (ABC) Membrane permeability ybhGFSR ( E. coli ) rhlE ( E. coli )Chloramphenicol Cephalosporin[26]BetIAccessory (67%)Glycine betaine synthesis betT (Enterobacteriales) betIBA (Enterobacteriales)Choline[27]EefRAccessory (47%)Multidrug efflux (RND) eefABC ( Enterobacter spp. , K. pneumoniae )No data available[28][29]FabRCore Accessory (93%) Fatty acid biosynthesis fabAB (Enterobacteriales)Unsaturated thioester[30]RamR Core Efflux regulation ramA (Enterobacteriales)Bile Berberine Ethidium bromide Dequalinium Crystal violet Rhodamine 6 g[31][32][33]RutRCore Accessory (93%) Pyrimidine utilisation Purine degradation Glutamine supply PH homeostasis rutABCDEFG ( E. coli ) carAB ( E. coli ) gadAXW ( E. coli ) gadIBC ( E. coli ) gly-hyi-glxR-ybbVW-allB-ybbY-glxK ( E. coli )Uracil Thymine[34][11][35]TetRAccessory (40%) Accessory (20%) Multidrug efflux (ABC)…”

“…SlmA contains this HTH and is therefore referred to by some authors as a TFTR. SlmA directly activates the transcription of the chb operon in V. cholerae [25], but is not believed to have any direct regulatory roles in E. coli [42]. In E. coli , SlmA acts as a nucleoid occlusion protein, interacting with target DNA and protein (FtsZ).…”

“…RutR and YbjK are known activators of at least one of their target genes [11, 35]. Nucleoid occlusion factor SlmA has no known transcriptional regulatory activity in E. coli but is a known activator in V. chloerae [25].…”

Escherichia coli CrfC Protein, a Nucleoid Partition Factor, Localizes to Nucleoid Poles via the Activities of Specific Nucleoid-Associated Proteins

“…Like HU, SlmA colocalizes throughout the entire nucleoid, except in the Ter macrodomain (Cho et al, 2011; Tonthat et al, 2011). SlmA binding distorts DNA, allowing cooperative binding of proteins and activation of transcription initiation of specific genes (Tonthat et al, 2013; Klancher et al, 2017). These observations suggest that SlmA organizes a specific nucleoid substructure by inducing the conformational changes in DNA and/or specific DNA–protein complexes.…”

Regulatory Hierarchies Controlling Virulence Gene Expression in Shigella flexneri and Vibrio cholerae

“…Chitin transport and metabolism depend on the chb operon in V. cholerae. The cell division protein SlmA binds to chb and regulates its expression, possibly in association with an unknown transcription factor that is under the control of the ChiS sensor-kinase ( Klancher et al, 2017 ). Cbp is a periplasmic chitin binding protein that regulates ChiS negatively when chitin is absent; binding chitin by Cbp relieves repression ( Li and Roseman, 2004 ) (Figure 6 ).…”