vp1524, a Vibrio parahaemolyticus NAD +-dependent deacetylase, regulates host response during infection by induction of host histone deacetylation

Abstract

Gram negative intracellular pathogen V. parahaemolyticus manifests its infection through a series of effector proteins released into the host via the type III secretion system. Most of these effector proteins alter signalling pathways of the host to facilitate survival and proliferation of bacteria inside host cells. Here, we report V. parahaemolyticus (serotype O3:K6) infection induced histone deacetylation in host intestinal epithelial cells, particularly deacetylation of H3K9, H3K56, H3K18 and H4K16 residues. We found a putative NAD+ dependent deacetylase, vp1524 (vpCobB) of Vibrio parahaemolyticus, was overexpressed during infection. Biochemical assays revealed that Vp1524 is a functional NAD+ dependent Sir2 family deacetylase in vitro, which was capable of deacetylating acetylated histones. Furthermore, we observed that vp1524 is expressed and localized to the nuclear periphery of the host cells during infection. Consequently, Vp1524 translocated to nuclear compartments of transfected cells, deacetylated histones, specifically causing deacetylation of those residues (K56, K16, K18) associated with V. parahaemolyticus infection. This infection induced deacetylation resulted in transcriptional repression of several host genes involved in epigenetic regulation, immune response, autophagy etc. Thus, our study shows that a V. parahaemolyticus lysine deacetylase Vp1524 is secreted inside the host cells during infection, modulating host gene expression through histone deacetylation.

An insight into the role of the N-terminal domain of Salmonella CobB in oligomerization and Zn2+ mediated inhibition of the deacetylase activity

“…Prokaryotic NAD + -dependent deacetylases, predominantly known as CobB, the mammalian SIRT5 isoforms, are fairly conserved in Gram-negative bacteria and have been extensively investigated in S. enterica and E. coli ( Mishra et al, 2022 ). Gram-negative species like Vibrio , Mycobacterium , Shigella , and Klebsiella are of clinical importance due to their ability to cause infection in the host.…”

“…The higher deacetylase activity of SeCobB S than that of SeCobB L is consistent with an earlier report. Only two such previous reports demonstrated eukaryotic histones as a substrate for a bacterial deacetylase ( Zhao et al, 2004 ; Mishra et al, 2022 ). In vitro deacetylation of core histones by SeCobB clearly indicates the ability of a bacterial deacetylase to alter host proteins during an infection.…”

“…The in vitro histone deacetylase assay was standardized in the laboratory ( Mishra et al, 2022 ). In brief, HCT-116 cells were treated with sodium butyrate (NaBU) for 24 h to hyperacetylate all the proteins including histones in the cells.…”

“…NAD + -dependent deacetylases are well studied in both Gram-negative and Gram-positive bacteria like CobB in E. coli ( de Diego Puente et al, 2015 ), Salmonella ( Tucker and Escalante-Semerena, 2010 ), Vibrio cholerae ( Liimatta et al, 2018 ), and Yersinia pestis ( Liu et al, 2018 ), Rv1151c in Mycobacterium ( Liu et al, 2014 ), SirtA in Streptomyces ( VanDrisse and Escalante-Semerena, 2018 ), and SirtN in B. subtilis ( Gardner and Escalante-Semerena, 2009 ). Multiple sequence alignments of CobB homologs in selective gastrointestinal bacteria demonstrate 70%–80% sequence homology and a conserved NAD + -binding domain [( Mishra et al, 2022 ), Supplementary Figure S1 ]. They play diverse roles in various bacterial systems such as regulation of the TacT–TacA toxin–antitoxin system ( VanDrisse et al, 2017 ) and PhoP–PhoQ two-component system in Salmonella ( Ren et al, 2016 ), biofilm formation in Mycobacterium tuberculosis , resistance to a first-line drug (isoniazid) in M. smegmatis ( Gu et al, 2015 ), chemotaxis in Y. pestis , and growth homeostasis in B. subtilis ( Gardner and Escalante-Semerena, 2009 ).…”