Redefining the H-NS protein family: a diversity of specialized core and accessory forms exhibit hierarchical transcriptional network integration.

Stephen Fitzgerald,Daniel M Stoebel,Tzu-Chiao Chao,Keith D Mackenzie,Andrew D S Cameron,Ebtihal Y Alshabib,Stefani C Kary

doi:10.1093/nar/gkaa709

Stephen Fitzgerald, Daniel M Stoebel + Show 5 more

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https://doi.org/10.1093/nar/gkaa709

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Abstract

H-NS is a nucleoid structuring protein and global repressor of virulence and horizontally-acquired genes in bacteria. H-NS can interact with itself or with homologous proteins, but protein family diversity and regulatory network overlap remain poorly defined. Here, we present a comprehensive phylogenetic analysis that revealed deep-branching clades, dispelling the presumption that H-NS is the progenitor of varied molecular backups. Each clade is composed exclusively of either chromosome-encoded or plasmid-encoded proteins. On chromosomes, stpA and newly discovered hlpP are core genes in specific genera, whereas hfp and newly discovered hlpC are sporadically distributed. Six clades of H-NS plasmid proteins (Hpp) exhibit ancient and dedicated associations with plasmids, including three clades with fidelity for plasmid incompatibility groups H, F or X. A proliferation of H-NS homologs in Erwiniaceae includes the first observation of potentially co-dependent H-NS forms. Conversely, the observed diversification of oligomerization domains may facilitate stable co-existence of divergent homologs in a genome. Transcriptomic and proteomic analysis in Salmonella revealed regulatory crosstalk and hierarchical control of H-NS homologs. We also discovered that H-NS is both a repressor and activator of Salmonella Pathogenicity Island 1 gene expression, and both regulatory modes are restored by Sfh (HppH) in the absence of H-NS.

Highlights

Bacterial nucleoid associated proteins (NAPs) are abundant DNA-binding proteins that perform the dual functions of regulating gene expression and shaping higherorder chromosome structures
The heat-stable nucleoidstructuring protein (H-NS), referred to as the histonelike nucleoid-structuring protein, is an archetypal NAP best studied as a repressor of gene expression in Escherichia coli, Salmonella enterica and other Gram-negative bacteria [1]
To establish a robust phylogeny of H-NS homologs that co-occur in Enterobacterales, we considered only bacterial strains encoding plasmid-borne H-NS homologs identified in the NCBI Microbial Plasmid database, and belonging to the families: Enterobacteriaceae, Erwiniaceae, Pectobacteriaceae and Yersiniaceae

Summary

Introduction

Bacterial nucleoid associated proteins (NAPs) are abundant DNA-binding proteins that perform the dual functions of regulating gene expression and shaping higherorder chromosome structures. H-NS performs two core cellular functions: it represses the expression of hundreds of gene targets, and it forms scaffolds that constrain chromosomal microdomains [2,3,4,5] This dual functionality allows H-NS to repress gene expression through a classical mechanism of competing with activator proteins for DNA binding sites in gene promoters, or H-NS can repress transcription at a broader level by restructuring regions of DNA to sequester gene promoters [6,7,8,9]. The ‘xenogeneic silencing’ of horizontally acquired genes has been observed

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