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

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.

Linear plasmids in Klebsiella and other Enterobacteriaceae

“…Sequences with homology to the transcriptional dual regulator hns were identified in all phylogroups except A (); however, the encoded proteins were highly divergent from one another (27–66 % pairwise homology between phylogroups) and the genes were classed as separate gene groups by panaroo (Table S2). Hns is a global regulator that can be plasmid encoded [36], and can regulate expression of both plasmid- and chromosomally encoded genes [37], impacting a wide range of phenotypes, including virulence [38], expression of genes on foreign DNA [39] and growth conditions [40]. Proteins with hits to known restriction/modification domains were also identified in all reference plasmids, these are frequently encoded by mobile elements and can function as toxin–antitoxin systems to force maintenance of those elements.…”

Physiological Robustness of Model Gram-Negative Bacteria in Response to Genome Rewiring

“…The effects on bacterial physiology of relocating these genes and of tinkering with their regulatory circuits through genetic rewiring will be described. While it should be noted that genes encoding NAP-like proteins are also found on extrachromosomal genetic elements [Doyle et al, 2007;Takeda et al, 2011;Fitzgerald et al, 2020], this topic is beyond the scope of the present discussion.…”

“…Sequence-specific DNA binding and bending protein [Mangan et al, 2006;Kasho et al, 2021;Pozdeev et al, 2022] StpA stpA Homodimer; can form heterodimers with H-NS and other H-NS-like proteins Similar properties to H-NS, but with a distinct production pattern [Leonard et al, 2009;Fitzgerald et al, 2015Fitzgerald et al, , 2020 Genome Rewiring and Bacterial Physiology…”

“…There appears to be no stage of growth at which H-NS is absent from the cell, although fluctuations in its intracellular concentration have been reported [Ueguchi et al, 1993;Dersch et al, 1993;Free and Dorman 1995;Atlung and Ingmer 1997]. H-NS is not essential, in part because it is accompanied by the paralogous StpA protein, with which it shares many properties [Fitzgerald et al, 2020].…”

RfaH Counter-Silences Inhibition of Transcript Elongation by H-NS–StpA Nucleoprotein Filaments in Pathogenic Escherichiacoli

“…Many enterobacteria contain multiple H-NS paralogs (e.g., StpA) and modulating proteins that bind H-NS filaments (e.g., Hha) ( 21 , 22 ). These paralogs and modulators may alter H-NS silencing by affecting H-NS bridging ( 19 , 22 – 25 ).…”