The architects of bacterial DNA bridges: a structurally and functionally conserved family of proteins

Abstract

Every organism across the tree of life compacts and organizes its genome with architectural chromatin proteins. While eukaryotes and archaea express histone proteins, the organization of bacterial chromosomes is dependent on nucleoid-associated proteins. In Escherichia coli and other proteobacteria, the histone-like nucleoid structuring protein (H-NS) acts as a global genome organizer and gene regulator. Functional analogues of H-NS have been found in other bacterial species: MvaT in Pseudomonas species, Lsr2 in actinomycetes and Rok in Bacillus species. These proteins complement hns − phenotypes and have similar DNA-binding properties, despite their lack of sequence homology. In this review, we focus on the structural and functional characteristics of these four architectural proteins. They are able to bridge DNA duplexes, which is key to genome compaction, gene regulation and their response to changing conditions in the environment. Structurally the domain organization and charge distribution of these proteins are conserved, which we suggest is at the basis of their conserved environment responsive behaviour. These observations could be used to find and validate new members of this protein family and to predict their response to environmental changes.

Molecular basis for the adaptive evolution of environment-sensing by H-NS proteins

“…These H-NS multimers form a superhelix that recapitulates the structure of plectonemic DNA, offering a mechanism for a stable concerted DNA coating by H-NS that results in gene silencing ( Arold et al, 2010 ). However, other modes of DNA association by H-NS were also proposed ( Qin et al, 2019 ).…”

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

“…The amino acids Q112, G113 and R114 form a ‘A/T-hook-like’ motif that interacts with the minor groove of double stranded DNA ( 34 ). These three positions are 100% conserved in all homolog clades except for HppX, which has highly divergent sequences at these positions and across the flanking DNA binding region.…”

Chromosome Segregation Proteins as Coordinators of Cell Cycle in Response to Environmental Conditions

“…In fact, exposure of M. smegmatis cells to stressful conditions modified ParA localization (Ginda et al, 2013;Pióro et al, 2019). Finally, it should be considered that environmental conditions such as increased temperature, pH or osmotic stress influence the chromosome topology (Dorman and Dorman, 2016;Qin et al, 2019), and changes of chromosome topology affect the binding of numerous DNAinteracting proteins including SMC and NAPs (Gruber and Errington, 2009;Dorman and Dorman, 2016;Tran et al, 2017;Qin et al, 2019). Consequently, the activities of segregation proteins may also be easily modified by changes in chromosome topology induced by environmental stress (Figure 2).…”