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1. Brucella MucR acts as an H-NS-like protein to silence virulence genes and structure the nucleoid

   https://doi.org/10.1128/mbio.02201-23  

   Barton, Ian S.; Ren, Zhongqing; Cribb, Connor B.; Pitzer, Joshua E.; Baglivo, Ilaria; Martin, Daniel W.; Wang, Xindan; Roop, R. Martin (December 2023, mBio)

   Parsek, Matthew (Ed.)

   ABSTRACT Histone-like nucleoid structuring (H-NS) and H-NS-like proteins serve as global gene silencers and work with antagonistic transcriptional activators (counter-silencers) to properly coordinate the expression of virulence genes in pathogenic bacteria. InBrucella, MucR has been proposed as a novel H-NS-like gene silencer, but direct experimental evidence is lacking. Here, we show that MucR serves as an H-NS-like silencer of theBrucella abortusgenes encoding the polar autotransporter adhesins BtaE and BmaC, the c-di-GMP-specific phosphodiesterase BpdB, and the quorum-sensing regulator BabR. We also demonstrate that the MarR-type transcriptional activator MdrA can displace MucR from thebtaEpromoter, supporting the existence of MucR counter-silencers inBrucella. Moreover, our chromatin immunoprecipitation (ChIP)-seq analysis identified 546 MucR enrichment peaks along the genome, including in the promoters of the genes encoding the Type IV secretion machinery and effectors and the quorum-sensing regulator VjbR. Importantly, MucR ChIP-seq peaks overlap with the previously described binding sites for the transcriptional activators VjbR, BvrR, and CtrA suggesting that these regulators serve as MucR counter-silencers and work in concert with MucR to coordinate virulence gene expression inBrucella. In addition, using chromosome conformation capture (Hi-C), we show that like H-NS inEscherichia coli, MucR alters the global structure of theBrucellanucleoid. Finally, a copy of theE. coli hnsrescues the distinctive growth defect and elevatedbtaEexpression of aB. abortus mucRmutant. Together, these findings solidify the role of MucR as a novel type of H-NS-like protein and suggest that MucR’s gene-silencing properties play a key role in virulence inBrucella. IMPORTANCEHistone-like nucleoid structuring (H-NS) and H-NS-like proteins coordinate host-associated behaviors in many pathogenic bacteria, often through forming silencer/counter-silencer pairs with signal-responsive transcriptional activators to tightly control gene expression.Brucellaand related bacteria do not encode H-NS or homologs of known H-NS-like proteins, and it is unclear if they have other proteins that perform analogous functions during pathogenesis. In this work, we provide compelling evidence for the role of MucR as a novel H-NS-like protein inBrucella. We show that MucR possesses many of the known functions attributed to H-NS and H-NS-like proteins, including the formation of silencer/counter-silencer pairs to control virulence gene expression and global structuring of the nucleoid. These results uncover a new role for MucR as a nucleoid structuring protein and support the importance of temporal control of gene expression inBrucellaand related bacteria. 

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2. Silver ions cause oscillation of bacterial length of Escherichia coli

   https://doi.org/10.1038/s41598-019-48113-4  

   Krishnamurthi, Venkata Rao; Chen, Jingyi; Wang, Yong (August 2019, Scientific Reports)

   Abstract Silver (Ag) in various forms have recently gained broad interest and been revisited due to their promising antimicrobial effects. Here we report our study on the morphological dynamics of live bacteria when subjected to Ag⁺ions. Using time-lapse microscopy, we observed oscillations of cell-length for a large fraction of bacteria exposed to 60μM of Ag⁺ions. In addition, we found that the responses of bacteria to Ag⁺ions were heterogeneous. We quantified the oscillations of cell-length with power spectral density, which appeared different from that of bacteria growing in the absence of Ag⁺ions. Furthermore, a model similar to the predator-prey argument was developed to understand the observed oscillations of cell-length upon exposure to Ag⁺ions. This model not only successfully produced the oscillations but also explained the observed heterogeneity in the bacterial responses to Ag⁺ions. 

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3. MucR protein: Three decades of studies have led to the identification of a new H‐NS ‐like protein

   https://doi.org/10.1111/mmi.15261  

   Baglivo, Ilaria; Malgieri, Gaetano; Roop, II, Roy_Martin; Barton, Ian_S; Wang, Xindan; Russo, Veronica; Pirone, Luciano; Pedone, Emilia_M; Pedone, Paolo_V (April 2024, Molecular Microbiology)

   Abstract MucR belongs to a large protein family whose members regulate the expression of virulence and symbiosis genes in α‐proteobacteria species. This protein and its homologs were initially studied as classical transcriptional regulators mostly involved in repression of target genes by binding their promoters. Very recent studies have led to the classification of MucR as a new type of Histone‐like Nucleoid Structuring (H‐NS) protein. Thus this review is an effort to put together a complete and unifying story demonstrating how genetic and biochemical findings on MucR suggested that this protein is not a classical transcriptional regulator, but functions as a novel type of H‐NS‐like protein, which binds AT‐rich regions of genomic DNA and regulates gene expression. 

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

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

   Fitzgerald, Stephen; Kary, Stefani C; Alshabib, Ebtihal Y; MacKenzie, Keith D; Stoebel, Daniel M; Chao, Tzu-Chiao; Cameron, Andrew D (September 2020, Nucleic Acids Research)

   null (Ed.)

   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. 

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5. A phage-encoded nucleoid associated protein compacts both host and phage DNA and derepresses H-NS silencing

   https://doi.org/10.1093/nar/gkab678  

   Son, Bokyung; Patterson-West, Jennifer; Arroyo-Mendoza, Melissa; Ramachandran, Revathy; Iben, James R; Zhu, Jingen; Rao, Venigalla; Dimitriadis, Emilios K; Hinton, Deborah M (August 2021, Nucleic Acids Research)

   Abstract Nucleoid Associated Proteins (NAPs) organize the bacterial chromosome within the nucleoid. The interaction of the NAP H-NS with DNA also represses specific host and xenogeneic genes. Previously, we showed that the bacteriophage T4 early protein MotB binds to DNA, co-purifies with H-NS/DNA, and improves phage fitness. Here we demonstrate using atomic force microscopy that MotB compacts the DNA with multiple MotB proteins at the center of the complex. These complexes differ from those observed with H-NS and other NAPs, but resemble those formed by the NAP-like proteins CbpA/Dps and yeast condensin. Fluorescent microscopy indicates that expression of motB in vivo, at levels like that during T4 infection, yields a significantly compacted nucleoid containing MotB and H-NS. motB overexpression dysregulates hundreds of host genes; ∼70% are within the hns regulon. In infected cells overexpressing motB, 33 T4 late genes are expressed early, and the T4 early gene repEB, involved in replication initiation, is up ∼5-fold. We postulate that MotB represents a phage-encoded NAP that aids infection in a previously unrecognized way. We speculate that MotB-induced compaction may generate more room for T4 replication/assembly and/or leads to beneficial global changes in host gene expression, including derepression of much of the hns regulon. 

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