and LEE− phenotypes among members of the EPEC population.
Ler is not a general antagonist of H‐NS because it binds only to a small subset of H‐NS targets in the genome, mostly those associated with the LEE pathogenicity island. The two proteins are dissimilar in amino acid sequence at their N‐termini but share similar C‐terminal domains, including the nucleic acid‐binding domain. However, a key arginine residue, found in Ler but not H‐NS, seems to underlie the more restricted range of Ler binding in DNA. Both proteins rely on an indirect readout mechanism for binding site recognition: in the case of Ler, the introduction of its arginine residue into the minor groove of DNA is permitted at only a subset of H‐NS binding sites (Cordeiro et al. 2011). This represents an interesting example of specialisation within the large family of H‐NS‐like proteins.
1.49 H‐NS Functional Homologues
Proteins performing a foreign‐gene‐silencing function analogous to that associated with H‐NS seem to be restricted to bacteria and to fall into four classes: H‐NS itself, Rok, MvaT, and Lsr2. In contrast, other types of NAP are widely distributed among prokaryotes. When a bacterium possesses one type of xenogeneic silencer, it typically will not also have an example of a different type, indicating specialisation between each protein type and its genome (Perez‐Rueda and Ibarra 2015).
1.50 H‐NS Functional Homologues: Rok from Bacillus spp.
The Rok protein was discovered in B. subtilis during an investigation of gene regulation in the competence system: Rok emerged as a transcription silencer of comK, the autoregulated master controller of competence (Hoa et al. 2002). Rok controls the expression of an extensive regulon of genes (Albano et al. 2005) and at some of its gene targets its activity is amplified by co‐binding of the DnaA protein (Seid et al. 2017). Rok binds to A+T‐rich DNA targets (Smits and Grossman 2010) and, like H‐NS, it has been implicated in the silencing of genes that have been acquired by HGT (Duan et al. 2018). Rok exhibits a higher preference for specific DNA sequences than other xenogenic silencer proteins (e.g. H‐NS) and these targets are relatively rare in the B. subtilis core genome, allowing Rok to focus on imported genes (Duan et al. 2018). Rok binds only in the DNA minor groove and uses a winged helix fold to do this. It avoids rigid poly‐A tracts with their very narrow minor grooves (Rohs et al. 2009), preferring 5′‐AACTA‐3′ and 5′‐TACTA‐3′ (both underrepresented in the core genome) and sequences that contain the flexible TpA step (Duan et al. 2018; Travers 2005).
1.51 H‐NS Functional Homologues: Lsr2 from Actinomycetes
The 12‐kDa Lsr2 NAP has been described as a functional analogue of H‐NS in actinomycetes, including Mycobacterium spp. (Datta et al. 2019a; Kriel et al. 2018). It targets genes that have high A+T content that are thought to have been acquired by HGT (Gordon et al. 2010). Like H‐NS, it can form DNA–protein–DNA bridges (Chen, J.M., et al. 2008), has a similar domain structure, and it can substitute functionally for H‐NS (Gordon et al. 2008). Lsr2 and H‐NS also bind DNA in the minor groove through a similar mechanism: using a so‐called AT‐hook‐like grip (Gordon et al. 2011). The similarities between Lsr2 and H‐NS are primarily functional and probably arose by convergent evolution: their amino acid sequences and their DNA‐binding domains have distinct tertiary structures (Gordon et al. 2010, 2011; Shindo et al. 1995). Like H‐NS, Lsr2 can polymerise along DNA to form stiff nucleoprotein structures from which other DNA‐binding proteins are excluded (Qu et al. 2013).
Rv3852 is a 13.8‐kDa protein that is highly conserved among Mycobacterium spp. and has been annotated as H‐NS because its N‐terminus resembles histone 1 from humans (Cole et al. 1998). Rv3852 is not an essential protein and a careful study of its properties rules out a role for it in controlling the virulence phenotype of Mycobacterium tuberculosis or in compacting the bacterial nucleoid (Odermatt et al. 2017).
1.52 H‐NS Functional Homologues: MvaT from Pseudomonas spp.
Identified originally as a transcription regulator of mvaAB, an operon involved in mevalonate metabolism in Pseudomonas mevalonii (Rosenthal and Rodwell 1998), MvaT is now recognised as a NAP with properties analogous to those of H‐NS (Castang and Dove 2010; Tendeng et al. 2003; Winardhi et al. 2012). MvaT binds to AT‐rich DNA in genes that have been acquired by HGT but it uses a binding mechanism that is distinct from other xenogeneic silencers: MvaT prefers binding sites that contain a series of flexible TpA steps and is tolerant of GC interruptions to the target sequence (Ding et al. 2015). MvaT has a paralogue, MvaU, with which it can form heteromeric complexes (Castang et al. 2008). Like MvaT, MvaU can bridge DNA and form filaments along the DNA that exclude other DNA‐binding proteins, enabling it to silence transcription (Winardhi et al. 2014). Mutants deficient in these proteins have altered phenotypes affecting prophage activation, pyocyanin expression biofilm production, and the elaboration of surface fimbriae (Li et al. 2009; Vallet et al. 2004; Vallet‐Gely et al. 2005).
Genes encoding MvaT‐like proteins are found on self‐transmissible plasmids and these proteins influence the transcriptome of the host cell in cooperation with their chromosomally encoded counterparts (Yun et al. 2015). Some bacteria express multiple members of the MvaT family; for example, Pseudomonas putida KT2440 encodes five MvaT orthologues: TurA, TurB, TurC, TurD, and TurE (Renzi et al. 2010). TurC, TurD, and TurE have species‐specific properties while TurA and TurB are similar to MvaT proteins found in all members of the Pseudomonadaceae. TurB is reported not to act generally as a repressor and to affect a smaller group of genes than TurA. These findings illustrate the versatile nature of MvaT‐like proteins and their capacity to acquire new functions through evolution (Renzi et al. 2010).
1.53 The Leucine‐responsive Regulatory Protein, LRP
The leucine‐responsive regulatory protein (LRP) DNA‐binding protein affects the expression of about 10% of the protein‐encoding genes in E. coli, many of which are involved in determining the structure of the bacterial surface, in transport, in metabolism, and in adaptation to stationary phase (Cho, B.K., et al. 2008, 2011; Engstrom and Mobley 2016; Tani et al. 2002). More recent data, based on ChIP‐seq and RNA‐seq analyses, have led to a revision of the estimate of LRP's influence to up to 38% of the E. coli genome (Kroner et al. 2019). In many cases, LRP interacts with target promoters in a poised mode, not influencing promoter activity until it operates in combination with other regulatory proteins; it also shifts between more‐ and less‐sequence specific DNA‐binding modes in response to nutrient signals (Kroner et al. 2019).
LRP contributes to the genetic switches that govern the phase‐variable expression of Pap and type 1 fimbriae in E. coli (and fimbriae in Salmonella), linking LRP to bacterial virulence and to biofilm formation (Aviv et al. 2017; Hernday et al. 2004; Kelly et al. 2009; Lahooti et al. 2005; McFarland et al. 2008). LRP is also a regulator of the stpA gene, encoding the H‐NS paralogue StpA that is both a DNA‐ and an RNA‐binding protein (Free and Dorman 1997; Sonden and Uhlin 1996). Together with StpA (and with H‐NS and FIS) LRP controls the transcription of rsd, the gene encoding the Rsd anti‐sigma factor that targets RpoD and, to a lesser extent, RpoS (Hofmann et al. 2011). These links confer on LRP the potential to influence transcription patterns throughout the genome.
The 18.8‐kDa LRP monomer forms octamers and hexadecamers and has the ability to wrap, bend, and bridge DNA (Chen et al. 2001); the B. subtilis homologue, LrpC, forms structures with DNA that are reminiscent of a eukaryotic histone core (Beloin et al. 2003b). LRP expression peaks at the transition from the exponential phase to the stationary phase of the growth cycle in rapidly growing E. coli (Landgraf et al. 1996). In keeping with its name, the interactions of LRP with its target genes can be potentiated, inhibited, or unaffected by leucine and other branched‐chain amino acids (Calvo and Matthews 1994;
