Structure and Function of the Bacterial Genome. Charles J. Dorman
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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; Lahooti et al. 2005; Peterson and Reich 2010). Leucine can also influence the oligomeric state of LRP, perhaps helping to explain the distinct effects (including no effects) that branched chain amino acids can have on different LRP regulated systems.
The LRP protein competes with the Dam methylase for access to two 5′‐GATC‐3′ sites in the pap and pef fimbrial operons of uropathogenic E. coli and Salmonella, respectively. This outcome of competition decides if the Dam sites will be methylated or not and this, in turn, determines if the fimbrial structural genes will be transcribed or not. The result is a stochastic switch that is reset by the synthesis of hemimethylated DNA during chromosome (pap) or virulence plasmid (pef) replication (Hernday et al. 2002; Nicholson and Low 2000). In contrast, LRP acts as a directionality determinant at the invertible fimS genetic switch that governs the phase‐variable expression of type 1 fimbriae in E. coli, an inversion event that is catalysed by two tyrosine integrases, FimB and FimE (Corcoran and Dorman 2009; Kelly et al. 2006). In the case of pap/pef, LRP is acting as a DNA‐binding protein in competition with a DNA modifying enzyme; in the case of fimS, LRP's ability to shape DNA is likely to be influencing the directionality of the On/Off invertible genetic switch. It also plays a role in virulence in M. tuberculosis by modulating the innate immune response of macrophage (Liu and Cai 2018). These examples illustrate the versatility of the LRP protein and its ability to influence diverse systems by different molecular mechanisms.
1.54 Small, Acid‐soluble Spore Proteins, SASPs
Aerobic and anaerobic spore‐forming bacteria rely on small, acid‐soluble spore proteins (SASPs) to protect their DNA from damage during the long (or very long) periods that may elapse between sporulation and spore germination. Most research on SASPs has been concerned with those produced by Bacillus spp. and Clostridium spp., aerobic and anaerobic organisms, respectively (Setkow 2007). The SASPs fall into two broad groups, the α/β type and the γ type. Their genes are transcribed with the G sigma factor (Nicholson et al. 1989), protect the genomic DNA in the spore, and after germination they are cannibalised as a source of amino acids by the emerging bacterial cell (Hackett and Setlow 1988; Setlow 1988). SASPs are specialists in that they are expressed specifically to accompany the genome during its period of storage in the spore and are degraded during germination; they do not have physiological roles in vegetative cells, yet they exhibit properties that are shared with NAPs. For example, they stiffen DNA, and eliminate DNA bends, they increase the persistence length of DNA and introduce supertwists into relaxed or nicked circular DNA (Griffith et al. 1994; Nicholson et al. 1990), including plasmids from spores (Nicholson and Setlow 1990). When cloned ssp genes expressing SASPs are introduced to E. coli, they induce nucleoid condensation; however, they also induce mutagenesis and cell killing (Setlow et al. 1991, 1992). The mutations accompanied expression of the B. subtilis SspC SASP and required RecA and Pol V, suggesting that the effects followed the arrest of replication forks in growing E. coli; a derivative of SspC that was deficient in DNA binding