et al. 2013; Le et al. 2013; Le and Laub 2016; Lioy et al. 2018; Meyer et al. 2018). Work that exploited site‐specific recombination as a measure of interaction frequency within the bacterial genome suggested that transcription activity and the associated changes in local DNA topology have a structural function in the nucleoid (Booker et al. 2010; Higgins 2014). Furthermore, the global level of DNA supercoiling in the nucleoid can be tuned by treating the bacterium with rifampicin, an inhibitor of RNA polymerase (Rovinskiy et al. 2012). Experiments with trimethylpsoralen crosslinking have provided evidence that a gradient of DNA supercoiling exists extending from the origin of chromosome replication to the Ter macrodomain (Lal et al. 2016). Bioinformatic and experimental studies show that the distribution of binding sites around the chromosome for DNA gyrase is non‐uniform, with more sites being detected close to the origin of replication (Jeong et al. 2004; Sobetzko et al. 2012; Sutormin et al. 2019). This could indicate that the Ori‐proximal part of the chromosome is the most underwound, contradicting the data from the psoralen‐binding‐and‐crosslinking studies (Lal et al. 2016). On the other hand, it may indicate a need to compensate for the paucity of negative supercoiling in the Ori‐proximal part of the chromosome that is predicted by those studies. Further evidence that the chromosome is not uniformly supercoiled has come from investigations in which supercoiling‐sensitive genes have been placed at different locations in the genome (Bryant et al. 2014). A comprehensive survey of the effects of gene position on transcription in E. coli showed that the propensity for transcription varies with chromosomal location: horizontally acquired genetic elements are associated with quiescent regions while ribosomal and other metabolic genes are in highly active zones (Scholz et al. 2019). It should be noted, however, that several studies which have explored the influence of gene position (including the possible contribution of differences in local DNA supercoiling) did not detect clear changes in the level of expression of the test gene(s) at different sites around the chromosome (Block et al. 2012; Brambilla and Sclavi 2015; Chandler and Pritchard 1975; Miller and Simons 1993; Pavitt and Higgins 1993; Schmid and Roth 1987; Sousa et al. 1997; Thompson and Gasson 2001; Ying et al. 2014).
1.34 Nucleoid‐associated Proteins (NAPs) and Nucleoid Structure
Sequence‐dependent DNA‐binding proteins such as MaoP, MatP, SeqA, and SlmA play important roles in the organisation of the chromosome in the nucleoid. Yet the term ‘nucleoid‐associated protein’, or NAP, is usually reserved for another group of DNA‐binding proteins, not all of which are sequence‐dependent for DNA binding. Most NAPs were discovered in roles other than organising the nucleoid. Several were first encountered as contributors to the efficient operation of site‐specific recombination systems in bacteria or their phage (reviewed in Dorman and Bogue 2016). Later, their more general contributions to cell physiology became appreciated. We have already encountered two, FIS and IHF, as components of the systems that govern the initiation of chromosome replication (Section 1.3). Originally, FIS was identified as an enhancer‐binding protein that improved the efficiency of the DNA inversion events responsible for phase‐variable expression of tail fibre genes in bacteriophage Mu, and for flagellar phase variation in Salmonella (Koch and Kahmann 1986; Johnson et al. 1986). IHF was detected as an essential factor for the site‐specific entry of the bacteriophage lambda genome into the attλ site on the chromosome of E. coli (Nash and Robertson 1981) (Section 1.35). These and other NAPs have emerged as important regulators of a multitude of bacterial genes (Dillon and Dorman 2010). They have mechanisms of action that typically involve the making of adjustments to local DNA architecture. In many cases, these adjustments affect gene expression at the level of transcription (or beyond) and include direct or indirect effects on nucleoid structure. A summary of the key features of some of the most important (i.e. best‐studied) NAPs is given in the following sections.
1.35 DNA Bending Protein Integration Host Factor (IHF)
IHF is essential both for the integration and the excision of bacteriophage lambda into/from the E. coli chromosome (Bushman et al. 1984; Seah et al. 2014) (Figure 1.17). These site‐specific recombination reactions are catalysed by the tyrosine integrase Int (Craig and Nash 1983; Han et al. 1994; Hoess et al. 1980; Kikuchi and Nash 1979; Tong et al. 2014). IHF is usually expressed as a heterodimer composed of an alpha and a beta subunit encoded by the ihfA and ihfB genes, respectively, which are located at different places on the chromosome (Haluzi et al. 1991; Mendelson et al. 1991; Miller and Friedman 1980; Nash et al. 1987). IHF has strict DNA sequence requirements for binding and its binding sites typically are located in A+T‐rich DNA (Miller and Friedman 1980). The protein inserts a looped beta strand with a proline amino acid at its apex into the minor groove of the DNA at the target site, producing a distortion that causes the DNA duplex to bend (Engelhorn and Geiselmann 1998; Engelhorn et al. 1995; Rice et al. 1996; Sun et al. 1996; Vivas et al. 2012) (Figure 1.18). The combined effects of the bends introduced by each subunit is to create a turn of up to 180° in the pathway taken by the DNA helix (Rice et al. 1996; Sugimura and Crothers 2006). This allows IHF to play important roles in nucleoid architecture, chromosome replication, site‐specific recombination, transposition, plasmid maintenance, and transcription regulation (Biek and Cohen 1989; Crellin et al. 2004; Dorman and Bogue 2016; Prieto et al. 2012; Ryan et al. 2004; Saha et al. 2013; Swinger and Rice 2004). In terms of amino acid sequence, protein structure, and subunit composition, IHF is a close relative of the HU NAP. Both proteins have an αβ heterodimeric structure and all four proteins have similar amino acid sequences (Dey et al. 2017). IHF appears to be a specialist member of the HU superfamily of DNA‐binding proteins, a group that includes relatives encoded by the human genome that contribute to chromosome partitioning (Burroughs et al. 2017). Although IHF is usually considered as acting in an αβ heterodimeric form, transcriptomic studies carried out in Salmonella indicate that bacteria expressing just the α, just the β, and both α and β subunits, are altered in expression of distinct‐yet‐overlapping groups of genes, implying that IHF can form homodimers that are biologically active (Mangan et al. 2006). Indeed, previous investigations have found that IHF homodimers have DNA‐binding activity (Hiszczynska‐Sawicka and Kur 1997; Werner et al. 1994; Zablewska and Kur 1995; Zulianello et al. 1994). When reading the older IHF literature, the reader should be aware that in 1996 the names of the genes were changed from himA and himD (where ‘him’ referred to H.I. Miller) to ihfA and ihfB, respectively (Weisberg et al. 1996).
Figure 1.17 Integration of bacteriophage lambda at the lambda attachment site on the E. coli chromosome and excision of the prophage. Integration and excision are catalysed by the phage‐encoded Int tyrosine integrase. In the integration step, the recombining sites at attP (on the phage) and attB (on the bacterial chromosome) undergo intermolecular site‐specific recombination to generate the lambda prophage. Excision recreates attB and attP from attL and attR, the direct repeats that form the boundaries between the prophage and chromosomal DNA. The nucleotide sequences of each of these four elements are shown in the figure. In addition to the Int recombinase, the integration step requires the architectural protein, integration host factor, IHF. Excision also requires IHF together with the phage‐encoded directionality factor, Xis, and the host‐encoded FIS protein. Xis is inhibitory to integration and FIS has a stimulatory effect on excision (see Ball and Johnson 1991; Seah et al. 2014). Binding sites for these proteins are represented by labelled arrows (P, Int), squares (H, IHF), ovals (X, Xis), and a triangle for a FIS (F) binding site. Binding sites in the P′ arm of the free circular phage genome have primes added to their designations and these are retained in the attL segment of the prophage. Not every protein‐binding site is occupied in each reaction. Occupied sites have a solid filling while unoccupied
