Structure and Function of the Bacterial Genome. Charles J. Dorman
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(Haykinson and Johnson 1993; Semsey et al. 2004). It also has RNA‐binding activity, enabling it to influence translation (Balandina et al. 2001).
Each HU subunit inserts a beta sheet with an apical proline amino acid into the minor groove of the DNA at the binding site, inducing the DNA to bend (Figure 1.18). The bend angle is typically in the range of 105°–140° and bends are not coplanar, having a dihedral angle that is consistent with the path taken in negatively supercoiled DNA (Swinger et al. 2003). The flexibility in the bend angle, coupled with the absence of a strict nucleotide sequence for DNA binding, may allow HU to participate as an architectural component in a wide variety of DNA‐based transactions.
The α and β subunits of HU are encoded, respectively, by the hupA and hupB genes, located at distinct positions on the chromosome: hupA hupB double mutants that fail to express the HU protein display a filamentous cell phenotype because of disruption of the cell cycle due to the arrest of DNA replication (Dri et al. 1991). HU interacts with the DnaA protein at oriC where it stimulates formation of the initiation complex in chromosome replication. Like IHF, HU is usually heterodimeric and is composed of an alpha and a beta subunit. The alpha subunit seems to have the primary responsibility for interacting with DnaA. This preference for the alpha subunit may facilitate enhanced HU–DnaA interaction at early stages of growth when an HU α2 homodimer predominates rather than the αβ heterodimer (Chodavarapu et al. 2008). HU can also influence chromosome replication initiation indirectly by repressing the expression of the gene that encodes SeqA (Lee, H., et al. 2001), the protein that sequesters oriC and excludes DnaA (Han et al. 2003; Slater et al. 1995; von Freiesleben et al. 1994).
The HU protein can form nucleosome‐like structures in E. coli that are dependent on the local HU‐to‐DNA ratio (Sagi et al. 2004). It has been described as insulating transcription units on the chromosome by preventing changes in DNA supercoiling caused by transcription in one unit from influencing an adjacent one (Berger et al. 2016). HU may be particularly important for the maintenance of DNA supercoiling levels in the Ter macrodomain as the bacterium enters the stationary phase of the growth cycle (Lal et al. 2016). It has been reported to induce, together with FIS, weak and transient domain boundaries around the E. coli chromosome (Wu et al. 2019).
In laboratory‐grown cultures, the subunit composition of the HU protein changes as a function of growth phase: In lag phase, as the bacterium adapts to its new environment, the α2 form of HU occurs; in exponential growth the αβ form predominates and the β2 form is detected as the culture enters stationary phase (Claret and Rouvière ‐Yaniv 1997). The changing subunit composition of HU and the different DNA interaction properties of the distinct HU forms may contribute to processes that differentially compact the chromosome in the nucleoid and affect gene expression patterns (Hammel et al. 2016). Transcriptomic studies in Salmonella have shown that each form of the HU protein seems to govern a distinct group of genes, with overlaps between the three sub‐regulons (Mangan et al. 2011).
1.37 The Very Versatile FIS Protein
FIS is the Factor for Inversion Stimulation, so called because it was discovered originally as an important architectural element in the DNA inversion mechanisms responsible for the phase‐variable expression of flagella in Salmonella (Johnson et al. 1986) and of tail fibre proteins in bacteriophage Mu (Koch and Kahmann 1986). FIS is now known to contribute to a wide range of molecular events in bacteria, including DNA replication (Cassler et al. 1995; Filutowisz et al. 1992; Gille et al. 1991), site‐specific recombination (Dhar et al. 2009; McLean et al. 2013), transposition (Weinreich and Reznikoff 1992), transcription regulation (Grainger et al. 2008; Hirvonen et al. 2001; Kelly et al. 2004; Pemberton et al. 2002), bacteriophage life cycles (Betermier et al. 1993; van Drunen et al. 1993; Papagiannis et al. 2007; Seah et al. 2014), illegitimate recombination (Shanado et al. 1997), and chromosome domain boundary formation (Hardy and Cozzarelli 2005; Wu et al. 2019).
1.38 FIS and the Early Exponential Phase of Growth
FIS is a homodimeric NAP that is encoded by the second gene in the dusB‐fis operon and shows strong homology to the DNA‐binding domain of the NtrC transcription factor (Bishop et al. 2002; Morett and Bork 1998). Transcription of the fis gene is maximal in the early stages of exponential growth and FIS plays an important role in boosting the expression of genes that encode components of the translational machinery of the cell (Appleman et al. 1998; Ball and Johnson 1991; Hirvonen et al. 2001; Osuna et al. 1995). FIS binds to the major groove of the DNA using a helix‐turn‐helix (HTH) motif that interacts with A+T‐rich sites that match a weak consensus sequence (Hancock et al. 2016). The protein uses an induced fit binding mechanism that compresses the minor groove between those parts of the major groove that accommodate the HTH motifs of the two subunits (Figure 1.18) (Hancock et al. 2016; Stella et al. 2010). This creates a bend in the DNA of 65° according to FIS‐DNA co‐crystal structure data (Stella et al. 2010) with bends of up to 90° also being reported (Kostrewa et al. 1992; Pan et al. 1996).
Transcription factors that introduce bends into DNA can facilitate additional contacts between DNA (including proteins bound to that DNA) located upstream of the promoter and bound RNA polymerase, increasing the efficiency of transcription initiation (Huo et al. 2006; Rivetti et al. 1999; Verbeek et al. 1991). FIS acts as a ‘conventional’ transcription factor at some promoters, making protein–protein contacts with RNA polymerase (Bokal et al. 1997) and its DNA‐bending activity has the potential to enhance the efficiency of the early stages of the transcription process. FIS can also influence promoter function without the need to contact RNA polymerase. The leuV operon consists of three genes that encode three of the four tRNA1Leu isoreceptors and its promoter is under the positive control of FIS. The single binding site for the FIS protein upstream of the leuV promoter is located in a DNA segment that is prone to becoming single‐stranded under the torsional stress imposed by negative supercoiling. This phenomenon is known as supercoiling‐induced DNA duplex destabilisation, SIDD (Benham 1992, 1993). Binding of the FIS protein to its site within the SIDD element displaces the tendency towards duplex destabilisation to the nearest susceptible site, in this case, the leuV promoter – assisting in the formation there of an open transcription complex (Opel et al. 2004). This mechanism is not peculiar to FIS and has been demonstrated for the IHF NAP too (Sheridan et al. 1998). It is likely to be used at many other promoters and represents an under‐researched aspect of the link between NAP binding, DNA topology, and promoter activation.
FIS has also been shown to create a nucleoprotein complex at promoters with a series of FIS‐binding sites that stabilise the topological state of the DNA in ways that favour transcription initiation (Rochman et al. 2004). Many of these promoters express genes that encode components of the translational apparatus, such as ribosomal proteins, tRNA, and rRNA (Champagne and Lapointe 1998; Newlands et al. 1992; Nilsson et al. 1990). Increased translation capacity is necessary to support rapid bacterial growth, so the stimulatory role of FIS during the lag‐to‐log phase of the growth cycle is important. Consistent with this is the observation that while mutants that lack the FIS protein remain viable, they display reduced competitive fitness when grown in co‐culture with their otherwise isogenic wild‐type parent (Schneider et al. 1997).
1.39 FIS and the Stringent Response
Stable RNA (tRNA and rRNA) genes that are stimulated by FIS are subject to control by the stringent response (Condon et al. 1995b; Potrykus and Cashel 2008). Here, an intracellular signal known as an ‘alarmone’ interferes with the ability of RNA polymerase to transcribe a subset of genes, including the stable RNA genes. The alarmone is guanosine tetraphosphate (ppGpp) or pentaphosphate (pppGpp) and it is synthesised in response to a build‐up of uncharged tRNA molecules and the interaction of the RelA protein with stalled ribosomes (Brown et al. 2016; Hauryliuk et al. 2015; Richter 1976) (see Section 6.18 for a more complete description