Structure and Function of the Bacterial Genome. Charles J. Dorman

detail to our picture of the nucleoid‐structuring contributions of MukBEF. However, the MukBEF‐Topo‐IV complex also has functions in chromosome segregation that do depend on the catalytic properties of Topo IV. The complex is responsible for the timely decatenation of newly replicated ori copies and their segregation (Figure 1.10), while also contributing to the management of DNA supercoiling set points (Zawadzki et al. 2015). The primary site of action of the MukBEF‐Topo‐IV complex has been regarded as ori, with MukBEF recruiting the topoisomerase to that region of the chromosome (Nicolas et al. 2014). It is becoming clear that MukBEF‐Topo‐IV has a much more dynamic relationship with the chromosome, both spatially and temporally, and that its relationship with the MatP protein in ter has an important management role in its choreography. The final stages of chromosome replication and the associated need to effect decatenation in a timely manner are consistent with a need to grant MukBEF‐Topo‐IV access to ter to perform the necessary cohesion/decatenation steps, with MatP then evicting the complex, making it available for re‐association with ori (Nolivos et al. 2016).

1.22 MatP, the matS Site and Ter Organisation

      The 17‐kDa MatP protein binds to 23 high‐affinity matS sites found exclusively within the Ter macrodomain of the E. coli chromosome (Mercier et al. 2008; Thiel et al. 2012). The Ter domains of both chromosome I and chromosome II of V. cholerae also have matS sites that are bound by MatP and these affect the spatiotemporal coordination of the replication and segregation of both chromosomes (Demarre et al. 2014). Counterparts of matS are present in the Ter regions of the chromosomes of Erwinia carotovora, S. enterica serovar Typhimurium LT2, and Yersinia pestis (Mercier et al. 2008). MatP forms bridged tetramers that link distant matS sites to condense the Ter DNA (Dupaigne et al. 2012). MatP interacts with ZapB, a cell division‐associated protein, to position the Ter macrodomain at the cell midpoint and to ensure its segregation (Espéli et al. 2012). With proteins ZapA, C, and D, ZapB functions to organise the Z ring that acts as a scaffold for the assembly of the complexes responsible for cell division (Buss et al. 2013). ZapB is dependent on ZapA for interaction with the tubulin‐like FtsZ protein (Galli and Gerdes 2010). MatP also interacts with the MukBEF‐Topo‐IV complex at the Ter macrodomain, displacing MukBEF from Ter and facilitating its interaction with the Ori macrodomain. This is part of a step‐wise process in which MukBEF manoeuvres the chromosome such that Ori and Ter adopt their assigned positions at the pole and mid‐cell, respectively, by the time cell division takes place (Lioy et al. 2018; Nolivos et al. 2016). Together with MukBEF and SeqA, MatP is part of a group of proteins found exclusively in bacteria that express the Dam methyltransferase (Brezellec et al. 2006; Mercier et al. 2008).

1.23 MaoP and the maoS Site

The MaoP protein is important for the organisation of the Ori macrodomain (Duigou and Boccard 2017; Valens et al. 2016). It binds to a 17‐bp sequence that lies adjacent to the maoP gene. Both MaoP and maoS are required for accurate positioning of Ori within the cell during the division cycle and for restricting the ability of the Ori macrodomain to interact with other territories of the chromosome, especially the Right Macrodomain and the NS‐Right region (Valens et al. 2016). MaoP has been described as belonging to a class of DNA‐binding proteins that has co‐evolved with Dam, including MatP (see below), MukBEF, and SeqA: all of these proteins are involved in chromosome replication/segregation (Brezellec et al. 2006; Valens et al. 2016).

1.24 SlmA and Nucleoid Occlusion

      The nucleoid is protected from bisection by the Z ring through a process known as nucleoid occlusion, or NO (Woldringh et al. 1991). If NO fails to occur the result is guillotining of the chromosome, fragmentation of the DNA, and cell death. In E. coli, the DNA‐binding SlmA protein plays a key role in NO through an interaction with FtsZ (Bernhardt and de Boer 2005). SlmA works by interfering with the polymerisation activity of FtsZ, inhibiting Z‐ring formation (Cho, H., et al. 2011). SlmA binds to DNA and to FtsZ simultaneously. Its DNA‐binding sites are distributed around the chromosome, but it does not bind in the Ter macrodomain. The inhibitory activity of SlmA on FtsZ polymerisation outside of Ter is thought to delay septum formation until after the Ter macrodomain has been replicated (Tonthat et al. 2011).

1.25 The Min System and Z Ring Localisation

      The cell division septum must be placed centrally if rod‐shaped bacteria like E. coli are to divide into daughter cells of equal size. This placement is achieved through a gradient of FtsZ‐inhibitor Min proteins. The gradients extend from regions of maximum Min density at the cell poles to a region of minimum density (and therefore minimum FtsZ inhibition) at mid‐cell (Bramkamp and van Baarle 2009; Monahan and Harry 2012; Rowlett and Margolin 2015). While nucleoid occlusion operates to prevent guillotining of the nucleoid by the closing division septum, the Min system works independently of the nucleoid and is concerned with the correct localisation of the septum. Indeed, bacteria that are rendered chromosomeless still tend to form the cell division septum at the mid cell (Sun et al. 1998).

      The term ‘Min’ is derived from ‘minicell’, a phenotype in E. coli min mutants (and other rod‐shaped bacteria) where eccentric placement of the division septum produces two daughter cells of uneven length, one of which is too small to accommodate a chromosome (Adler et al. 1967; Reeve et al. 1973), although it can house plasmids (Roozen et al. 1971).

E. coli uses the MinC protein to inhibit FtsZ polymerisation (Hu et al. 1999; Hu and Lutkenhaus 2000) but, unlike B. subtilis, it lacks a cell‐pole‐anchoring protein that can be used to recruit MinC and other Min complex components to that part of the envelope. It relies instead on a MinC protein gradient extending from each pole to the midcell, with MinC forming a complex with the membrane‐binding MinD ParA‐like ATPase protein (de Boer et al. 1989, 1991; Hu and Lutkenhaus 2003). A third protein, MinE, is used to target the MinCD complex to the cell poles, with MinE (and phospholipid) stimulating the ATPase activity of MinD (Hu and Lutkenhaus 2001). MinE binds to the membrane at the pole, targeting MinCD complexes, displacing both MinC and MinD and stimulating ATP hydrolysis by MinD (Loose et al. 2011; Park et al. 2011). MinE and MinD set up a high‐speed oscillating system in which MinC is trafficked from pole to pole, on average spending a minimum of time at mid‐cell and most of the time at the poles (Raskin and de Boer 1997; Hu and Lutkenhaus 1999; Hu et al. 2002). It is the relative paucity of MinC at mid‐cell that diminishes the inhibitory influence on FtsZ polymerisation and Z‐ring formation (Hu and Lutkenhaus 1999; Raskin and de Boer 1999a,b). In addition to inhibiting FtsZ polymerisation by protein‐protein interaction, the oscillation of MinC populations from pole to pole has an impact on the distribution of other FtsZ‐interactors. Together with FtsZ itself, the ZapA, ZapB, and ZipA proteins oscillate oppositely to MinC and with a similar dynamic pattern. ZapB does not bind FtsZ directly but through ZapA, which does bind FtsZ. ZipA, with FtsA, connects FtsZ to the cytoplasmic membrane (Pichoff and Lutkenhaus 2005) while ZapA‐ZapB stimulates Z‐ring formation and stabilises it (Buss et al. 2013; Galli and Gerdes 2010; Gueiros‐Filho and Losick 2002). Therefore, the oscillatory movements of MinC proteins probably trigger periodic assembly and disassembly of the Z ring complexes (Bisicchia et al. 2013; Thanedar and Margolin 2004).

      B. subtilis possesses the cell‐pole‐targeting protein DivIVA, which is involved both in chromosome attachment at the pole in sporulating cells (Section 1.10) and in directing the cellular localisation of MinC (Cha and Stewart 1997; Edwards and Errington 1997). The utility of DivIVA as a general pole‐targeting protein arises from its ability to sense cell membrane curvature, which is maximal at the poles (Edwards et al. 2000; Lenarcic et al. 2009). The MinC protein is bound by MinD and an adaptor protein, MinJ, connects this complex to DivIVA (Bramkamp et al. 2008; Patrick and Kearns 2008). As the division septum develops, invagination of the membrane, and the associated membrane curvature, recruit DivIVA from the pole to the mid‐cell (which is the soon‐to‐be pole