Structure and Function of the Bacterial Genome. Charles J. Dorman
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fulfils this role in C. crescentus by forming a matrix at the pole and interacting with the ParB‐parS complex at oriC (Bowman et al. 2008; Ebersbach et al. 2008). Displacement of parS to a different chromosome site interferes with this arrangement: while parS continues to be located at the pole oriC, from which parS is now disconnected, lies elsewhere in the cell (Umbarger et al. 2011).
The cytoplasmic protein HubP connects the origin of replication of ChrI to the cell pole in V. cholerae. The connection is made between HubP and the ParAI‐ParBI‐parS complex. In addition to its membrane location, the HubP protein is connected to the cell wall through a peptidoglycan‐binding LysM motif, a feature that is required for its polar localisation (Yamaichi et al. 2012).
Polar attachment of the chromosome occurs in B. subtilis at the onset of sporulation. The RacA protein interacts with the DivIVA membrane protein that is located at the cell pole (Ben‐Yehuda et al. 2003; Lenarcic et al. 2009; Oliva et al. 2010; Ramamurthi and Losick 2009; Wu and Errington 2003). RacA also binds to ram (RacA binding motifs) that are found in 25 copies at oriC (Ben‐Yehuda et al. 2005). In the absence of RacA or DivIVA, sporulating bacteria fail to position the chromosome correctly and have the oriC at mid‐cell. This misplacement leads to the production of prespore compartments without chromosomes (Ben‐Yehuda et al. 2003). B. subtilis cells do not have their chromosomes attached to the cell pole during vegetative growth, although their origins occupy positions that alternate between pole‐proximal and at quarter‐cell, arrangements that require the cytoplasmic SMC complex (Wang, X., et al. 2014), just as the MukBEF equivalent in E. coli is required for that organism's chromosome to exhibit its customary ori‐Ter orientation during rapid growth (Danilova et al. 2007).
1.11 Some Bacterial Chromosomes Are Linear
Most of the literature on bacterial chromosomes describes work with covalently closed, circular molecules. On the face of it, chromosome circularity is not essential for survival: work with E. coli has shown that linearisation of its circular chromosome through a phage‐mediated process that leaves the ends closed by DNA hairpins does not interfere significantly with the life of the bacterium (Cui et al. 2007). Going in the other direction, the linear chromosome of Streptomyces lividans can be circularised without killing the microbe, although its genetic instability increases (Volff et al. 1997).
Some organisms have linear chromosomes naturally. For example, Borrelia burgdorferi, the spirochete and causative agent of Lyme disease, has a complex genome consisting of a linear chromosome and 23 plasmids, some of which are circular while others are linear (Chaconas and Kobryn 2010). Essential metabolic functions are encoded by the plasmids, so these are parts of the core genome and not simply ancillary components. The ends of the linear DNA molecules are closed covalently by hairpin telomere‐like structures (Barbour and Garon 1987). Such structures are not found widely in bacteria; other examples have been reported in the plant pathogen Agrobacterium tumefaciens and in some phage (Chaconas and Kobryn 2010; Slater et al. 2013). Telomere resolvases, enzymes that are related to the integrase family of tyrosine site‐specific recombinases, promote fusions between the linear replicons at their telomeres, driving genome evolution (Huang et al. 2017). Replication of linear replicons in Borrelia spp. is thought to occur bidirectionally from a central origin, producing a double‐stranded dimeric circle that is resolved by the telomere resolvase (ResT in B. burgdorferi) to produce two linear molecules with closed telomeres at their ends. Positive DNA supercoiling, probably arising from the local overwinding of the DNA during replication, assists telomere resolution (Bankhead et al. 2006). Although the role of DNA supercoiling, positive or negative, in linear replicons has not been studied comprehensively, there is some evidence that it is a factor in setting the level of transcription of promoters found on linear plasmids when those replicons are artificially circularised. This has led to the proposal that linear replicons may avoid instability caused by topological changes in circular molecules (Beaurepaire and Chaconas 2007). Streptomyces spp. also have linear chromosomes and linear plasmids, and intra‐replicon interactions mediated by ‘terminal proteins’ that are covalently bound to the telomeres allow the creation of negatively supercoiled DNA circles from the linear replicons (Tsai et al. 2011). These negative supercoils are relaxed by DNA topoisomerase I, which is a component of the telomere complex in Streptomyces. It has been proposed that negative supercoiling is likely to be important for both DNA replication and for transcription, especially of genes located close to the telomeres (Tsai et al. 2011).
1.12 Some Bacteria Have More than One Chromosome
Among bacteria that have more than one chromosome are the well‐studied organisms A. tumefaciens (Allardet‐Servent et al. 1993), Brucella spp. (Jumas‐Bilak et al. 1998), Rhodobacter sphaeroides spp. (Choudhary et al. 2007; Suwanto and Kaplan 1989), and Vibrio spp. (Val et al. 2014). Of the organisms listed here, A. tumefaciens, has one circular and one linear chromosome; the others have two circular chromosomes. Paracoccus denitrificans is a bacterium that has three chromosomes (Winterstein and Ludwig 1998).
Are all of the chromosomes in a multi‐chromosome genome ‘equal’? It appears that one chromosome is usually the primary replicon, with the other being relegated to secondary chromosome status. For example, the two chromosomes of the pathogen V. cholerae are designated chromosomes, ChrI and ChrII, with ChrI having the majority of the metabolically important and virulence‐associated genes. ChrII does harbour essential genes, so its designation as a second chromosome is justified, despite its having plasmid‐like features. For example, the origin of replication of ChrII shows structural features that are similar to those of plasmids, which is consistent with the secondary chromosome having evolved from an ancestral plasmid (Orlova et al. 2017). The plasmid‐like nature of ChrII is also emphasised by its encoding plasmid RK2‐like toxin systems that ensure post‐segregation killing of those V. cholerae cells that lose ChrII (Yuan et al. 2011). The replication initiation system of ChrI resembles that of E. coli: initiation of replication of each chromosome is independent of, but coordinated with, that of the other (Duigou et al. 2006). ChrII begins replicating later in the cell cycle than the larger ChrI, but both finish together. This has been interpreted as a mechanism that compensates for the differences in size of the two molecules and the need to end replication simultaneously so that the chromosomes can be segregated together and that any dimers can be resolved simultaneously (Rasmussen et al. 2007). Further investigation has revealed the generality of coordinated termination of replication in members of the Vibrionaceae with two chromosomes (Kemter et al. 2018). ChrI and ChrII each possess their own ParAB‐parS systems and use these for efficient segregation of chromosome copies at cell division (Fogel and Waldor 2005; Yamaichi et al. 2007, 2011).
1.13 Plasmids
In many bacteria, autonomously replicating and segregating genetic elements called plasmids accompany the chromosome in the cell. Like most bacterial chromosomes, plasmids are usually covalently closed, circular DNA molecules, but this is not always the case: some are linear. Certain plasmids are categorised as additional chromosomes (or ‘chromids’) due to their size, their carriage of genes normally found on bona fide chromosomes, their unitary copy number, and/or the coordination of their replication and segregation with the main chromosome (Barloy‐Hubler and Jebbar 2008; Fournes et al. 2018). Other very big plasmids are called ‘mega‐plasmids’ and can encode functions required for symbiosis or virulence (Schwartz 2008). In general, plasmids carry genes that are useful rather than essential, so their loss is not usually fatal to the cell; in contrast, loss of the chromosome is fatal.
Plasmids came to attention due to their involvement in bacterial sex (the Fertility, or F factor) and when it was discovered that they carried genes for resistance to antimicrobial agents, including antibiotics (R factors). Investigations of these phenomena led to the discovery of plasmid conjugation and the existence of other mobile genetic elements such as transposons and integrons. Plasmid studies revealed a wealth of information about plasmid replication processes, segregation systems, and copy number control mechanisms. This field also