Chapter 26 : Second Chromosomes and Megaplasmids in Bacteria

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This chapter reviews some aspects of the many major secondary DNA replicons that have been characterized from organisms that possess multireplicon genomes. Nonprimary replicons are often referred to as secondary chromosomes if they are essential for cell viability or as megaplasmids. A modern source of ambiguity in genomic biology is whether certain replicons represent megaplasmids or second chromosomes. Multircplicon genomes in bacteria could conceivably arise by a number of mechanisms, but two general mechanisms seem most plausible. A major secondary replicon may derive from an ancestral chromosome via an excision event where the excised DNA possesses an origin of replication that is either a duplicated copy of the region or a second, redundant origin that was previously resident on that part of the ancestral chromosome. Chromosome I has an origin of replication typical of other bacterial chromosomes, and the region encodes the , , , and genes. A greater proportion of chromosome II is also devoted to genes encoding transporters and solute binding proteins and to genes encoding enzymes required in central intermediary metabolism. The linear chromosome encodes and other genes required for synthesis of several cell surface polysaccharides and also the cellulose synthesis genes that are required for host attachment. Copies of genes required for the synthesis of some amino acids and for certain enzyme cofactors are carried uniquely on the megaplasmid as are the flagellar genes.

Citation: MacLellan S, Sibley C, Finan T. 2004. Second Chromosomes and Megaplasmids in Bacteria, p 529-542. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch26
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Image of Figure 1.
Figure 1.

Cladogram of ParA ATPases. Amino acid sequences were obtained from tbe NCBI database and aligned using ClustalX. In the case of multiple ParA-like sequences on a replicon, the ParA sequence closest to the origin of replication was used. The maximum likelihood tree was generated with a quartet puzzling program, TreePuzzle 5.0. Branch lengths were computed using a model of substitution and rate heterogeneity ( ). Support for the internal branches of the quartet puzzling tree topology is shown in percent values at each node. Accession numbers are provided in the descending order they appear in the tree: NP_700354, NP_541070, NP_109505, NP_534416, AAB69096, NP_436589, NP_53616I, NP_535377, AAC83387, NP_436540, CAA62234, CAA28295, NP.233494, NP_763081, AAA99230, CAA28769, NP_085829, CAA62234, NP_720345, NP_387441, NP_532810, NP_699034, NP.538927, NP_105341, NP_76727l, NP_422547, NP_220452, NP_742172, NP_391977, NP_521445, NP_720272, NP_232399, NP_759973.

Citation: MacLellan S, Sibley C, Finan T. 2004. Second Chromosomes and Megaplasmids in Bacteria, p 529-542. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch26
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Table 1.

Examples of multipartite bacterial genomes

Citation: MacLellan S, Sibley C, Finan T. 2004. Second Chromosomes and Megaplasmids in Bacteria, p 529-542. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch26

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