Second Chromosomes and Megaplasmids in Bacteria

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 oriC 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 dnaA, dnaN, recF, and gyrA 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 exoC 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.