Evolution of exceptionally large genes in prokaryotes

Analysis of bacterial genomic sequences revealed an average bacterial gene size of approximately 1 kb. However, genes with a size >10 kb were also noted. This study investigates the prevalence, possible function, and origin of exceptionally large-size genes (ELSGs; >10 kb) in prokaryotes. Forty-two ELSGs (0.03%) were identified after searching more than 170,000 genes in 46 bacterial and 11 archaeal species. These ELSGs were found in diverse species including both archaeal and eubacterial kingdoms. Homology analysis of these ELSGs indicates that, other than encoding nonribosomal peptide synthesis enzymes, many ELSGs likely encode cell surface proteins. The ELSGs have different degrees of codon usage bias, and evidence of gene expression is observed in some cases. Both intragenic domain duplication and gene recombination are major means contributing to gene size expansion in these ELSGs. Direct evidence of gene fusion was identified in only one ELSG. Finally, several ELSGs showed recent horizontal transfer signatures. In summary, ELSGs are commonly present in prokaryotes. Aside from their large size, the evolutionary process of ELSGs is quite heterogeneous.