Compositional discordance between prokaryotic plasmids and host chromosomes.
BACKGROUND
Most plasmids depend on the host replication machinery and possess partitioning genes. These properties confine plasmids to a limited range of hosts, yielding a close and presumably stable relationship between plasmid and host. Hence, it is anticipated that due to amelioration the dinucleotide composition of plasmids is similar to that of the genome of their hosts. However, plasmids are also thought to play a major role in horizontal gene transfer and thus are frequently exchanged between hosts, suggesting dinucleotide composition dissimilarity between plasmid and host genome. We compared the dinucleotide composition of a large collection of plasmids with that of their host genomes to shed more light on this enigma.


RESULTS
The dinucleotide frequency, coined the genome signature, facilitates the identification of putative horizontally transferred DNA in complete genome sequences, since it was found to be typical for a certain genome, and similar between related species. By comparison of the genome signature of 230 plasmid sequences with that of the genome of each respective host, we found that in general the genome signature of plasmids is dissimilar from that of their host genome.


CONCLUSIONS
Our results show that the genome signature of plasmids does not resemble that of their host genome. This indicates either absence of amelioration or a less stable relationship between plasmids and their host. We propose an indiscriminate lifestyle for plasmids preserving the genome signature discordance between these episomes and host chromosomes.
van Passel
Mark W J
MW
Academic Medical Center, Department of Medical Microbiology, Amsterdam, The Netherlands. m.w.vanpassel@amc.uva.nl
Bart
Aldert
A
Luyf
Angela C M
AC
van Kampen
Antoine H C
AH
van der Ende
Arie
A
D001482:Base Composition; D025065:Borrelia burgdorferi / Q000235:genetics; D002875:Chromosomes / Q000737:chemistry* / Q000235:genetics*; D002876:Chromosomes, Bacterial / Q000737:chemistry / Q000235:genetics; D004247:DNA / Q000737:chemistry / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D022761:Gene Transfer, Horizontal; D023281:Genomics; D054884:Host-Pathogen Interactions / Q000235:genetics*; D010957:Plasmids / Q000737:chemistry* / Q000235:genetics*; D011387:Prokaryotic Cells
D004269:DNA, Bacterial; D004247:DNA