Comparative analyses of base compositions, DNA sizes, and dinucleotide frequency profiles in archaeal and bacterial chromosomes and plasmids.

Hiromi Nishida

doi:10.1155/2012/342482

Abstract

In the present paper, I compared guanine-cytosine (GC) contents, DNA sizes, and dinucleotide frequency profiles in 109 archaeal chromosomes, 59 archaeal plasmids, 1379 bacterial chromosomes, and 854 bacterial plasmids. In more than 80% of archaeal and bacterial plasmids, the GC content was lower than that of the host chromosome. Furthermore, most of the differences in GC content found between a plasmid and its host chromosome were less than 10%, and the GC content in plasmids and host chromosomes was highly correlated (Pearson's correlation coefficient r = 0.965 in bacteria and 0.917 in archaea). These results support the hypothesis that horizontal gene transfers have occurred frequently via plasmid distribution during evolution. GC content and chromosome size were more highly correlated in bacteria (r = 0.460) than in archaea (r = 0.195). Interestingly, there was a tendency for archaea with plasmids to have higher GC content in the chromosome and plasmid than those without plasmids. Thus, the dinucleotide frequency profile of the archaeal plasmids has a bias toward high GC content.

Highlights

DNA base composition, guanine-cytosine (GC) content, is a bacterial taxonomic marker
109 archaeal chromosomes, 59 archaeal plasmids, 1379 bacterial chromosomes, and 854 bacterial plasmids were used from the database OligoWeb, searching oligonucleotide frequencies
The GC contents of bacterial plasmids were found to be lower than those of the host chromosomes (Figure 1, Supplementary Table S1), which is consistent with a previous study [11]

Summary

Introduction

DNA base composition, guanine-cytosine (GC) content, is a bacterial taxonomic marker. Assessing the dinucleotide frequency profile, a genome signature, of a genomic DNA sequence is a powerful tool to compare different chromosomes and plasmids [2,3,4,5,6]. GC content and DNA size are correlated [7,8,9,10]. Plasmids, and inserted sequences, the GC contents are lower than those of their host chromosomes [11]. Replication of and transcription from plasmid DNA are controlled mainly by factors encoded by the chromosome of the host organism. It is hypothesized that the GC content and genome signature of a plasmid are similar to those of the chromosome of the host organism. It is believed that horizontal gene transfers have occurred frequently via plasmid distribution during evolution [12]

Methods

Results

Conclusion