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 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 () than in archaea (). 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.

Summary: The γ‐butyrolactone regulatory system triggers secondary metabolism and/or morphological development in the Gram‐positive, soil‐dwelling, filamentous bacterial genus Streptomyces . The representative of the γ‐butyrolactones is A‐factor in Streptomyces griseus . AfsA is an enzyme for A‐factor biosynthesis and ArpA is the A‐factor receptor protein that serves as a transcriptional factor by using A‐factor as the ligand. Analysis of evolutional relations between AfsA including its homologues and ArpA including its homologues, all of which are widely distributed in Streptomyces , revealed great differences in the topologies of their phylogenetic trees. Therefore, the combinations of AfsA homologues and ArpA homologues in a given Streptomyces strain appear to have changed during the evolution. Even if an afsA homologue and an arpA homologue locate adjacently on the chromosome, the evolutional history of the individuals was found to be different in some Streptomyces strains. In addition, the phylogenetic analyses suggested that the ancestral ArpA protein had existed and functioned as a DNA‐binding protein, not as a γ‐butyrolactone receptor, before the appearance of a γ‐butyrolactone receptor protein in the course of the bacterial evolution. Some Streptomyces strains have plasmids encoding AfsA/ArpA homologues, which suggests that plasmids have played an important role in the distribution of afsA / arpA homologues. During the evolution, once a Streptomyces strain acquired different afsA / arpA homologues, it may have developed a new γ‐butyrolactone regulatory system reconstructing the regulatory systems for secondary metabolism and/or morphogenesis. This idea is consistent with the diverged combination of AfsA homologues and ArpA homologues in a Streptomyces strain.

Background: Plasmids are extrachromosomal elements that replicate autonomously, and many can be transmitted between bacterial cells through conjugation. Although the transcription pattern of genes on a plasmid can be altered by a change in host background, the expression range of plasmid genes that will result in phenotypic variation has not been quantitatively investigated. Results: Using a microarray with evenly tiled probes at a density of 9 bp, we mapped and quantified the transcripts of the carbazole catabolic plasmid pCAR1 in its original host Pseudomonas resinovorans CA10 and the transconjugant P. putida KT2440(pCAR1) during growth on either carbazole or succinate as the sole carbon source. We identified the operons in pCAR1, which consisted of nearly identical transcription units despite the difference in host background during growth on the same carbon source. In accordance with previous studies, the catabolic operons for carbazole degradation were upregulated during growth on carbazole in both hosts. However, our tiling array results also showed that several operons flanking the transfer gene cluster were transcribed at significantly higher levels in the transconjugant than in the original host. The number of transcripts and the positions of the transcription start sites agreed with our quantitative RT-PCR and primer extension results. Conclusion: Our tiling array results indicate that the levels of transcription for the operons on a plasmid can vary by host background. High-resolution mapping using an unbiased tiling array is a valuable tool for the simultaneous identification and quantification of prokaryotic transcriptomes including polycistronic operons and non-coding RNAs.