Causal analysis of CpG suppression in the Mycoplasma genome

M. Goto, T. Washio, Masaru Tomita

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Some bacterial genomes are known to have low CpG dinucleotide frequencies. While their causes are not clearly understood, the frequency of CpG is suppressed significantly in the genome of Mycoplasma genitalium, but not in that of Mycoplasma pneumoniae. We compared orthologous gene pairs of the two closely related species to analyze CpG substitution patterns between these two genomes. We also divided genome sequences into three regions: protein-coding, noncoding, and RNA-coding, and obtained the CpG frequencies for each region for each organism. It was found that the observed/expected ratio of CpG dinucleotides is low in both the protein-coding and noncoding regions; while that ratio is in the normal range in the RNA-coding region. Our results indicate that CpG suppression of the Mycoplasma genome is not caused by (1) biased usage amino acid; (2) biased usage of synonymous codon; or (3) methylation effects by the CpG methyltransferase in the genomes of their hosts. Instead, we consider it likely that a certain global pressure, such as genome-wide pressure for the advantages of DNA stability or replication, has the effect of decreasing CpG over the entire genome, which, in turn, resulted in the biased codon usage.

Original languageEnglish
Pages (from-to)51-58
Number of pages8
JournalMicrobial and Comparative Genomics
Volume5
Issue number1
Publication statusPublished - 2000

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Mycoplasma
Genes
Genome
Codon
Open Reading Frames
Mycoplasma genitalium
Bacterial Genomes
Pressure
Mycoplasma pneumoniae
Untranslated RNA
Methyltransferases
Methylation
Reference Values
RNA
Amino Acids
Proteins
Substitution reactions
DNA

ASJC Scopus subject areas

  • Molecular Biology
  • Applied Microbiology and Biotechnology

Cite this

Causal analysis of CpG suppression in the Mycoplasma genome. / Goto, M.; Washio, T.; Tomita, Masaru.

In: Microbial and Comparative Genomics, Vol. 5, No. 1, 2000, p. 51-58.

Research output: Contribution to journalArticle

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