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ISSN
1672-9145
Acta Biochim Biophys Sin
2005, 37(1): 1–10
CN 31-1940/Q
Analysis of Synonymous Codon Usage Bias in Chlamydia
Hui LÜ, Wei-Ming ZHAO*, Yan
ZHENG, Hong WANG, Mei QI, and Xiu-Ping YU
Department of
Medical Microbiology, School of Medicine, Shandong University, Jinan 250012,
China
Abstract Chlamydiae are obligate
intracellular bacterial pathogens that cause ocular and sexually transmitted diseases,
and are associated with cardiovascular diseases. The analysis of codon usage
may improve our understanding of the evolution and pathogenesis of Chlamydia
and allow reengineering of target genes to improve their expression for gene
therapy. Here, we analyzed the codon usage of C. muridarum, C.
trachomatis (here indicating biovar trachoma and LGV), C. pneumoniae,
and C. psittaci using the codon usage database and the CUSP (Create a codon
usage table) program of EMBOSS (The European Molecular Biology Open Software
Suite). The results show that the four genomes have similar codon usage
patterns, with a strong bias towards the codons with A and T at the third codon
position. Compared with Homo sapiens, the four chlamydial species show
discordant seven or eight preferred codons. The ENC (effective number of codons
used in a gene)-plot reveals that the genetic heterogeneity in Chlamydia
is constrained by the G+C content, while translational selection and gene
length exert relatively weaker influences. Moreover, mutational pressure
appears to be the major determinant of the codon usage variation among the
chlamydial genes. In addition, we compared the codon preferences of C.
trachomatis with those of E. coli, yeast, adenovirus and Homo
sapiens. There are 23 codons showing distinct usage differences between C.
trachomatis and E. coli, 24 between C. trachomatis and
adenovirus, 21 between C. trachomatis and Homo sapiens, but only
six codons between C. trachomatis and yeast. Therefore, the yeast system
may be more suitable for the expression of chlamydial genes. Finally, we
compared the codon preferences of C. trachomatis with those of six
eukaryotes, eight prokaryotes and 23 viruses. There is a strong positive
correlation between the differences in coding GC content and the variations in
codon bias (r=0.905, P<0.001). We conclude that the variation
of codon bias between C. trachomatis and other organisms is much less
influenced by phylogenetic lineage and primarily determined by the extent of
disparities in GC content.
Key words Chlamydia; codon usage
bias; GC content; gene expression
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Received: September 29,
2004
Accepted: December 10, 2004
This work was supported by the grants from the National Natural
Science Foundation of China (No. 30271193), International Cooperation and Exchange
Fund from the NSFC (No. 30170045) and the Natural Science Foundation of
Shandong Province (No. Y2002004)
*Corresponding author: Tel, 86-531-8382579; E-mail,
[email protected]