Molecular Biology and Evolution, Vol 16, 1484-1495, Copyright © 1999 by Society for Molecular Biology and Evolution
B Lafay and PM Sharp
The pattern of codon usage in the amitochondriate diplomonad Giardia
lamblia has been investigated. Very extensive heterogeneity was evident
among a sample of 65 genes. A discrete group of genes featured unusual
codon usage due to the amino acid composition of their products: these
variant surface proteins (VSPs) are unusually rich in Cys and, to a lesser
extent, Gly and Thr. Among the remaining 50 genes, correspondence analysis
revealed a single major source of variation in synonymous codon usage. This
trend was related to the extent of use of a particular subset of 21 codons
which are inferred to be those which are optimal for translation; at one
end of this trend were genes expected to be expressed at low levels with
near random codon usage, while at the other extreme were genes expressed at
high levels in which these optimal codons are used almost exclusively.
These optimal codons all end in C or G so G + C content at silent sites
varies enormously among genes, from values around 40%, expected to reflect
the background level of the genome, up to nearly 100%. Although VSP genes
are occasionally extremely highly expressed, they do not, in general, have
high frequencies of optimal codons, presumably because their high
expression is only intermittent. These results indicate that natural
selection has been very effective in shaping codon usage in G. lamblia.
These analyses focused on sequences from strains placed within G. lamblia
"assemblage A"; a few sequences from other strains revealed extensive
divergence at silent sites, including some divergence in the pattern of
codon usage.
ORIGINAL ARTICLE
Synonymous codon usage variation among Giardia lamblia genes and isolates
Institute of Genetics, University of Nottingham, Queens Medical Centre, England. lafay@com.univ-mrs.fr
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