Synonymous codon usage in Cryptosporidium parvum: identification of two distinct trends among genes

RJ Grocock, PM Sharp*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

The usage of alternative synonymous codons in the apicomplexan Cryptosporidium parvum has been investigated. A data set of 54 genes was analysed. Overall. A- and U-ending codons predominate. as expected in an A + T-rich genome. Two trends of codon usage variation among genes were identified using correspondence analysis. The primary trend is in the extent of usage of a subset of presumably translationally optimal codons. that are used at significantly higher frequencies in genes expected to be expressed at high levels. Fifteen of the 18 codons identified as optimal are more G + C-rich than the otherwise common codons. so that codon selection associated with translation opposes the general mutation bias, Among 40 genes with lower frequencies of these optimal codons, a secondary trend in G + C content was identified. In these genes, G + C content at synonymously variable third positions of codons is correlated with that in 5' and 3' flanking sequences, indicative of regional variation in G + C content, perhaps reflecting regional variation in mutational biases. (C) 2001 Australian Society for Parasitology Inc. Published by Elsevier Science Ltd. All rights reserved.

Original languageEnglish
Pages (from-to)402-412
Number of pages11
JournalInternational Journal For Parasitology
Volume31
Issue number4
Publication statusPublished - Apr 2001

Keywords

  • ESCHERICHIA-COLI
  • G+C CONTENT
  • TRANSLATIONAL SELECTION
  • BIAS
  • ENTAMOEBA-HISTOLYTICA
  • DROSOPHILA-MELANOGASTER
  • Cryptosporidium parvum
  • EXPRESSED GENES
  • GENOME
  • UNICELLULAR ORGANISMS
  • gene expression
  • codon usage
  • mutation bias
  • SACCHAROMYCES-CEREVISIAE

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