title: Analysis of the distribution of functionally relevant rare codons.
abstract: BACKGROUND
  The substitution of rare codons with more frequent codons is a commonly applied method in heterologous gene expression to increase protein yields. However, in some cases these substitutions lead to a decrease of protein solubility or activity. To predict these functionally relevant rare codons, a method was developed which is based on an analysis of multisequence alignments of homologous protein families.
  
  
  RESULTS
  The method successfully predicts functionally relevant codons in fatty acid binding protein and chloramphenicol acetyltransferase which had been experimentally determined. However, the analysis of 16 homologous protein families belonging to the alpha/beta hydrolase fold showed that functionally rare codons share no common location in respect to the tertiary and secondary structure.
  
  
  CONCLUSIONS
  A systematic analysis of multisequence alignments of homologous protein families can be used to predict rare codons with a potential impact on protein expression. Our analysis showed that most genes contain at least one putative rare codon rich region. Rare codons located near to those regions should be excluded in an approach of improving protein expression by an exchange of rare codons by more frequent codons.
authors.affiliation: Institute of Technical Biochemistry, Allmandring 31, 70569 Stuttgart, Germany. Michael.Widmann@itb.uni-stuttgart.de
authors.forename: Michael
authors.initials: M
authors.lastname: Widmann
authors.forename: Marie
authors.initials: M
authors.lastname: Clairo
authors.forename: Jürgen
authors.initials: J
authors.lastname: Dippon
authors.forename: Jürgen
authors.initials: J
authors.lastname: Pleiss
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D015500:Chloramphenicol O-Acetyltransferase / Q000737:chemistry / Q000235:genetics*; D003062:Codon; D048209:Echinococcus granulosus / Q000737:chemistry; D004926:Escherichia coli / Q000201:enzymology; D050556:Fatty Acid-Binding Proteins / Q000737:chemistry / Q000235:genetics*; D006867:Hydrolases / Q000737:chemistry / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D014176:Protein Biosynthesis; D017510:Protein Folding; D017386:Sequence Homology, Amino Acid
chemical_list: D003062:Codon; D050556:Fatty Acid-Binding Proteins; D015500:Chloramphenicol O-Acetyltransferase; D006867:Hydrolases