Codon usage bias and mutation constraints reduce the level of error minimization of the genetic code

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

Studies on the origin of the genetic code compare measures of the degree of error minimization of the standard code with measures produced by random variant codes but do not take into account codon usage, which was probably highly biased during the origin of the code. Codon usage bias could play an important role in the minimization of the chemical distances between amino acids because the importance of errors depends also on the frequency of the different codons. Here I show that when codon usage is taken into account, the degree of error minimization of the standard code may be dramatically reduced, and shifting to alternative codes often increases the degree of error minimization. This is especially true with a high CG content, which was probably the case during the origin of the code. I also show that the frequency of codes that perform better than the standard code, in terms of relative efficiency, is much higher in the neighborhood of the standard code itself, even when not considering codon usage bias; therefore alternative codes that differ only slightly from the standard code are more likely to evolve than some previous analyses suggested. My conclusions are that the standard genetic code is far from being an optimum with respect to error minimization and must have arisen for reasons other than error minimization.

Original languageEnglish (US)
Pages (from-to)258-266
Number of pages9
JournalJournal Of Molecular Evolution
Volume59
Issue number2
DOIs
StatePublished - Aug 1 2004

Fingerprint

Genetic Code
genetic code
codons
Codon
mutation
Mutation
code
amino acids
Amino Acids

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

@article{298bb376fd904f459bf0fd3f54dc4310,
title = "Codon usage bias and mutation constraints reduce the level of error minimization of the genetic code",
abstract = "Studies on the origin of the genetic code compare measures of the degree of error minimization of the standard code with measures produced by random variant codes but do not take into account codon usage, which was probably highly biased during the origin of the code. Codon usage bias could play an important role in the minimization of the chemical distances between amino acids because the importance of errors depends also on the frequency of the different codons. Here I show that when codon usage is taken into account, the degree of error minimization of the standard code may be dramatically reduced, and shifting to alternative codes often increases the degree of error minimization. This is especially true with a high CG content, which was probably the case during the origin of the code. I also show that the frequency of codes that perform better than the standard code, in terms of relative efficiency, is much higher in the neighborhood of the standard code itself, even when not considering codon usage bias; therefore alternative codes that differ only slightly from the standard code are more likely to evolve than some previous analyses suggested. My conclusions are that the standard genetic code is far from being an optimum with respect to error minimization and must have arisen for reasons other than error minimization.",
author = "Marco Archetti",
year = "2004",
month = "8",
day = "1",
doi = "10.1007/s00239-004-2620-0",
language = "English (US)",
volume = "59",
pages = "258--266",
journal = "Journal of Molecular Evolution",
issn = "0022-2844",
publisher = "Springer New York",
number = "2",

}

Codon usage bias and mutation constraints reduce the level of error minimization of the genetic code. / Archetti, Marco.

In: Journal Of Molecular Evolution, Vol. 59, No. 2, 01.08.2004, p. 258-266.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Codon usage bias and mutation constraints reduce the level of error minimization of the genetic code

AU - Archetti, Marco

PY - 2004/8/1

Y1 - 2004/8/1

N2 - Studies on the origin of the genetic code compare measures of the degree of error minimization of the standard code with measures produced by random variant codes but do not take into account codon usage, which was probably highly biased during the origin of the code. Codon usage bias could play an important role in the minimization of the chemical distances between amino acids because the importance of errors depends also on the frequency of the different codons. Here I show that when codon usage is taken into account, the degree of error minimization of the standard code may be dramatically reduced, and shifting to alternative codes often increases the degree of error minimization. This is especially true with a high CG content, which was probably the case during the origin of the code. I also show that the frequency of codes that perform better than the standard code, in terms of relative efficiency, is much higher in the neighborhood of the standard code itself, even when not considering codon usage bias; therefore alternative codes that differ only slightly from the standard code are more likely to evolve than some previous analyses suggested. My conclusions are that the standard genetic code is far from being an optimum with respect to error minimization and must have arisen for reasons other than error minimization.

AB - Studies on the origin of the genetic code compare measures of the degree of error minimization of the standard code with measures produced by random variant codes but do not take into account codon usage, which was probably highly biased during the origin of the code. Codon usage bias could play an important role in the minimization of the chemical distances between amino acids because the importance of errors depends also on the frequency of the different codons. Here I show that when codon usage is taken into account, the degree of error minimization of the standard code may be dramatically reduced, and shifting to alternative codes often increases the degree of error minimization. This is especially true with a high CG content, which was probably the case during the origin of the code. I also show that the frequency of codes that perform better than the standard code, in terms of relative efficiency, is much higher in the neighborhood of the standard code itself, even when not considering codon usage bias; therefore alternative codes that differ only slightly from the standard code are more likely to evolve than some previous analyses suggested. My conclusions are that the standard genetic code is far from being an optimum with respect to error minimization and must have arisen for reasons other than error minimization.

UR - http://www.scopus.com/inward/record.url?scp=4043056141&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=4043056141&partnerID=8YFLogxK

U2 - 10.1007/s00239-004-2620-0

DO - 10.1007/s00239-004-2620-0

M3 - Article

C2 - 15486699

AN - SCOPUS:4043056141

VL - 59

SP - 258

EP - 266

JO - Journal of Molecular Evolution

JF - Journal of Molecular Evolution

SN - 0022-2844

IS - 2

ER -