当前位置： SCI文献检索 > PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA期刊下所有文献 > Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli.

Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli.

Abstract：

:The degeneracy of the genetic code allows nucleic acids to encode amino acid identity as well as noncoding information for gene regulation and genome maintenance. The rare arginine codons AGA and AGG (AGR) present a case study in codon choice, with AGRs encoding important transcriptional and translational properties distinct from the other synonymous alternatives (CGN). We created a strain of Escherichia coli with all 123 instances of AGR codons removed from all essential genes. We readily replaced 110 AGR codons with the synonymous CGU codons, but the remaining 13 "recalcitrant" AGRs required diversification to identify viable alternatives. Successful replacement codons tended to conserve local ribosomal binding site-like motifs and local mRNA secondary structure, sometimes at the expense of amino acid identity. Based on these observations, we empirically defined metrics for a multidimensional "safe replacement zone" (SRZ) within which alternative codons are more likely to be viable. To evaluate synonymous and nonsynonymous alternatives to essential AGRs further, we implemented a CRISPR/Cas9-based method to deplete a diversified population of a wild-type allele, allowing us to evaluate exhaustively the fitness impact of all 64 codon alternatives. Using this method, we confirmed the relevance of the SRZ by tracking codon fitness over time in 14 different genes, finding that codons that fall outside the SRZ are rapidly depleted from a growing population. Our unbiased and systematic strategy for identifying unpredicted design flaws in synthetic genomes and for elucidating rules governing codon choice will be crucial for designing genomes exhibiting radically altered genetic codes.

journal_name

Proc Natl Acad Sci U S A

journal_title

Proceedings of the National Academy of Sciences of the United States of America

authors

Napolitano MG,Landon M,Gregg CJ,Lajoie MJ,Govindarajan L,Mosberg JA,Kuznetsov G,Goodman DB,Vargas-Rodriguez O,Isaacs FJ,Söll D,Church GM

doi

10.1073/pnas.1605856113

subject

Has Abstract

pub_date

2016-09-20 00:00:00

pages

E5588-97

issue

eissn

0027-8424

issn

1091-6490

pii

1605856113

journal_volume

113

pub_type

杂志文章

在线工具

Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli.