Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation

To investigate the possible influence of the local rates of translation on protein folding, 16 consecutive rare (in Escherichia coli) codons in the chloramphenicol acetyltransferase (CAT) gene have been replaced by frequent ones. Site‐directed silent mutagenesis reduced the pauses in translation of CAT in E. coli S30 extract cell‐free system and led to the acceleration of the overall rate of CAT protein synthesis. At the same time, the silently mutated protein (with unaltered protein sequence) synthesized in the E. coli S30 extract system was shown to possess 20% lower specific activity. The data suggest that kinetics of protein translation can affect the in vivo protein‐folding pathway, leading to increased levels of protein misfolding.

[1]  A. Brown,et al.  The folding of the bifunctional TRP3 protein in yeast is influenced by a translational pause which lies in a region of structural divergence with Escherichia coli indoleglycerol-phosphate synthase. , 1994, European journal of biochemistry.

[2]  Søren Brunak,et al.  Protein structure and the sequential structure of mRNA: α‐Helix and β‐sheet signals at the nucleotide level , 1996 .

[3]  V. Gurevich,et al.  Preparative in vitro mRNA synthesis using SP6 and T7 RNA polymerases. , 1991, Analytical biochemistry.

[4]  G. Kramer,et al.  Co-translational folding. , 1999, Current opinion in structural biology.

[5]  A. Brown,et al.  The efficiency of folding of some proteins is increased by controlled rates of translation in vivo. A hypothesis. , 1987, Journal of molecular biology.

[6]  Ellis Rj,et al.  Discovery of molecular chaperones. , 1996 .

[7]  M Yarus,et al.  Codon contexts from weakly expressed genes reduce expression in vivo. , 1989, Journal of molecular biology.

[8]  G. Kramer,et al.  The effect of a hydrophobic N-terminal probe on translational pausing of chloramphenicol acetyl transferase and rhodanese. , 1999, Journal of molecular biology.

[9]  A. Helenius,et al.  Cotranslational folding and calnexin binding during glycoprotein synthesis. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[10]  F. Hartl,et al.  Co-translational domain folding as the structural basis for the rapid de novo folding of firefly luciferase , 1999, Nature Structural Biology.

[11]  C. Kurland,et al.  Errors of heterologous protein expression. , 1996, Current opinion in biotechnology.

[12]  A. Fedorov,et al.  Protein folding and assembly in a cell-free expression system. , 1998, Methods in enzymology.

[13]  Xie Tao,et al.  The relationship between synonymous codon usage and protein structure , 1998 .

[14]  W V Shaw,et al.  Structure of chloramphenicol acetyltransferase at 1.75-A resolution. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[15]  W. V. Shaw,et al.  O-Acetyltransferases for chloramphenicol and other natural products , 1997, Antimicrobial agents and chemotherapy.

[16]  Stephen Neidle,et al.  An Integrated Sequence-Structure Database incorporating matching mRNA sequence, amino acid sequence and protein three-dimensional structure data , 1998, Nucleic Acids Res..

[17]  M. Orešič,et al.  Specific correlations between relative synonymous codon usage and protein secondary structure. , 1998, Journal of molecular biology.

[18]  H. Schägger,et al.  Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. , 1987, Analytical biochemistry.

[19]  A. Komar,et al.  Kinetics of translation of γB crystallin and its circularly permutated variant in an in vitro cell‐free system: possible relations to codon distribution and protein folding , 1995, FEBS letters.

[20]  M Yarus,et al.  Rates of aminoacyl-tRNA selection at 29 sense codons in vivo. , 1989, Journal of molecular biology.

[21]  M. Sørensen,et al.  Absolute in vivo translation rates of individual codons in Escherichia coli. The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate. , 1991, Journal of molecular biology.

[22]  R. Kopito,et al.  Cotranslational Ubiquitination of Cystic Fibrosis Transmembrane Conductance Regulator in Vitro * , 1998, The Journal of Biological Chemistry.

[23]  R. Jaenicke,et al.  What does protein refolding in vitro tell us about protein folding in the cell? , 1993, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[24]  T. Ikemura.  Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. , 1981, Journal of molecular biology.

[25]  Judith Frydman,et al.  Folding of nascent polypeptide chains in a high molecular mass assembly with molecular chaperones , 1994, Nature.

[26]  S. Anderson,et al.  Proper and improper folding of proteins in the cellular environment. , 1991, Annual review of microbiology.

[27]  M. Coffey,et al.  Co‐translational trimerization of the reovirus cell attachment protein. , 1996, The EMBO journal.

[28]  W. Greene,et al.  Cotranslational Biogenesis of NF-κB p50 by the 26S Proteasome , 1998, Cell.

[29]  A. Suyama,et al.  Two types of linkage between codon usage and gene‐expression levels , 1991, FEBS letters.

[30]  D. Wetlaufer,et al.  Folding of protein fragments. , 1981, Advances in protein chemistry.

[31]  E. V. Makeyev,et al.  Folding of firefly luciferase during translation in a cell‐free system. , 1994, The EMBO journal.

[32]  David W. E. Smith.  Problems of Translating Heterologous Genes in Expression Systems: The Role of tRNA , 1996, Biotechnology progress.

[33]  E. V. Makeyev,et al.  Cotranslational folding of proteins. , 1995, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[34]  P Argos,et al.  Ribosome‐mediated translational pause and protein domain organization , 1996, Protein science : a publication of the Protein Society.

[35]  R. Jaenicke.  Role of accessory proteins in protein folding , 1993 .

[36]  A. Plückthun,et al.  Recent advances in producing and selecting functional proteins by using cell-free translation. , 1998, Current opinion in biotechnology.

[37]  I. Adzhubei,et al.  Nonuniform size distribution of nascent globin peptides, evidence for pause localization sites, and a cotranslational protein-folding model , 1991, Journal of protein chemistry.

[38]  H. Gilbert.  Protein chaperones and protein folding. , 1994, Current opinion in biotechnology.

[39]  E. Fisher,et al.  Regulated Co-translational Ubiquitination of Apolipoprotein B100 , 1998, The Journal of Biological Chemistry.

[40]  E. Craig,et al.  Protein Folding In Vivo: Unraveling Complex Pathways , 1997, Cell.

[41]  F. Hartl,et al.  Recombination of protein domains facilitated by co-translational folding in eukaryotes , 1997, Nature.

[42]  P Argos,et al.  Protein secondary structural types are differentially coded on messenger RNA , 1996, Protein science : a publication of the Protein Society.

[43]  A. Bera,et al.  Refolding of denatured lactate dehydrogenase by Escherichia coli ribosomes. , 1994, The Biochemical journal.

[44]  A. Horwich,et al.  GroEL‐Mediated protein folding , 1997, Protein science : a publication of the Protein Society.

[45]  A. Fedorov,et al.  Cotranslational Protein Folding* , 1997, The Journal of Biological Chemistry.

[46]  A. Fedorov,et al.  Contribution of cotranslational folding to the rate of formation of native protein structure. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[47]  J Solomovici,et al.  Does Escherichia coli optimize the economics of the translation process? , 1997, Journal of theoretical biology.

[48]  Logan S. Ahlstrom,et al.  Chaperone-assisted protein folding. , 1997, Current opinion in structural biology.

[49]  A. Leslie.  Refined crystal structure of type III chloramphenicol acetyltransferase at 1.75 A resolution. , 1990, Journal of molecular biology.

[50]  J. Vockley,et al.  High-level expression of an altered cDNA encoding human isovaleryl-CoA dehydrogenase in Escherichia coli. , 1995, Gene.

[51]  Stephen Neidle,et al.  Non‐random usage of ‘degenerate’ codons is related to protein three‐dimensional structure , 1996, FEBS letters.

[52]  C. Dasgupta,et al.  Reactivation of denatured proteins by 23S ribosomal RNA: role of domain V. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[53]  A. Weiss,et al.  Total synthesis and expression in Escherichia coli of a gene encoding human tropoelastin. , 1995, Gene.

[54]  D. Andrews,et al.  The signal recognition particle receptor alpha subunit assembles co‐translationally on the endoplasmic reticulum membrane during an mRNA‐encoded translation pause in vitro. , 1996, The EMBO journal.

[55]  A. Spirin,et al.  Cotranslational Folding of Globin* , 1997, The Journal of Biological Chemistry.

[56]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[57]  M. Huang,et al.  Aurintricarboxylic acid: inhibitor of initiation of protein synthesis. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[58]  D. Zhu.  Oligodeoxynucleotide-directed cleavage and repair of a single-stranded vector: a method of site-specific mutagenesis. , 1989, Analytical biochemistry.

[59]  K. V. van Wijk,et al.  Co-translational Assembly of the D1 Protein into Photosystem II* , 1999, The Journal of Biological Chemistry.

[60]  G. Kramer,et al.  Ribosomes and ribosomal RNA as chaperones for folding of proteins. , 1997, Folding & design.