Selective charging of tRNA isoacceptors explains patterns of codon usage.
We modeled how the charged levels of different transfer RNAs (tRNAs) that carry the same amino acid (isoacceptors) respond when this amino acid becomes growth-limiting. The charged levels will approach zero for some isoacceptors (such as tRNA2Leu) and remain high for others (such as tRNA4Leu), as determined by the concentrations of isoacceptors and how often their codons occur in protein synthesis. The theory accounts for (synonymous) codons for the same amino acid that are used in ribosome-mediated transcriptional attenuation, the choices of synonymous codons in trans-translating transfermessenger RNA, and the overrepresentation of rare codons in messenger RNAs for amino acid biosynthetic enzymes.
Elf
Johan
J
Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, 751 24 Uppsala, Sweden.
Nilsson
Daniel
D
Tenson
Tanel
T
Ehrenberg
Mans
M
D000596:Amino Acids / Q000378:metabolism*; D000604:Amino Acyl-tRNA Synthetases / Q000378:metabolism; D003062:Codon; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000096:biosynthesis / Q000235:genetics; D018965:Frameshifting, Ribosomal; D015964:Gene Expression Regulation, Bacterial; D007700:Kinetics; D008433:Mathematics; D008957:Models, Genetic; D009876:Operon; D014176:Protein Biosynthesis; D011755:Pyrophosphatases / Q000235:genetics / Q000378:metabolism; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012343:RNA, Transfer / Q000235:genetics / Q000378:metabolism; D012346:RNA, Transfer, Amino Acyl / Q000235:genetics / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism
D000596:Amino Acids; D003062:Codon; D029968:Escherichia coli Proteins; D012329:RNA, Bacterial; D012333:RNA, Messenger; D012346:RNA, Transfer, Amino Acyl; C096222:tmRNA; D012343:RNA, Transfer; C027627:guanosine-3',5'-bis(diphosphate) 3'-pyrophosphatase; D011755:Pyrophosphatases; D000604:Amino Acyl-tRNA Synthetases