Codon optimality controls differential mRNA translation during amino acid starvation.
It is common wisdom that codon usage bias has evolved in the selection for efficient translation, in which highly expressed genes are encoded predominantly by optimal codons. However, a growing body of evidence suggests regulatory roles for non-optimal codons in translation dynamics. Here we report that in mammalian cells, non-optimal codons play a critical role in promoting selective mRNA translation during amino acid starvation. During starvation, in contrast to genes encoding ribosomal proteins whose translation is highly sensitive to amino acid deprivation, translation of genes involved in the cellular protein degradation pathways remains unaffected. We found that these two gene groups bear different codon composition, with non-optimal codons being highly enriched in genes encoding the ubiquitin-proteasome system. Supporting the selective tRNA charging model originally proposed in Escherichia coli, we demonstrated that tRNA isoacceptors decoding rare codons are maintained in translating ribosomes under amino acid starvation. Finally, using luciferase reporters fused with endogenous gene-derived sequences, we show that codon optimality contributes to differential mRNA translation in response to amino acid starvation. These results highlight the physiological significance of codon usage bias in cellular adaptation to stress.
Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA.
Mridusmita
M
Saikia
Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illnois 60637, USA.
Xiaoyun
X
Wang
Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA.
Yuanhui
Y
Mao
Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA.
Ji
J
Wan
Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illnois 60637, USA.
Tao
T
Pan
Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA.
Shu-Bing
SB
Qian
D000596:Amino Acids / Q000378:metabolism*; D003062:Codon; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000235:genetics*; D012343:RNA, Transfer / Q000235:genetics; D012270:Ribosomes / Q000378:metabolism
D000596:Amino Acids; D003062:Codon; D012333:RNA, Messenger; D012343:RNA, Transfer
adaptation; codon bias; genetic code; starvation; tRNA; translation