A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons.
Ambiguity in genetic codes exists in cases where certain stop codons are alternatively used to encode non-canonical amino acids. In selenoprotein transcripts, the UGA codon may either represent a translation termination signal or a selenocysteine (Sec) codon. Translating UGA to Sec requires selenium and specialized Sec incorporation machinery such as the interaction between the SECIS element and SBP2 protein, but how these factors quantitatively affect alternative assignments of UGA has not been fully investigated. We developed a model simulating the UGA decoding process. Our model is based on the following assumptions: (1) charged Sec-specific tRNAs (Sec-tRNASec) and release factors compete for a UGA site, (2) Sec-tRNASec abundance is limited by the concentrations of selenium and Sec-specific tRNA (tRNASec) precursors, and (3) all synthesis reactions follow first-order kinetics. We demonstrated that this model captured two prominent characteristics observed from experimental data. First, UGA to Sec decoding increases with elevated selenium availability, but saturates under high selenium supply. Second, the efficiency of Sec incorporation is reduced with increasing selenoprotein synthesis. We measured the expressions of four selenoprotein constructs and estimated their model parameters. Their inferred Sec incorporation efficiencies did not correlate well with their SECIS-SBP2 binding affinities, suggesting the existence of additional factors determining the hierarchy of selenoprotein synthesis under selenium deficiency. This model provides a framework to systematically study the interplay of factors affecting the dual definitions of a genetic codon.
Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
Yen-Fu
YF
Chen
Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.|Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.
Hsiu-Chuan
HC
Lin
Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.|Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.
Kai-Neng
KN
Chuang
Institute of Statistical Science, Academia Sinica, Taipei, Taiwan.
Chih-Hsu
0000-0003-4034-8960
CH
Lin
Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.|Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.
Hsueh-Chi S
HS
Yen
Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.|Institute of Statistical Science, Academia Sinica, Taipei, Taiwan.
Chen-Hsiang
0000-0002-9224-5800
CH
Yeang
D018387:Codon, Initiator / Q000235:genetics*; D018388:Codon, Terminator / Q000235:genetics*; D003198:Computer Simulation; D008957:Models, Genetic; D014176:Protein Biosynthesis / Q000235:genetics; D011506:Proteins / Q000235:genetics*; D017279:Selenocysteine / Q000235:genetics*; D051140:Selenoproteins / Q000096:biosynthesis / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods
D018387:Codon, Initiator; D018388:Codon, Terminator; D011506:Proteins; D051140:Selenoproteins; D017279:Selenocysteine