Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis

Aaron Fluitt, Elsje Pienaar, Hendrik J Viljoen

Research output: Contribution to journalArticle

82 Citations (Scopus)

Abstract

It is generally accepted that the translation rate depends on the availability of cognate aa-tRNAs. In this study it is shown that the key factor that determines translation rate is the competition between near-cognate and cognate aa-tRNAs. The transport mechanism in the cytoplasm is diffusion, thus the competition between cognate, near-cognate and non-cognate aa-tRNAs to bind to the ribosome is a stochastic process. Two competition measures are introduced; C(i) and R(i) (i = 1, 64) are quotients of the arrival frequencies of near-cognates vs. cognates and non-cognates vs. cognates, respectively. Furthermore, the reaction rates of bound cognates differ from those of bound near-cognates. If a near-cognate aa-tRNA binds to the A site of the ribosome, it may be rejected at the anti-codon recognition step or proofreading step or it may be accepted. Regardless of its fate, the near-cognates and non-cognates have caused delays of varying duration to the observed rate of translation. Rate constants have been measured at a temperature of 20 °C by (Gromadski, K.B., Rodnina, M.V., 2004. Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol. Cell 13, 191-200). These rate constants have been re-evaluated at 37 °C, using experimental data at 24.5 °C and 37 °C (Varenne, S., et al., 1984. Translation in a non-uniform process: effect of tRNA availability on the rate of elongation of nascent polypeptide chains. J. Mol. Biol. 180, 549-576). The key results of the study are: (i) the average time (at 37 °C) to add an amino acid, as defined by the ith codon, to the nascent peptide chain is: τ(i) = 9.06 + 1.445 × [10.48C(i) + 0.5R(i)] (in ms); (ii) the misreading frequency is directly proportional to the near-cognate competition, E(i) = 0.0009C(i); (iii) the competition from near-cognates, and not the availability of cognate aa-tRNAs, is the most important factor that determines the translation rate - the four codons with highest near-cognate competition (in the case of E. coli) are [GCC] > [CGG] > [AGG] > [GGA], which overlap only partially with the rarest codons: [AGG] < [CCA] < [GCC] < [CAC]; (iv) based on the kinetic rates at 37 °C, the average time to insert a cognate amino acid is 9.06 ms and the average delay to process a near-cognate aa-tRNA is 10.45 ms and (vii) the model also provides estimates of the vacancy times of the A site of the ribosome - an important factor in frameshifting.

Original languageEnglish (US)
Pages (from-to)335-346
Number of pages12
JournalComputational Biology and Chemistry
Volume31
Issue number5-6
DOIs
StatePublished - Oct 1 2007

Fingerprint

ribosomes
Transfer RNA
Ribosomes
Peptides
Fidelity
peptides
Kinetics
Synthesis
kinetics
synthesis
Codon
availability
Availability
amino acids
Amino acids
Time-average
Rate constants
Rate Constant
Amino Acids
Stochastic Processes

Keywords

  • Mistranslation frequencies
  • Ribosome kinetics
  • Translation
  • tRNA availability

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Organic Chemistry
  • Computational Mathematics

Cite this

Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis. / Fluitt, Aaron; Pienaar, Elsje; Viljoen, Hendrik J.

In: Computational Biology and Chemistry, Vol. 31, No. 5-6, 01.10.2007, p. 335-346.

Research output: Contribution to journalArticle

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N2 - It is generally accepted that the translation rate depends on the availability of cognate aa-tRNAs. In this study it is shown that the key factor that determines translation rate is the competition between near-cognate and cognate aa-tRNAs. The transport mechanism in the cytoplasm is diffusion, thus the competition between cognate, near-cognate and non-cognate aa-tRNAs to bind to the ribosome is a stochastic process. Two competition measures are introduced; C(i) and R(i) (i = 1, 64) are quotients of the arrival frequencies of near-cognates vs. cognates and non-cognates vs. cognates, respectively. Furthermore, the reaction rates of bound cognates differ from those of bound near-cognates. If a near-cognate aa-tRNA binds to the A site of the ribosome, it may be rejected at the anti-codon recognition step or proofreading step or it may be accepted. Regardless of its fate, the near-cognates and non-cognates have caused delays of varying duration to the observed rate of translation. Rate constants have been measured at a temperature of 20 °C by (Gromadski, K.B., Rodnina, M.V., 2004. Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol. Cell 13, 191-200). These rate constants have been re-evaluated at 37 °C, using experimental data at 24.5 °C and 37 °C (Varenne, S., et al., 1984. Translation in a non-uniform process: effect of tRNA availability on the rate of elongation of nascent polypeptide chains. J. Mol. Biol. 180, 549-576). The key results of the study are: (i) the average time (at 37 °C) to add an amino acid, as defined by the ith codon, to the nascent peptide chain is: τ(i) = 9.06 + 1.445 × [10.48C(i) + 0.5R(i)] (in ms); (ii) the misreading frequency is directly proportional to the near-cognate competition, E(i) = 0.0009C(i); (iii) the competition from near-cognates, and not the availability of cognate aa-tRNAs, is the most important factor that determines the translation rate - the four codons with highest near-cognate competition (in the case of E. coli) are [GCC] > [CGG] > [AGG] > [GGA], which overlap only partially with the rarest codons: [AGG] < [CCA] < [GCC] < [CAC]; (iv) based on the kinetic rates at 37 °C, the average time to insert a cognate amino acid is 9.06 ms and the average delay to process a near-cognate aa-tRNA is 10.45 ms and (vii) the model also provides estimates of the vacancy times of the A site of the ribosome - an important factor in frameshifting.

AB - It is generally accepted that the translation rate depends on the availability of cognate aa-tRNAs. In this study it is shown that the key factor that determines translation rate is the competition between near-cognate and cognate aa-tRNAs. The transport mechanism in the cytoplasm is diffusion, thus the competition between cognate, near-cognate and non-cognate aa-tRNAs to bind to the ribosome is a stochastic process. Two competition measures are introduced; C(i) and R(i) (i = 1, 64) are quotients of the arrival frequencies of near-cognates vs. cognates and non-cognates vs. cognates, respectively. Furthermore, the reaction rates of bound cognates differ from those of bound near-cognates. If a near-cognate aa-tRNA binds to the A site of the ribosome, it may be rejected at the anti-codon recognition step or proofreading step or it may be accepted. Regardless of its fate, the near-cognates and non-cognates have caused delays of varying duration to the observed rate of translation. Rate constants have been measured at a temperature of 20 °C by (Gromadski, K.B., Rodnina, M.V., 2004. Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol. Cell 13, 191-200). These rate constants have been re-evaluated at 37 °C, using experimental data at 24.5 °C and 37 °C (Varenne, S., et al., 1984. Translation in a non-uniform process: effect of tRNA availability on the rate of elongation of nascent polypeptide chains. J. Mol. Biol. 180, 549-576). The key results of the study are: (i) the average time (at 37 °C) to add an amino acid, as defined by the ith codon, to the nascent peptide chain is: τ(i) = 9.06 + 1.445 × [10.48C(i) + 0.5R(i)] (in ms); (ii) the misreading frequency is directly proportional to the near-cognate competition, E(i) = 0.0009C(i); (iii) the competition from near-cognates, and not the availability of cognate aa-tRNAs, is the most important factor that determines the translation rate - the four codons with highest near-cognate competition (in the case of E. coli) are [GCC] > [CGG] > [AGG] > [GGA], which overlap only partially with the rarest codons: [AGG] < [CCA] < [GCC] < [CAC]; (iv) based on the kinetic rates at 37 °C, the average time to insert a cognate amino acid is 9.06 ms and the average delay to process a near-cognate aa-tRNA is 10.45 ms and (vii) the model also provides estimates of the vacancy times of the A site of the ribosome - an important factor in frameshifting.

KW - Mistranslation frequencies

KW - Ribosome kinetics

KW - Translation

KW - tRNA availability

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