Fidelity of bacterial translation initiation: a stochastic kinetic model

During the initiation stage of protein synthesis, a ribosomal initiation complex (IC) is assembled on a messenger RNA (mRNA) template. In bacteria, the speed and accuracy of this assembly process are regulated by the complementary activities of three essential initiation factors (IFs). Selection of an authentic N-formylmethionyl-transfer RNA (fMet-tRNA\textsuperscript{fMet}) and the canonical, triplet-nucleotide mRNA start codon are crucial events during assembly of a canonical, ribosomal 70S IC. Mis-initiation due to the aberrant selection of an elongator tRNA or a non-canonical start codon are rare events that result in the assembly of a pseudo 70S IC or a non-canonical 70S IC, respectively. Here, we have developed a theoretical model for the stochastic kinetics of canonical-, pseudo-, and non-canonical 70S IC assembly that includes all of the major steps of the IC assembly process that have been observed and characterized in ensemble kinetic-, single-molecule kinetic-, and structural studies of the fidelity of translation initiation. Specifically, we use the rates of the individual steps in the IC assembly process and the formalism of first-passage times to derive exact analytical expressions for the probability distributions for the assembly of canonical-, pseudo- and non-canonical 70S ICs. In order to illustrate the power of this analytical approach, we compare the theoretically predicted first-passage time distributions with the corresponding computer simulation data. We also compare the mean times required for completion of these assemblies with experimental estimates. In addition to generating new, testable hypotheses, our theoretical model can also be easily extended as new experimental 70S IC assembly data become available, thereby providing a versatile tool for interpreting these data and developing advanced models of the mechanism and regulation of translation initiation.

[1]  M. Ehrenberg,et al.  A conformational switch in initiation factor 2 controls the fidelity of translation initiation in bacteria , 2017, Nature Communications.

[2]  V. Ramakrishnan,et al.  Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation , 2016, Cell.

[3]  D. Chowdhury,et al.  A Generalized Michaelis–Menten Equation in Protein Synthesis: Effects of Mis-Charged Cognate tRNA and Mis-Reading of Codon , 2015, Bulletin of Mathematical Biology.

[4]  M. Rodnina,et al.  Directional transition from initiation to elongation in bacterial translation , 2015, Nucleic acids research.

[5]  R. L. Gonzalez,et al.  Ribosomal initiation complex-driven changes in the stability and dynamics of initiation factor 2 regulate the fidelity of translation initiation. , 2015, Journal of molecular biology.

[6]  Daniel D Macdougall,et al.  Translation initiation factor 3 regulates switching between different modes of ribosomal subunit joining. , 2015, Journal of molecular biology.

[7]  Anton Zilman,et al.  First Passage processes in cellular biology , 2015, 1503.00291.

[8]  Sidney Redner,et al.  First-passage phenomena and their applications , 2014 .

[9]  J. Remme,et al.  Initiation with Elongator tRNAs , 2013, Journal of bacteriology.

[10]  Pohl Milón,et al.  Real-time assembly landscape of bacterial 30S translation initiation complex , 2012, Nature Structural &Molecular Biology.

[11]  K. Fredrick,et al.  Role of helix 44 of 16S rRNA in the fidelity of translation initiation. , 2012, RNA.

[12]  M. Ehrenberg,et al.  Activation of initiation factor 2 by ligands and mutations for rapid docking of ribosomal subunits , 2011, The EMBO journal.

[13]  D. Chowdhury,et al.  Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding , 2010, Physical biology.

[14]  M. Ehrenberg,et al.  Error-prone initiation factor 2 mutations reduce the fitness cost of antibiotic resistance , 2010, Molecular microbiology.

[15]  D. Chowdhury,et al.  Stochastic kinetics of ribosomes: single motor properties and collective behavior. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

[16]  Bruno P. Klaholz,et al.  Structure of the 30S translation initiation complex , 2008, Nature.

[17]  M. Rodnina,et al.  Kinetic checkpoint at a late step in translation initiation. , 2008, Molecular cell.

[18]  C. Gualerzi,et al.  A quantitative kinetic scheme for 70 S translation initiation complex formation. , 2007, Journal of molecular biology.

[19]  V. Hatzimanikatis,et al.  A model for protein translation: polysome self-organization leads to maximum protein synthesis rates. , 2007, Biophysical journal.

[20]  M. Ehrenberg,et al.  How initiation factors maximize the accuracy of tRNA selection in initiation of bacterial protein synthesis. , 2006, Molecular cell.

[21]  Måns Ehrenberg,et al.  How initiation factors tune the rate of initiation of protein synthesis in bacteria , 2006, The EMBO journal.

[22]  D. Chowdhury,et al.  Traffic of interacting ribosomes: effects of single-machine mechanochemistry on protein synthesis. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[23]  S. Joseph,et al.  Unfolding of mRNA secondary structure by the bacterial translation initiation complex. , 2006, Molecular cell.

[24]  J. Stoyanov.  A Guide to First‐passage Processes , 2003 .

[25]  T. Misteli.  The concept of self-organization in cellular architecture , 2001, The Journal of cell biology.

[26]  U. RajBhandary,et al.  Altered discrimination of start codons and initiator tRNAs by mutant initiation factor 3. , 2001, RNA.

[27]  Frederick C. Neidhardt,et al.  Effect of Temperature on In Vivo Protein Synthetic Capacity in Escherichia coli , 1998, Journal of bacteriology.

[28]  S. Lovett,et al.  IF3-mediated suppression of a GUA initiation codon mutation in the recJ gene of Escherichia coli , 1997, Journal of bacteriology.

[29]  R. Simons,et al.  Escherichia coli translation initiation factor 3 discriminates the initiation codon in vivo , 1996, Molecular microbiology.

[30]  M. Springer,et al.  The role of the AUU initiation codon in the negative feedback regulation of the gene for translation initiation factor IF3 in Escherichia coli , 1996, Molecular microbiology.

[31]  M. Springer,et al.  Physiological effects of translation initiation factor IF3 and ribosomal protein L20 limitation inEscherichia coli , 1996, Molecular and General Genetics MGG.

[32]  Y. Mechulam,et al.  Disruption of the gene for Met-tRNA(fMet) formyltransferase severely impairs growth of Escherichia coli , 1992, Journal of bacteriology.

[33]  Joachim Frank,et al.  Molecular machines in biology : workshop of the cell , 2011 .

[34]  D. Morris,et al.  Dynamic model of the process of protein synthesis in eukaryotic cells. , 2007, Bulletin of mathematical biology.

[35]  Masuhiro Kogoma.  総論;総論;Introduction , 2006 .