Biology:Bacterial initiation factor

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Short description: Protein that stabilizes the initiation complex for polypeptide translation

A bacterial initiation factor (IF) is a protein that stabilizes the initiation complex for polypeptide translation.

Translation initiation is essential to protein synthesis and regulates mRNA translation fidelity and efficiency in bacteria.[1] The 30S ribosomal subunit, initiator tRNA, and mRNA form an initiation complex for elongation.[2] This complex process requires three essential protein factors in bacteria – IF1, IF2, and IF3.[3] These factors bind to the 30S subunit and promote correct initiation codon selection on the mRNA.[4] IF1, the smallest factor at 8.2 kDa, blocks elongator tRNA binding at the A-site.[5] IF2 is the major component that transports initiator tRNA to the P-site.[6] IF3 checks P-site codon-anticodon pairing and rejects incorrect initiation complexes.[7]

The orderly mechanism of initiation starts with IF3 attaching to the 30S subunit and changing its shape.[8] IF1 joins next, followed by mRNA binding, and starts codon-P-site interaction.[9] IF2 enters with the initiator tRNA and places it on the start codon.[6] GTP hydrolysis by IF2 releases it and IF3, enabling 50S subunit joining.[10] The coordinated binding and activities of IF1, IF2, and IF3 are essential for the rapid and precise translation initiation in bacteria. They facilitate start codon selection and assemble an active, protein-synthesis-ready 70S ribosome.

IF1

Main page: Biology:Bacterial initiation factor 1

Bacterial initiation factor 1 associates with the 30S ribosomal subunit in the A site and prevents an aminoacyl-tRNA from entering. It modulates IF2 binding to the ribosome by increasing its affinity. It may also prevent the 50S subunit from binding, stopping the formation of the 70S subunit. It also contains a β-domain fold common for nucleic acid-binding proteins. It is a homolog of eIF1A. Initiation factor IF-1 is the smallest translation factor at only 8.2kDa.[11] Beyond blocking the A-site, it affects the dynamics of ribosome association and dissociation. IF-1 enhances dissociation with IF-3, likely by inducing conformational changes in the 30S subunit.[12] It also increases the binding affinity of IF-2 to the 30S subunit, possibly by altering the subunit configuration.[13] Though IF-1 occupies the A-site, it does so in a way that is distinct from tRNA binding. Structural studies show IF-1 inserts a loop into the minor groove of helix 44 of 16S rRNA, flipping out bases A1492 and A1493.[14] This insertion repositions nucleotides of helix 44, transmitting a conformational change over a 70Å distance and rotating the head of the 30S subunit. IF-1 mutants can exhibit cold-sensitive phenotypes, indicating a role for the factor in cold shock adaptation.[15] Certain mutations also lead to o of genes at low temperatures, suggesting IF-1 is involved in gene regulation.[16] IF-1 actively modifies ribosome structure and dynamics during initiation, in addition to just blocking the A-site.

IF2

Main page: Biology:Bacterial initiation factor 2

The IF2 initiation factor is a crucial component in the process of protein synthesis. The largest among the three indispensable translation initiation factors is IF-2, which possesses a molecular mass of 97 kDa.[17][18] The protein has many domains, including an N-terminal domain, a GTPase domain, a linker region, C1, C2, and C-terminal domains. The GTPase domain encompasses the G1-G5 motif, which is responsible for the binding and hydrolysis of GTP.[19] The activity of IF2 is regulated by conformational changes induced by the binding and hydrolysis of GTP.[6] The primary function of IF-2 is to transport the initiator fMet-tRNA to the P-site of the 30S ribosomal subunit.[20] The C2 domain of IF2 has a unique recognition and binding affinity towards the initiator tRNA. The IF-2 protein has been observed to form a ternary complex when interacting with GTP and fMet-tRNA.[21] This complex has been found to interact with the 30S subunit.[6] The initiation of mRNA translation involves the placement of the start codon in the P-site through the codon-anticodon base matching with the tRNA anti-codon.[22] IF2 regulates start codon selection accuracy and inhibits elongator tRNAs' binding by selectively binding to fMet-tRNA.[23] Additionally, it relocates the initiator tRNA on the 30S subunit to enhance the optimum contact with the P-site.[24] Furthermore, IF2 exhibits RNA chaperone activity, which enables it to rectify misfolded RNA structures. In general, the IF2 protein plays a crucial role in coordinating many steps of translation initiation, including the binding of mRNA and fMet-tRNA to the start codon, the joining of sub-units, and the activation of GTPase.

IF3

Main page: Biology:Prokaryotic initiation factor-3

Initiation factor IF3 is a small protein of 21 kDa containing two compact α/β domains (IF3C and IF3N) connected by a flexible lysine-rich linker.[25][26] Most IF3 functions are mediated by the IF3C domain, while IF3N regulates 30S subunit binding. Bacterial initiation factor 3 (infC) is not universally found in all bacterial species but in E. coli it is required for the 30S subunit to bind to the initiation site in mRNA. IF3 is required by the small subunit to form initiation complexes, but has to be released to allow the 50S subunit to bind.[27][28] IF3 attaches to the platform side of the 30S subunit, close to helices 23, 24, 25, 26 and 45 of 16S rRNA, as well as ribosomal proteins S7, S11, and S12.[29] The IF3C domain interacts with the 30S subunit via its conserved basic residues R99, R116, R147 and R168 .[30] A major function of IF3 is inspecting codon-anticodon pairing at the P-site during start codon selection.[7] It accelerates the dissociation of non-canonical initiation complexes containing mismatched or incorrect tRNAs.[31][32] IF3 also inspects the initiator tRNA, rejecting elongator tRNAs and it also promotes the dissociation of the 70S ribosome into subunits, providing a pool of free 30S subunits for initiation.[9] Another key role of IF3 is repositioning mRNA on the 30S subunit from a standby site to the P-site decoding site for start codon selection.[33][34] IF3 works cooperatively with IF1 and IF2 during initiation and modulates IF2 binding and enhances the fidelity of start codon selection.

References

  1. ↑ "Initiation of protein synthesis in bacteria". Microbiology and Molecular Biology Reviews 69 (1): 101–123. March 2005. doi:10.1128/mmbr.69.1.101-123.2005. PMID 15755955. 
  2. ↑ "How ribosomes select initiator regions in mRNA: base pair formation between the 3' terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli". Proceedings of the National Academy of Sciences of the United States of America 72 (12): 4734–4738. December 1975. doi:10.1073/pnas.72.12.4734. PMID 1107998. Bibcode: 1975PNAS...72.4734S. 
  3. ↑ "Initiation of mRNA translation in prokaryotes". Biochemistry 29 (25): 5881–5889. June 1990. doi:10.1021/bi00477a001. PMID 2200518. 
  4. ↑ "Prokaryotic translation: the interactive pathway leading to initiation". Trends in Genetics 10 (11): 402–407. November 1994. doi:10.1016/0168-9525(94)90057-4. PMID 7809946. 
  5. ↑ "Interaction of Escherichia coli translation-initiation factor IF-1 with ribosomes". European Journal of Biochemistry 178 (2): 351–355. December 1988. doi:10.1111/j.1432-1033.1988.tb14457.x. PMID 3061814. 
  6. ↑ 6.0 6.1 6.2 6.3 "Late events in translation initiation. Adjustment of fMet-tRNA in the ribosomal P-site". Journal of Molecular Biology 256 (4): 667–675. March 1996. doi:10.1006/jmbi.1996.0116. PMID 8642589. 
  7. ↑ 7.0 7.1 "Escherichia coli translation initiation factor 3 discriminates the initiation codon in vivo". Molecular Microbiology 21 (2): 347–360. July 1996. doi:10.1046/j.1365-2958.1996.6371354.x. PMID 8858589. 
  8. ↑ "The real-time path of translation factor IF3 onto and off the ribosome". Molecular Cell 25 (2): 285–296. January 2007. doi:10.1016/j.molcel.2006.12.011. PMID 17244535. 
  9. ↑ 9.0 9.1 "From stand-by to decoding site. Adjustment of the mRNA on the 30S ribosomal subunit under the influence of the initiation factors". RNA 1 (8): 772–782. October 1995. PMID 7493323. PMC 1369318. http://rnajournal.cshlp.org/content/1/8/772. 
  10. ↑ "The roles of initiation factor 2 and guanosine triphosphate in initiation of protein synthesis". The EMBO Journal 22 (20): 5593–5601. October 2003. doi:10.1093/emboj/cdg525. PMID 14532131. 
  11. ↑ "Structure-function relationship in Escherichia coli translational initiation factors. Characterization of IF1 by high-resolution 1H-NMR spectroscopy". FEBS Letters 236 (2): 303–308. August 1988. doi:10.1016/0014-5793(88)80042-5. PMID 3044826. 
  12. ↑ "The effects of initiation factors IF-1 and IF-3 on the dissociation of Escherichia coli 70 S ribosomes". FEBS Letters 97 (1): 105–10. January 1979. doi:10.1016/0014-5793(79)80062-9. PMID 367813. 
  13. ↑ "Interaction of Escherichia coli translation-initiation factor IF-1 with ribosomes". European Journal of Biochemistry 178 (2): 351–355. December 1988. doi:10.1111/j.1432-1033.1988.tb14457.x. PMID 3061814. 
  14. ↑ "Crystal structure of an initiation factor bound to the 30S ribosomal subunit". Science 291 (5503): 498–501. January 2001. doi:10.1126/science.1057766. PMID 11228145. Bibcode: 2001Sci...291..498C. 
  15. ↑ "Generation and characterization of functional mutants in the translation initiation factor IF1 of Escherichia coli". European Journal of Biochemistry 271 (3): 534–544. February 2004. doi:10.1046/j.1432-1033.2003.03954.x. PMID 14728680. 
  16. ↑ "In vivo involvement of mutated initiation factor IF1 in gene expression control at the translational level". FEBS Letters 579 (5): 995–1000. February 2005. doi:10.1016/j.febslet.2004.12.072. PMID 15710381. 
  17. ↑ "Initiation factors in the early events of mRNA translation in bacteria". Cold Spring Harbor Symposia on Quantitative Biology 66: 363–376. 2001-01-01. doi:10.1101/sqb.2001.66.363. PMID 12762039. 
  18. ↑ "A six-domain structural model for Escherichia coli translation initiation factor IF2. Characterisation of twelve surface epitopes". Biochemistry and Molecular Biology International 46 (5): 1027–1041. December 1998. doi:10.1080/15216549800204582. PMID 9861457. 
  19. ↑ "X-Ray structures of the universal translation initiation factor IF2/eIF5B: conformational changes on GDP and GTP binding". Cell 103 (5): 781–792. November 2000. doi:10.1016/s0092-8674(00)00181-1. PMID 11114334. 
  20. ↑ "The C-terminal subdomain (IF2 C-2) contains the entire fMet-tRNA binding site of initiation factor IF2". The Journal of Biological Chemistry 275 (4): 2447–2454. January 2000. doi:10.1074/jbc.275.4.2447. PMID 10644698. 
  21. ↑ "Real-time assembly landscape of bacterial 30S translation initiation complex". Nature Structural & Molecular Biology 19 (6): 609–615. May 2012. doi:10.1038/nsmb.2285. PMID 22562136. 
  22. ↑ "Initiation factor IF 2 binds to the alpha-sarcin loop and helix 89 of Escherichia coli 23S ribosomal RNA". RNA 7 (8): 1173–1179. August 2001. doi:10.1017/S1355838201010366. PMID 11497435. 
  23. ↑ "Late events of translation initiation in bacteria: a kinetic analysis". The EMBO Journal 19 (9): 2127–2136. May 2000. doi:10.1093/emboj/19.9.2127. PMID 10790378. 
  24. ↑ "Chaperone properties of bacterial elongation factor EF-G and initiation factor IF2". The Journal of Biological Chemistry 275 (2): 855–860. January 2000. doi:10.1074/jbc.275.2.855. PMID 10625618. 
  25. ↑ "X-ray crystallography shows that translational initiation factor IF3 consists of two compact alpha/beta domains linked by an alpha-helix". The EMBO Journal 14 (16): 4056–4064. August 1995. doi:10.1002/j.1460-2075.1995.tb00077.x. PMID 7664745. 
  26. ↑ "Translation initiation factor IF3: two domains, five functions, one mechanism?". The EMBO Journal 20 (16): 4560–4569. August 2001. doi:10.1093/emboj/20.16.4560. PMID 11500382. 
  27. ↑ "Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3". The EMBO Journal 20 (8): 1829–1839. April 2001. doi:10.1093/emboj/20.8.1829. PMID 11296217. 
  28. ↑ "Location of translational initiation factor IF3 on the small ribosomal subunit". Proceedings of the National Academy of Sciences of the United States of America 96 (8): 4301–4306. April 1999. doi:10.1073/pnas.96.8.4301. PMID 10200257. Bibcode: 1999PNAS...96.4301M. 
  29. ↑ "Mapping the active sites of bacterial translation initiation factor IF3". Journal of Molecular Biology 331 (3): 541–556. August 2003. doi:10.1016/S0022-2836(03)00731-9. PMID 12899827. 
  30. ↑ "Escherichia coli translation initiation factor 3 discriminates the initiation codon in vivo". Molecular Microbiology 21 (2): 347–360. July 1996. doi:10.1046/j.1365-2958.1996.6371354.x. PMID 8858589. 
  31. ↑ "Domains of initiator tRNA and initiation codon crucial for initiator tRNA selection by Escherichia coli IF3". Genes & Development 4 (10): 1790–1800. October 1990. doi:10.1101/gad.4.10.1790. PMID 1701151. 
  32. ↑ "Light-scattering studies showing the effect of initiation factors on the reversible dissociation of Escherichia coli ribosomes". Journal of Molecular Biology 94 (3): 461–478. May 1975. doi:10.1016/0022-2836(75)90215-6. PMID 1100842. 
  33. ↑ "Effect of Escherichia coli initiation factors on the kinetics of N-Acphe-tRNAPhe binding to 30S ribosomal subunits. A fluorescence stopped-flow study". Biochemistry 22 (3): 690–694. February 1983. doi:10.1021/bi00272a025. PMID 6340723. 
  34. ↑ "Discrimination by Escherichia coli initiation factor IF3 against initiation on non-canonical codons relies on complementarity rules". Journal of Molecular Biology 290 (4): 825–837. July 1999. doi:10.1006/jmbi.1999.2881. PMID 10398584. 

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