View source for Biology:Bacterial initiation factor

{{Short description|Protein that stabilizes the initiation complex for polypeptide translation}}
A '''bacterial initiation factor''' (IF) is a [[Biology:Protein|protein]] that stabilizes the initiation complex for polypeptide [[Biology:Translation|translation]].

Translation initiation is essential to protein synthesis and regulates [[Biology:Messenger RNA|mRNA]] translation fidelity and efficiency in [[Biology:Bacteria|bacteria]].<ref>{{cite journal | vauthors = Laursen BS, Sørensen HP, Mortensen KK, Sperling-Petersen HU | title = Initiation of protein synthesis in bacteria | journal = Microbiology and Molecular Biology Reviews | volume = 69 | issue = 1 | pages = 101–123 | date = March 2005 | pmid = 15755955 | pmc = 1082788 | doi = 10.1128/mmbr.69.1.101-123.2005 }}</ref> The [[Biology:Prokaryotic small ribosomal subunit|30S ribosomal subunit]], initiator [[Biology:Transfer RNA|tRNA]], and mRNA form an initiation complex for elongation.<ref>{{cite journal | vauthors = Steitz JA, Jakes K | title = 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 | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 72 | issue = 12 | pages = 4734–4738 | date = December 1975 | pmid = 1107998 | pmc = 388805 | doi = 10.1073/pnas.72.12.4734 | bibcode = 1975PNAS...72.4734S | doi-access = free }}</ref> This complex process requires three essential protein factors in bacteria – IF1, IF2, and IF3.<ref>{{cite journal | vauthors = Gualerzi CO, Pon CL | title = Initiation of mRNA translation in prokaryotes | journal = Biochemistry | volume = 29 | issue = 25 | pages = 5881–5889 | date = June 1990 | pmid = 2200518 | doi = 10.1021/bi00477a001 }}</ref> These factors bind to the 30S subunit and promote correct initiation codon selection on the mRNA.<ref>{{cite journal | vauthors = McCarthy JE, Brimacombe R | title = Prokaryotic translation: the interactive pathway leading to initiation | journal = Trends in Genetics | volume = 10 | issue = 11 | pages = 402–407 | date = November 1994 | pmid = 7809946 | doi = 10.1016/0168-9525(94)90057-4 }}</ref> IF1, the smallest factor at 8.2 kDa, blocks elongator tRNA binding at the A-site.<ref>{{cite journal | vauthors = Celano B, Pawlik RT, Gualerzi CO | title = Interaction of Escherichia coli translation-initiation factor IF-1 with ribosomes | journal = European Journal of Biochemistry | volume = 178 | issue = 2 | pages = 351–355 | date = December 1988 | pmid = 3061814 | doi = 10.1111/j.1432-1033.1988.tb14457.x | doi-access = free }}</ref> IF2 is the major component that transports initiator tRNA to the P-site.<ref name="La Teana_1996">{{cite journal | vauthors = La Teana A, Pon CL, Gualerzi CO | title = Late events in translation initiation. Adjustment of fMet-tRNA in the ribosomal P-site | journal = Journal of Molecular Biology | volume = 256 | issue = 4 | pages = 667–675 | date = March 1996 | pmid = 8642589 | doi = 10.1006/jmbi.1996.0116 }}</ref> IF3 checks P-site codon-anticodon pairing and rejects incorrect initiation complexes.<ref name="Sussman_1996">{{cite journal | vauthors = Sussman JK, Simons EL, Simons RW | title = Escherichia coli translation initiation factor 3 discriminates the initiation codon in vivo | journal = Molecular Microbiology | volume = 21 | issue = 2 | pages = 347–360 | date = July 1996 | pmid = 8858589 | doi = 10.1046/j.1365-2958.1996.6371354.x | s2cid = 31289254 }}</ref>

The orderly mechanism of initiation starts with IF3 attaching to the 30S subunit and changing its shape.<ref>{{cite journal | vauthors = Fabbretti A, Pon CL, Hennelly SP, Hill WE, Lodmell JS, Gualerzi CO | title = The real-time path of translation factor IF3 onto and off the ribosome | journal = Molecular Cell | volume = 25 | issue = 2 | pages = 285–296 | date = January 2007 | pmid = 17244535 | doi = 10.1016/j.molcel.2006.12.011 | doi-access = free }}</ref> IF1 joins next, followed by mRNA binding, and starts codon-P-site interaction.<ref name="La Teana_1995">{{cite journal | vauthors = La Teana A, Gualerzi CO, Brimacombe R | title = From stand-by to decoding site. Adjustment of the mRNA on the 30S ribosomal subunit under the influence of the initiation factors | journal = RNA | volume = 1 | issue = 8 | pages = 772–782 | date = October 1995 | pmid = 7493323 | pmc = 1369318 | url = http://rnajournal.cshlp.org/content/1/8/772 }}</ref> IF2 enters with the initiator tRNA and places it on the start codon.<ref name="La Teana_1996" /> GTP hydrolysis by IF2 releases it and IF3, enabling 50S subunit joining.<ref>{{cite journal | vauthors = Antoun A, Pavlov MY, Andersson K, Tenson T, Ehrenberg M | title = The roles of initiation factor 2 and guanosine triphosphate in initiation of protein synthesis | journal = The EMBO Journal | volume = 22 | issue = 20 | pages = 5593–5601 | date = October 2003 | pmid = 14532131 | pmc = 213779 | doi = 10.1093/emboj/cdg525 }}</ref> The coordinated binding and activities of IF1, IF2, and IF3 are essential for the rapid and precise translation initiation in bacteria. They facilitate [[Biology:Start codon|start codon]] selection and assemble an active, protein-synthesis-ready 70S ribosome.

== IF1 ==
{{main|Biology:Bacterial initiation factor 1}}
[[Biology:Bacterial initiation factor 1|Bacterial initiation factor 1]] associates with the [[Biology:Prokaryotic small ribosomal subunit|30S ribosomal subunit]] in the A site and prevents an [[Biology:Aminoacyl-tRNA|aminoacyl-tRNA]] from entering. It modulates IF2 binding to the [[Biology:Ribosome|ribosome]] by increasing its affinity. It may also prevent the [[Biology:Prokaryotic large ribosomal subunit|50S subunit]] from binding, stopping the formation of the 70S subunit. It also contains a β-domain fold common for [[Biology:Nucleic acid|nucleic]] acid-binding proteins. It is a homolog of eIF1A. Initiation factor IF-1 is the smallest [[Biology:Translation|translation]] factor at only 8.2kDa.<ref>{{cite journal | vauthors = Paci M, Pon CL, Gualerzi CO | title = Structure-function relationship in Escherichia coli translational initiation factors. Characterization of IF1 by high-resolution 1H-NMR spectroscopy | journal = FEBS Letters | volume = 236 | issue = 2 | pages = 303–308 | date = August 1988 | pmid = 3044826 | doi = 10.1016/0014-5793(88)80042-5 | s2cid = 31852223 | doi-access = free }}</ref> 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.<ref name="pmid367813">{{cite journal | vauthors = Dottavio-Martin D, Suttle DP, Ravel JM | title = The effects of initiation factors IF-1 and IF-3 on the dissociation of Escherichia coli 70 S ribosomes | journal = FEBS Letters | volume = 97 | issue = 1 | pages = 105–10 | date = January 1979 | pmid = 367813 | doi = 10.1016/0014-5793(79)80062-9 | s2cid = 39582391 | doi-access = free }}</ref> It also increases the binding affinity of IF-2 to the 30S subunit, possibly by altering the subunit configuration.<ref>{{cite journal | vauthors = Celano B, Pawlik RT, Gualerzi CO | title = Interaction of Escherichia coli translation-initiation factor IF-1 with ribosomes | journal = European Journal of Biochemistry | volume = 178 | issue = 2 | pages = 351–355 | date = December 1988 | pmid = 3061814 | doi = 10.1111/j.1432-1033.1988.tb14457.x | doi-access = free }}</ref> Though IF-1 occupies the A-site, it does so in a way that is distinct from [[Biology:Transfer RNA|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.<ref>{{cite journal | vauthors = Carter AP, Clemons WM, Brodersen DE, Morgan-Warren RJ, Hartsch T, Wimberly BT, Ramakrishnan V | title = Crystal structure of an initiation factor bound to the 30S ribosomal subunit | journal = Science | volume = 291 | issue = 5503 | pages = 498–501 | date = January 2001 | pmid = 11228145 | doi = 10.1126/science.1057766 | bibcode = 2001Sci...291..498C }}</ref> This insertion repositions [[Biology:Nucleotide|nucleotide]]s 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.<ref>{{cite journal | vauthors = Croitoru V, Bucheli-Witschel M, Hägg P, Abdulkarim F, Isaksson LA | title = Generation and characterization of functional mutants in the translation initiation factor IF1 of Escherichia coli | journal = European Journal of Biochemistry | volume = 271 | issue = 3 | pages = 534–544 | date = February 2004 | pmid = 14728680 | doi = 10.1046/j.1432-1033.2003.03954.x | doi-access = free }}</ref> Certain mutations also lead to o of genes at low temperatures, suggesting IF-1 is involved in [[Biology:Regulation of gene expression|gene regulation]].<ref>{{cite journal | vauthors = Croitoru VV, Bucheli-Witschel M, Isaksson LA | title = In vivo involvement of mutated initiation factor IF1 in gene expression control at the translational level | journal = FEBS Letters | volume = 579 | issue = 5 | pages = 995–1000 | date = February 2005 | pmid = 15710381 | doi = 10.1016/j.febslet.2004.12.072 | s2cid = 37744376 | doi-access = free }}</ref> IF-1 actively modifies ribosome structure and dynamics during initiation, in addition to just blocking the A-site.

== IF2 ==
{{main|Biology:Bacterial initiation factor 2}}
The [[Biology:Bacterial initiation factor 2|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.<ref>{{cite journal | vauthors = Gualerzi CO, Brandi L, Caserta E, Garofalo C, Lammi M, La Teana A, Petrelli D, Spurio R, Tomsic J, Pon CL | display-authors = 6 | title = Initiation factors in the early events of mRNA translation in bacteria | journal = Cold Spring Harbor Symposia on Quantitative Biology | volume = 66 | pages = 363–376 | date = 2001-01-01 | pmid = 12762039 | doi = 10.1101/sqb.2001.66.363 }}</ref><ref>{{cite journal | vauthors = Mortensen KK, Kildsgaard J, Moreno JM, Steffensen SA, Egebjerg J, Sperling-Petersen HU | title = A six-domain structural model for Escherichia coli translation initiation factor IF2. Characterisation of twelve surface epitopes | journal = Biochemistry and Molecular Biology International | volume = 46 | issue = 5 | pages = 1027–1041 | date = December 1998 | pmid = 9861457 | doi = 10.1080/15216549800204582 | s2cid = 24983166 }}</ref> 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.<ref>{{cite journal | vauthors = Roll-Mecak A, Cao C, Dever TE, Burley SK | title = X-Ray structures of the universal translation initiation factor IF2/eIF5B: conformational changes on GDP and GTP binding | journal = Cell | volume = 103 | issue = 5 | pages = 781–792 | date = November 2000 | pmid = 11114334 | doi = 10.1016/s0092-8674(00)00181-1 | s2cid = 16829369 | doi-access = free }}</ref> The activity of IF2 is regulated by conformational changes induced by the binding and hydrolysis of GTP.<ref name="La Teana_1996" /> The primary function of IF-2 is to transport the initiator fMet-tRNA to the P-site of the 30S ribosomal subunit.<ref>{{cite journal | vauthors = Spurio R, Brandi L, Caserta E, Pon CL, Gualerzi CO, Misselwitz R, Krafft C, Welfle K, Welfle H | display-authors = 6 | title = The C-terminal subdomain (IF2 C-2) contains the entire fMet-tRNA binding site of initiation factor IF2 | journal = The Journal of Biological Chemistry | volume = 275 | issue = 4 | pages = 2447–2454 | date = January 2000 | pmid = 10644698 | doi = 10.1074/jbc.275.4.2447 | doi-access = free }}</ref> 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.<ref>{{cite journal | vauthors = Milón P, Maracci C, Filonava L, Gualerzi CO, Rodnina MV | title = Real-time assembly landscape of bacterial 30S translation initiation complex | journal = Nature Structural & Molecular Biology | volume = 19 | issue = 6 | pages = 609–615 | date = May 2012 | pmid = 22562136 | doi = 10.1038/nsmb.2285 | hdl = 11858/00-001M-0000-000F-9BC6-4 | s2cid = 15128390 | hdl-access = free }}</ref> This complex has been found to interact with the 30S subunit.<ref name="La Teana_1996" /> 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.<ref>{{cite journal | vauthors = La Teana A, Gualerzi CO, Dahlberg AE | title = Initiation factor IF 2 binds to the alpha-sarcin loop and helix 89 of Escherichia coli 23S ribosomal RNA | journal = RNA | volume = 7 | issue = 8 | pages = 1173–1179 | date = August 2001 | pmid = 11497435 | pmc = 1370164 | doi = 10.1017/S1355838201010366 }}</ref> IF2 regulates start codon selection accuracy and inhibits elongator tRNAs' binding by selectively binding to fMet-tRNA.<ref>{{cite journal | vauthors = Tomsic J, Vitali LA, Daviter T, Savelsbergh A, Spurio R, Striebeck P, Wintermeyer W, Rodnina MV, Gualerzi CO | display-authors = 6 | title = Late events of translation initiation in bacteria: a kinetic analysis | journal = The EMBO Journal | volume = 19 | issue = 9 | pages = 2127–2136 | date = May 2000 | pmid = 10790378 | pmc = 305682 | doi = 10.1093/emboj/19.9.2127 }}</ref> Additionally, it relocates the initiator tRNA on the 30S subunit to enhance the optimum contact with the P-site.<ref>{{cite journal | vauthors = Caldas T, Laalami S, Richarme G | title = Chaperone properties of bacterial elongation factor EF-G and initiation factor IF2 | journal = The Journal of Biological Chemistry | volume = 275 | issue = 2 | pages = 855–860 | date = January 2000 | pmid = 10625618 | doi = 10.1074/jbc.275.2.855 | doi-access = free }}</ref> 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|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.<ref>{{cite journal | vauthors = Biou V, Shu F, Ramakrishnan V | title = X-ray crystallography shows that translational initiation factor IF3 consists of two compact alpha/beta domains linked by an alpha-helix | journal = The EMBO Journal | volume = 14 | issue = 16 | pages = 4056–4064 | date = August 1995 | pmid = 7664745 | pmc = 394484 | doi = 10.1002/j.1460-2075.1995.tb00077.x }}</ref><ref>{{cite journal | vauthors = Petrelli D, LaTeana A, Garofalo C, Spurio R, Pon CL, Gualerzi CO | title = Translation initiation factor IF3: two domains, five functions, one mechanism? | journal = The EMBO Journal | volume = 20 | issue = 16 | pages = 4560–4569 | date = August 2001 | pmid = 11500382 | pmc = 125572 | doi = 10.1093/emboj/20.16.4560 }}</ref> Most IF3 functions are mediated by the IF3C domain, while IF3N regulates 30S subunit binding. [[Biology:Prokaryotic initiation factor-3|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.<ref>{{cite journal | vauthors = Pioletti M, Schlünzen F, Harms J, Zarivach R, Glühmann M, Avila H, Bashan A, Bartels H, Auerbach T, Jacobi C, Hartsch T, Yonath A, Franceschi F | display-authors = 6 | title = Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3 | journal = The EMBO Journal | volume = 20 | issue = 8 | pages = 1829–1839 | date = April 2001 | pmid = 11296217 | pmc = 125237 | doi = 10.1093/emboj/20.8.1829 }}</ref><ref>{{cite journal | vauthors = McCutcheon JP, Agrawal RK, Philips SM, Grassucci RA, Gerchman SE, Clemons WM, Ramakrishnan V, Frank J | display-authors = 6 | title = Location of translational initiation factor IF3 on the small ribosomal subunit | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 96 | issue = 8 | pages = 4301–4306 | date = April 1999 | pmid = 10200257 | pmc = 16327 | doi = 10.1073/pnas.96.8.4301 | doi-access = free | bibcode = 1999PNAS...96.4301M }}</ref> 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.<ref>{{cite journal | vauthors = Petrelli D, Garofalo C, Lammi M, Spurio R, Pon CL, Gualerzi CO, La Teana A | title = Mapping the active sites of bacterial translation initiation factor IF3 | journal = Journal of Molecular Biology | volume = 331 | issue = 3 | pages = 541–556 | date = August 2003 | pmid = 12899827 | doi = 10.1016/S0022-2836(03)00731-9 }}</ref> The IF3C domain interacts with the 30S subunit via its conserved basic residues R99, R116, R147 and R168 .<ref>{{cite journal | vauthors = Sussman JK, Simons EL, Simons RW | title = Escherichia coli translation initiation factor 3 discriminates the initiation codon in vivo | journal = Molecular Microbiology | volume = 21 | issue = 2 | pages = 347–360 | date = July 1996 | pmid = 8858589 | doi = 10.1046/j.1365-2958.1996.6371354.x | s2cid = 31289254 }}</ref> A major function of IF3 is inspecting codon-anticodon pairing at the P-site during start codon selection.<ref name="Sussman_1996" /> It accelerates the dissociation of non-canonical initiation complexes containing mismatched or incorrect tRNAs.<ref>{{cite journal | vauthors = Hartz D, Binkley J, Hollingsworth T, Gold L | title = Domains of initiator tRNA and initiation codon crucial for initiator tRNA selection by Escherichia coli IF3 | journal = Genes & Development | volume = 4 | issue = 10 | pages = 1790–1800 | date = October 1990 | pmid = 1701151 | doi = 10.1101/gad.4.10.1790 | s2cid = 30323548 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Grunberg-Manago M, Dessen P, Pantaloni D, Godefroy-Colburn T, Wolfe AD, Dondon J | title = Light-scattering studies showing the effect of initiation factors on the reversible dissociation of Escherichia coli ribosomes | journal = Journal of Molecular Biology | volume = 94 | issue = 3 | pages = 461–478 | date = May 1975 | pmid = 1100842 | doi = 10.1016/0022-2836(75)90215-6 }}</ref> 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.<ref name="La Teana_1995" /> 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.<ref>{{cite journal | vauthors = Wintermeyer W, Gualerzi C | title = Effect of Escherichia coli initiation factors on the kinetics of N-Acphe-tRNAPhe binding to 30S ribosomal subunits. A fluorescence stopped-flow study | journal = Biochemistry | volume = 22 | issue = 3 | pages = 690–694 | date = February 1983 | pmid = 6340723 | doi = 10.1021/bi00272a025 }}</ref><ref>{{cite journal | vauthors = Meinnel T, Sacerdot C, Graffe M, Blanquet S, Springer M | title = Discrimination by Escherichia coli initiation factor IF3 against initiation on non-canonical codons relies on complementarity rules | journal = Journal of Molecular Biology | volume = 290 | issue = 4 | pages = 825–837 | date = July 1999 | pmid = 10398584 | doi = 10.1006/jmbi.1999.2881 }}</ref> IF3 works cooperatively with IF1 and IF2 during initiation and modulates IF2 binding and enhances the fidelity of start codon selection.

== References ==
{{Reflist}}

== External links ==
* {{MeshName|Prokaryotic+Initiation+Factors}}

{{GeneticTranslation}}

[[Category:Molecular biology]]
[[Category:Protein biosynthesis]]
[[Category:Gene expression]]

{{Sourceattribution|Bacterial initiation factor}}