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Release factor

Not to be confused with a "releasing factor" in the sense of a releasing hormone.
Peptide chain release factor, bacterial Class 1
Identifiers
SymbolPCRF
PfamPF03462
InterProIPR005139
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary
Peptide chain release factor, bacterial Class 1, PTH domain, GGQ
Identifiers
SymbolRF-1
PfamPF00472
Pfam clanCL0337
InterProIPR000352
PROSITEPS00745
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary
Peptide chain release factor eRF1/aRF1
Identifiers
Symbol?
InterProIPR004403

A release factor is a protein that allows for the termination of translation by recognizing the termination codon or stop codon in an mRNA sequence. They are named so because they release new peptides from the ribosome.

Background

During translation of mRNA, most codons are recognized by "charged" tRNA molecules, called aminoacyl-tRNAs because they are adhered to specific amino acids corresponding to each tRNA's anticodon. In the standard genetic code, there are three mRNA stop codons: UAG ("amber"), UAA ("ochre"), and UGA ("opal" or "umber"). Although these stop codons are triplets just like ordinary codons, they are not decoded by tRNAs. It was discovered by Mario Capecchi in 1967 that, instead, tRNAs do not ordinarily recognize stop codons at all, and that what he named "release factor" was not a tRNA molecule but a protein.[1] Later, it was demonstrated that different release factors recognize different stop codons.[2]

Classification

There are two classes of release factors. Class 1 release factors recognize stop codons; they bind to the A site of the ribosome in a way mimicking that of tRNA, releasing the new polypeptide as it disassembles the ribosome.[3][4] Class 2 release factors are GTPases that enhance the activity of class 1 release factors. It helps the class 1 RF dissociate from the ribosome.[5]

Bacterial release factors include RF1, RF2, and RF3 (or PrfA, PrfB, PrfC in the "peptide release factor" gene nomenclature). RF1 and RF2 are class 1 RFs: RF1 recognizes UAA and UAG while RF2 recognizes UAA and UGA. RF3 is the class 2 release factor.[6] Eukaryotic and archaeal release factors are named analogously, with the naming changed to "eRF" for "eukaryotic release factor" and vice versa. a/eRF1 can recognize all three stop codons, while eRF3 (archaea use aEF-1α instead) works just like RF3.[6][7]

The bacterial and archaeo-eukaryotic release factors are believed to have evolved separately. The two groups class 1 factors do not show sequence or structural homology with each other.[8][9] The homology in class 2 is restricted to the fact that both are GTPases. It is believed that (b)RF3 evolved from EF-G while eRF3 evolved from eEF1α.[10]

In line with their symbiotic origin, eukaryotic mitochondria and plastids use bacterial-type class I release factors.[11] As of April 2019, no definite reports of an organellar class II release factor can be found.

Human genes

Structure and function

Crystal structures have been solved for bacterial 70S ribosome bound to each of the three release factors, revealing details in codon recognition by RF1/2 and the EF-G-like rotation of RF3.[12] Cryo-EM structures have been obtained for eukaryotic mamallian 80S ribosome bound to eRF1 and/or eRF3, providing a view of structural rearrangements caused by the factors. Fitting the EM images to previously known crystal structures of individual parts provides identification and a more detailed view of the process.[13][14]

In both systems, the class II (e)RF3 binds to the universal GTPase site on the ribosome, while the class I RFs occupy the A site.[12]

Bacterial

The bacterial class 1 release factors can be divided into four domains. The catalytically-important domains are:[12]

  • The "tripeptide anticodon" motif in domain 2, P[AV]T in RF1 and SPF in RF2. Only one residue actually participates in stop codon recognition via hydrogen bonding.
  • The GGQ motif in domain 3, critical for peptidyl-tRNA hydrolase (PTH) activity.

As RF1/2 sits in the A site of the ribosome, domains 2, 3, and 4 occupy the space that tRNAs load into during elongation. Stop codon recognition activates the RF, promoting a compact to open conformation change,[15] sending the GGQ motif to the peptidyl transferase center (PTC) next to the 3′ end of the P-site tRNA. By hydrolysis of the peptidyl-tRNA ester bond, which displayed pH-dependence in vitro,[16] the peptide is cut loose and released. RF3 is still needed to release RF1/2 from this translation termination complex.[12]

After releasing the peptide, ribosomal recycling is still required to empty the P-site tRNA and mRNA out to make the ribosome usable again. This is done by splitting the ribosome with factors like IF1–IF3 or RRF–EF-G.[17]

Eukaryotic and archaeal

eRF1 can be broken down into four domains: N-terminal (N), Middle (M), C-terminal (C), plus a minidomain:

  • The N domain is responsible for stop codon recognition. Motifs include TASNIKS and YxCxxxF.
  • A GGQ motif in the M domain is critical for peptidyl-tRNA hydrolase (PTH) activity.

Unlike in the bacterial version, eRF1–eRF3–GTP binds together into a sub-complex, via a GRFTLRD motif on RF3. Stop codon recognition makes eRF3 hydrolyze the GTP, and the resulting movement puts the GGQ into the PTC to allow for hydrolysis. The movement also causes a +2-nt movement of the toeprint of the pre-termination complex.[13] The archaeal aRF1–EF1α–GTP complex is similar.[18] The triggering mechanism is similar to that of aa-tRNA–EF-Tu–GTP.[14]

A homologous system is Dom34/Pelota–Hbs1, a eukaryotic system that breaks up stalled ribosomes. It does not have GGQ.[14] The recycling and breakup is mediated by ABCE1.[19][20]

References

  1. ^ Capecchi MR (September 1967). "Polypeptide chain termination in vitro: isolation of a release factor". Proceedings of the National Academy of Sciences of the United States of America. 58 (3): 1144–1151. Bibcode:1967PNAS...58.1144C. doi:10.1073/pnas.58.3.1144. PMC 335760. PMID 5233840.
  2. ^ Scolnick E, Tompkins R, Caskey T, Nirenberg M (October 1968). "Release factors differing in specificity for terminator codons". Proceedings of the National Academy of Sciences of the United States of America. 61 (2): 768–774. Bibcode:1968PNAS...61..768S. doi:10.1073/pnas.61.2.768. PMC 225226. PMID 4879404.
  3. ^ Brown CM, Tate WP (December 1994). "Direct recognition of mRNA stop signals by Escherichia coli polypeptide chain release factor two". The Journal of Biological Chemistry. 269 (52): 33164–33170. doi:10.1016/S0021-9258(20)30112-5. PMID 7806547.
  4. ^ Scarlett DJ, McCaughan KK, Wilson DN, Tate WP (April 2003). "Mapping functionally important motifs SPF and GGQ of the decoding release factor RF2 to the Escherichia coli ribosome by hydroxyl radical footprinting. Implications for macromolecular mimicry and structural changes in RF2". The Journal of Biological Chemistry. 278 (17): 15095–15104. doi:10.1074/jbc.M211024200. PMID 12458201.
  5. ^ Jakobsen CG, Segaard TM, Jean-Jean O, Frolova L, Justesen J (2001). "[Identification of a novel termination release factor eRF3b expressing the eRF3 activity in vitro and in vivo]". Molekuliarnaia Biologiia. 35 (4): 672–681. PMID 11524954.
  6. ^ a b Weaver RF (2005). Molecular Biology. New York, NY: McGraw-Hill. pp. 616–621. ISBN 978-0-07-284611-9.
  7. ^ Saito K, Kobayashi K, Wada M, Kikuno I, Takusagawa A, Mochizuki M, et al. (November 2010). "Omnipotent role of archaeal elongation factor 1 alpha (EF1α in translational elongation and termination, and quality control of protein synthesis". Proceedings of the National Academy of Sciences of the United States of America. 107 (45): 19242–19247. Bibcode:2010PNAS..10719242S. doi:10.1073/pnas.1009599107. PMC 2984191. PMID 20974926.
  8. ^ Buckingham RH, Grentzmann G, Kisselev L (May 1997). "Polypeptide chain release factors". Molecular Microbiology. 24 (3): 449–456. doi:10.1046/j.1365-2958.1997.3711734.x. PMID 9179839. Standard methods of sequence comparison do not show significant similarity between the prokaryotic factors RF1/2 and RF1
  9. ^ Kisselev L (January 2002). "Polypeptide Release Factors in Prokaryotes and Eukaryotes". Structure. 10 (1): 8–9. doi:10.1016/S0969-2126(01)00703-1. PMID 11796105.
  10. ^ Inagaki Y, Ford Doolittle W (June 2000). "Evolution of the eukaryotic translation termination system: origins of release factors". Molecular Biology and Evolution. 17 (6): 882–889. doi:10.1093/oxfordjournals.molbev.a026368. PMID 10833194.
  11. ^ Duarte I, Nabuurs SB, Magno R, Huynen M (November 2012). "Evolution and diversification of the organellar release factor family". Molecular Biology and Evolution. 29 (11): 3497–3512. doi:10.1093/molbev/mss157. PMC 3472500. PMID 22688947.
  12. ^ a b c d Zhou J, Korostelev A, Lancaster L, Noller HF (December 2012). "Crystal structures of 70S ribosomes bound to release factors RF1, RF2 and RF3". Current Opinion in Structural Biology. 22 (6): 733–742. doi:10.1016/j.sbi.2012.08.004. PMC 3982307. PMID 22999888.
  13. ^ a b Taylor D, Unbehaun A, Li W, Das S, Lei J, Liao HY, et al. (November 2012). "Cryo-EM structure of the mammalian eukaryotic release factor eRF1-eRF3-associated termination complex". Proceedings of the National Academy of Sciences of the United States of America. 109 (45): 18413–18418. Bibcode:2012PNAS..10918413T. doi:10.1073/pnas.1216730109. PMC 3494903. PMID 23091004.
  14. ^ a b c des Georges A, Hashem Y, Unbehaun A, Grassucci RA, Taylor D, Hellen CU, et al. (March 2014). "Structure of the mammalian ribosomal pre-termination complex associated with eRF1.eRF3.GDPNP". Nucleic Acids Research. 42 (5): 3409–3418. doi:10.1093/nar/gkt1279. PMC 3950680. PMID 24335085.
  15. ^ Fu Z, Indrisiunaite G, Kaledhonkar S, Shah B, Sun M, Chen B, et al. (June 2019). "The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy". Nature Communications. 10 (1): 2579. Bibcode:2019NatCo..10.2579F. doi:10.1038/s41467-019-10608-z. PMC 6561943. PMID 31189921.
  16. ^ Indrisiunaite G, Pavlov MY, Heurgué-Hamard V, Ehrenberg M (May 2015). "On the pH dependence of class-1 RF-dependent termination of mRNA translation". Journal of Molecular Biology. Translation: Regulation and Dynamics. 427 (9): 1848–1860. doi:10.1016/j.jmb.2015.01.007. PMID 25619162.
  17. ^ Pavlov MY, Antoun A, Lovmar M, Ehrenberg M (June 2008). "Complementary roles of initiation factor 1 and ribosome recycling factor in 70S ribosome splitting". The EMBO Journal. 27 (12): 1706–1717. doi:10.1038/emboj.2008.99. PMC 2435134. PMID 18497739.
  18. ^ Kobayashi K, Saito K, Ishitani R, Ito K, Nureki O (October 2012). "Structural basis for translation termination by archaeal RF1 and GTP-bound EF1α complex". Nucleic Acids Research. 40 (18): 9319–9328. doi:10.1093/nar/gks660. PMC 3467058. PMID 22772989.
  19. ^ Becker T, Franckenberg S, Wickles S, Shoemaker CJ, Anger AM, Armache JP, et al. (February 2012). "Structural basis of highly conserved ribosome recycling in eukaryotes and archaea". Nature. 482 (7386): 501–506. Bibcode:2012Natur.482..501B. doi:10.1038/nature10829. PMC 6878762. PMID 22358840.
  20. ^ Hellen CU (October 2018). "Translation Termination and Ribosome Recycling in Eukaryotes". Cold Spring Harbor Perspectives in Biology. 10 (10): a032656. doi:10.1101/cshperspect.a032656. PMC 6169810. PMID 29735640.
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