Elongation factor

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Ternary complex of EF-Tu (blue), tRNA (red) and GTP (yellow). Taken from PDB Molecule of the Month Elongation factors, September 2006.

Elongation factors are a set of proteins that function at the ribosome, during protein synthesis, to facilitate translational elongation from the formation of the first to the last peptide bond of a growing polypeptide. Most common elongation factors in prokaryotes are EF-Tu, EF-Ts, EF-G.^[1] Bacteria and eukaryotes use elongation factors that are largely homologous to each other, but with distinct structures and different research nomenclatures.^[2]

Elongation is the most rapid step in translation.^[3] In bacteria, it proceeds at a rate of 15 to 20 amino acids added per second (about 45-60 nucleotides per second).^{[citation needed]} In eukaryotes the rate is about two amino acids per second (about 6 nucleotides read per second).^{[citation needed]} Elongation factors play a role in orchestrating the events of this process, and in ensuring the high accuracy translation at these speeds.^{[citation needed]}

Nomenclature of homologous EFs

Elongation factors
Bacterial	Eukaryotic/Archaeal	Function
EF-Tu	eEF-1A (α)^[2]	mediates the entry of the aminoacyl tRNA into a free site of the ribosome.^[4]
EF-Ts	eEF-1B (β γ)^[2]	serves as the guanine nucleotide exchange factor for EF-Tu, catalyzing the release of GDP from EF-Tu.^[2]
EF-G	eEF-2	catalyzes the translocation of the tRNA and mRNA down the ribosome at the end of each round of polypeptide elongation. Causes large conformation changes.^[5]
EF-P	eIF-5A	possibly stimulates formation of peptide bonds and resolves stalls.^[6]
EF-4	(None)	Proofreading
Note that EIF5A, the archaeal and eukaryotic homolog to EF-P, was named as an initiation factor but now considered an elongation factor as well.^[6]

In addition to their cytoplasmic machinery, eukaryotic mitochondria and plastids have their own translation machinery, each with their own set of bacterial-type elongation factors.^[7]^[8] In humans, they include TUFM, TSFM, GFM1, GFM2, GUF1; the nominal release factor MTRFR may also play a role in elongation.^[9]

In bacteria, selenocysteinyl-tRNA requires a special elongation factor SelB (P14081) related to EF-Tu. A few homologs are also found in archaea, but the functions are unknown.^[10]

As a target

Elongation factors are targets for the toxins of some pathogens. For instance, Corynebacterium diphtheriae produces diphtheria toxin, which alters protein function in the host by inactivating elongation factor (EF-2). This results in the pathology and symptoms associated with diphtheria. Likewise, Pseudomonas aeruginosa exotoxin A inactivates EF-2.^[11]

References

^ Parker, J. (2001). "Elongation Factors; Translation". Encyclopedia of Genetics. pp. 610–611. doi:10.1006/rwgn.2001.0402. ISBN 9780122270802.
^ ^a ^b ^c ^d Sasikumar, Arjun N.; Perez, Winder B.; Kinzy, Terri Goss (July 2012). "The Many Roles of the Eukaryotic Elongation Factor 1 Complex". Wiley Interdisciplinary Reviews. RNA. 3 (4): 543–555. doi:10.1002/wrna.1118. ISSN 1757-7004. PMC 3374885. PMID 22555874.
^ Prabhakar, Arjun; Choi, Junhong; Wang, Jinfan; Petrov, Alexey; Puglisi, Joseph D. (July 2017). "Dynamic basis of fidelity and speed in translation: Coordinated multistep mechanisms of elongation and termination". Protein Science. 26 (7): 1352–1362. doi:10.1002/pro.3190. ISSN 0961-8368. PMC 5477533. PMID 28480640.
^ Weijland A, Harmark K, Cool RH, Anborgh PH, Parmeggiani A (March 1992). "Elongation factor Tu: a molecular switch in protein biosynthesis". Molecular Microbiology. 6 (6): 683–8. doi:10.1111/j.1365-2958.1992.tb01516.x. PMID 1573997.
^ Jørgensen, R; Ortiz, PA; Carr-Schmid, A; Nissen, P; Kinzy, TG; Andersen, GR (May 2003). "Two crystal structures demonstrate large conformational changes in the eukaryotic ribosomal translocase". Nature Structural Biology. 10 (5): 379–85. doi:10.1038/nsb923. PMID 12692531. S2CID 4795260.
^ ^a ^b Rossi, D; Kuroshu, R; Zanelli, CF; Valentini, SR (2013). "eIF5A and EF-P: two unique translation factors are now traveling the same road". Wiley Interdisciplinary Reviews. RNA. 5 (2): 209–22. doi:10.1002/wrna.1211. PMID 24402910. S2CID 25447826.
^ Manuell, Andrea L; Quispe, Joel; Mayfield, Stephen P; Petsko, Gregory A (7 August 2007). "Structure of the Chloroplast Ribosome: Novel Domains for Translation Regulation". PLOS Biology. 5 (8): e209. doi:10.1371/journal.pbio.0050209. PMC 1939882. PMID 17683199.
^ G C Atkinson; S L Baldauf (2011). "Evolution of elongation factor G and the origins of mitochondrial and chloroplast forms". Molecular Biology and Evolution. 28 (3): 1281–92. doi:10.1093/molbev/msq316. PMID 21097998.
^ "KEGG DISEASE: Combined oxidative phosphorylation deficiency". www.genome.jp.
^ Atkinson, Gemma C; Hauryliuk, Vasili; Tenson, Tanel (21 January 2011). "An ancient family of SelB elongation factor-like proteins with a broad but disjunct distribution across archaea". BMC Evolutionary Biology. 11 (1): 22. doi:10.1186/1471-2148-11-22. PMC 3037878. PMID 21255425.
^ Lee H, Iglewski WJ (1984). "Cellular ADP-ribosyltransferase with the same mechanism of action as diphtheria toxin and Pseudomonas toxin A". Proc. Natl. Acad. Sci. U.S.A. 81 (9): 2703–7. Bibcode:1984PNAS...81.2703L. doi:10.1073/pnas.81.9.2703. PMC 345138. PMID 6326138.

Further reading

Alberts, B. et al. (2002). Molecular Biology of the Cell, 4th ed. New York: Garland Science. ISBN 0-8153-3218-1.^{[page needed]}
Berg, J. M. et al. (2002). Biochemistry, 5th ed. New York: W.H. Freeman and Company. ISBN 0-7167-3051-0.^{[page needed]}
Singh, B. D. (2002). Fundamentals of Genetics, New Delhi, India: Kalyani Publishers. ISBN 81-7663-109-4.^{[page needed]}

External links

nobelprize.org Explaining the function of eukaryotic elongation factors
Elongation+Factor at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
Peptide+Elongation+Factor+G at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
Peptide+Elongation+Factor+Tu at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
EC 3.6.5.3

Protein biosynthesis: translation (bacterial, archaeal, eukaryotic)

Proteins

Initiation factor

eIF1	eIF1 B SUI1 family eIF1A Y
eIF2	α kinase β γ eIF2A eIF2B 1 2 3 4 5 eIF2D
eIF3	A B C D E F G H I J K L M
eIF4	A 1 2 3 E1 2 3 G 1 2 3 B H
eIF5	EIF5 EIF5A 2 5B
eIF6	EIF6

Elongation factor

Bacterial/Mitochondrial	EF-Tu EF-Ts EF-G EF-4 EF-P TSFM GFM1 GFM2
Archaeal/Eukaryotic	a/eEF-1 A1 2 3 B P1 P2 P3 D E G a/eEF-2

Class 1
- eRF1
Class 2/RF3
- GSPT1
- GSPT2

Ribosomal Proteins

60S subunit	RPL3 RPL4 RPL5 RPL6 RPL7 RPL7A RPL8 RPL9 RPL10 RPL10A RPL10-like RPL11 RPL12 RPL13 RPL13A RPL14 RPL15 RPL17 RPL18 RPL18A RPL19 RPL21 RPL22 RPL23 RPL23A RPL24 RPL26 RPL27 RPL27A RPL28 RPL29 RPL30 RPL31 RPL32 RPL34 RPL35 RPL35A RPL36 RPL36A RPL37 RPL37A RPL38 RPL39 RPL40 RPL41 RPLP0 RPLP1 RPLP2 RRP15-like RSL24D1
40S subunit	RPSA RPS2 RPS3 RPS3A RPS4 (RPS4X, RPS4Y1, RPS4Y2) RPS5 RPS6 RPS7 RPS8 RPS9 RPS10 RPS11 RPS12 RPS13 RPS14 RPS15 RPS15A RPS16 RPS17 RPS18 RPS19 RPS20 RPS21 RPS23 RPS24 RPS25 RPS26 RPS27 RPS27A RPS28 RPS29 RPS30 RACK1

39S subunit	MRPL1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42
28S subunit	MRPS1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

Other concepts

Hydrolases: acid anhydride hydrolases (EC 3.6)

3.6.3-4: ATPase

3.6.3

Cu++ (3.6.3.4)	Menkes/ATP7A Wilson/ATP7B
Ca+ (3.6.3.8)	SERCA ATP2A1 ATP2A2 ATP2A3 Plasma membrane ATP2B1 ATP2B2 ATP2B3 ATP2B4 SPCA ATP2C1 ATP2C2
Na+/K+ (3.6.3.9)	ATP1A1 ATP1A2 ATP1A3 ATP1A4 ATP1B1 ATP1B2 ATP1B3 ATP1B4
H+/K+ (3.6.3.10)	ATP4A
Other P-type ATPase	ATP8B1 ATP10A ATP11B ATP12A ATP13A2 ATP13A3

3.6.4

3.6.5.1: Heterotrimeric G protein	G_αs G_olf G_αi GNAI1 GNAI2 GNAI3 Transducin GNAT1 GNAT2 Gustducin GNAT3 G_αq/11 GNAQ GNA11 G_α12/13 GNA12 GNA13
3.6.5.2: Small GTPase > Ras superfamily	Rho family of GTPases: Cdc42 CDC42 TC10 TCL RhoUV RhoU RhoV Rac Rac1 2 3 RhoG RhoBTB 1 2 RhoH Rho A B C Rnd 1 2 3 RhoDF RhoF RhoD other: Ras HRAS KRAS NRAS Rab RAB23 RAB27 Arf ARF6 SAR1B ARL13B ARL6 Ran Rheb Rap RGK
3.6.5.3: Protein-synthesizing GTPase	Prokaryotic IF-2 EF-Tu EF-G Eukaryotic
3.6.5.5-6: Polymerization motors	dynamin superfamily Dynamin Guanylate-binding protein Mitofusin-1 MX1 and MX2 OPA1 Tubulin

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