Journal of Biosciences

, Volume 31, Issue 2, pp 281–289 | Cite as

Mechanism of recycling of post-termination ribosomal complexes in eubacteria: A new role of initiation factor 3

  • Anuradha Seshadri
  • Umesh Varshney


Ribosome recycling is a process which dissociates the post-termination complexes (post-TC) consisting of mRNA-bound ribosomes harbouring deacylated tRNA(s). Ribosome recycling factor (RRF), and elongation factor G (EFG) participate in this crucial process to free the ribosomal subunits for a new round of translation. We discuss the overall pathway of ribosome recycling in eubacteria with especial reference to the important role of the initiation factor 3 (IF3) in this process. Depending on the step(s) at which IF3 function is implicated, three models have been proposed. In model 1, RRF and EFG dissociate the post-TCs into the 50S and 30S subunits, mRNAand tRNA(s). In this model, IF3, which binds to the 30S subunit, merely keeps the dissociated subunits apart by its anti-association activity. In model 2, RRF and EFG separate the 50S subunit from the post-TC. IF3 then dissociates the remaining complex of mRNA, tRNA and the 30S subunit, and keeps the ribosomal subunits apart from each other. However, in model 3, both the genetic and biochemical evidence support a more active role for IF3 even at the step of dissociation of the post-TC by RRF and EFG into the 50S and 30S subunits.


EFG IF3 post-TC protein synthesis RF specific interactions 

Abbreviations Used


Elongation factor G

IF 3

initiation factor 3


post termination complex


release factor


ribosome recycling factor


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Agrawal R K, Sharma M R, Kiel M C, Hirokawa G, Booth T M, Spahn C M, Grassucci R A, Kaji A and Frank J 2004 Visualization of ribosome-recycling factor on theEscherichia coli 70S ribosome: functional implications;Proc. Natl. Acad. Sci. USA 101 8900–8905PubMedCrossRefGoogle Scholar
  2. Buckingham R H, Grentzmann G and Kisselev L 1997 Polypeptide chain release factors;Mol. Microbiol. 24 449–456PubMedCrossRefGoogle Scholar
  3. Cate J H, Yusupov M M, Yusupova G Z, Earnest T N and Noller H F 1999 X-ray crystal structures of 70S ribosome functional complexes;Science 285 2095–2104PubMedCrossRefGoogle Scholar
  4. Dallas A and Noller H F 2001 Interaction of translation initiation factor 3 with the 30S ribosomal subunit;Mol. Cell 8 855–864PubMedCrossRefGoogle Scholar
  5. Fraser C M, Gocayne J D, White O, Adams M D, Clayton R A, Fleischmann R D, Bult C J, Kerlavage A R, Sutton G, Kelley J M, Fritchman R D, Weidman J F, Small K V, Sandusky M, Fuhrmann J, Nguyen D, Utterback T R, Saudek D M, Phillips C A, Merrick J M, Tomb J F, Dougherty B A, Bott K F, Hu P C, Lucier T S, Peterson S N, Smith H O, Hutchison C A 3rd and Venter J C 1995 The minimal gene complement ofMycoplasma genitalium;Science 270 397–403PubMedCrossRefGoogle Scholar
  6. Freistroffer D V, Pavlov M Y, MacDougall J, Buckingham R H and Ehrenberg M 1997 Release factor RF3 inE. coli accelerates the dissociation of release factors RF1 and RF2 from the ribosome in a GTP-dependent manner;EMBO J. 16 4126–4133PubMedCrossRefGoogle Scholar
  7. Fujiwara T, Ito K, Yamami T and Nakamura Y 2004 Ribosome recycling factor disassembles the post-termination ribosomal complex independent of the ribosomal translocase activity of elongation factor G;Mol. Microbiol. 53 517–528PubMedCrossRefGoogle Scholar
  8. Gabashvili I S, Agrawal R K, Spahn C M, Grassucci R A, Svergun D I, Frank J and Penczek P 2000 Solution structure of theE. coli 70S ribosome at 11.5 å resolution;Cell 100 537–549PubMedCrossRefGoogle Scholar
  9. Gao H, Sengupta J, Valle M, Korostelev A, Eswar N, Stagg S M, Van Roey P, Agrawal R K, Harvey S C, Sali A, Chapman M S and Frank J 2003 Study of the structural dynamics of theE. coli 70S ribosome using real-space refinement;Cell 113 789–801PubMedCrossRefGoogle Scholar
  10. Gao N, Zavialov A V, Li W, Sengupta J, Valle M, Gursky R R Ehrenberg M and Frank J 2005 Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies;Mol. Cell 18 663–674PubMedCrossRefGoogle Scholar
  11. Hershey J W B 1983 Protein synthesis; inEscherichia coli and Salmonella typhimurium: Cellular and molecular biology (eds) F C Neidhardt, J L Ingraham, K B Low, B Magasanik, M Schaechter and H E Umbarger (Washington D C: American Society for Microbiology) pp 613–647Google Scholar
  12. Heurgue-Hamard V, Karimi R, Mora L, MacDougall J, Leboeuf C, Grentzmann G, Ehrenberg M and Buckingham R H 1998 Ribosome release factor RF4 and termination factor RF3 are involved in dissociation of peptidyl-tRNA from the ribosome;EMBOJ. 17 808–816CrossRefGoogle Scholar
  13. Hirashima A and Kaji A 1972 Factor-dependent release of ribosomes from messenger RNA — Requirement for two heat-stable factors;J. Mol. Biol. 65 43–58PubMedCrossRefGoogle Scholar
  14. Hirokawa G, Kiel M C, Muto A, Selmer M, Raj V S, Liljas A, Igarashi K, Kaji H and Kaji A 2002 Post-termination complex disassembly by ribosome recycling factor, a functional tRNA mimic;EMBO J. 21 2272–2281PubMedCrossRefGoogle Scholar
  15. Hirokawa G, Inokuchi H, Kaji H, Igarashi K and Kaji A 2004In vivo effect of inactivation of ribosome recycling factor — fate of ribosomes after unscheduled translation downstream of open reading frame;Mol. Microbiol. 54 1011–1021PubMedCrossRefGoogle Scholar
  16. Hirokawa G, Nijman R M, Raj V S, Kaji H, Igarashi K and Kaji A 2005 The role of ribosome recycling factor in dissociation of 70S ribosomes into subunits;RNA 11 1317–1328PubMedCrossRefGoogle Scholar
  17. Hirokawa G, Demeshkina N, Iwakura N, Kaji H and Kaji A 2006 The ribosome-recycling step: consensus or controversy?;Trends Biochem. Sci. 31 141–149CrossRefGoogle Scholar
  18. Ito K, Fujiwara T, Toyoda T and Nakamura Y 2002 Elongation factor G participates in ribosome disassembly by interacting with ribosome recycling factor at their tRNA-mimicry domains;Mol. Cell 9 1263–1272PubMedCrossRefGoogle Scholar
  19. Janosi L, Shimizu I and Kaji A 1994 Ribosome recycling factor (ribosome releasing factor) is essential for bacterial growth;Proc. Natl. Acad. Sci. USA 91 4249–4253PubMedCrossRefGoogle Scholar
  20. Janosi L, Ricker R and Kaji A 1996 Dual functions of ribosome recycling factor in protein biosynthesis: disassembling the termination complex and preventing translational errors;Biochimie 78 959–969PubMedCrossRefGoogle Scholar
  21. Janosi L, Mottagui-Tabar S, Isaksson L A, Sekine Y, Ohtsubo E, Zhang S, Goon S, Nelken S, Shuda M and Kaji A 1998 Evidence forin vivo ribosome recycling, the fourth step in protein biosynthesis;EMBO J. 17 1141–1151PubMedCrossRefGoogle Scholar
  22. Kaji A, Teyssier E and Hirokawa G 1998 Disassembly of the post-termination complex and reduction of translational error by ribosome recycling factor (RRF) — A possible new target for antibacterial agents;Biochem. Biophys. Res. Commun. 250 1–4PubMedCrossRefGoogle Scholar
  23. Karimi R, Pavlov M Y, Buckingham R H and Ehrenberg M 1999 Novel roles for classical factors at the interface between translation termination and initiation;Mol. Cell 3 601–609PubMedCrossRefGoogle Scholar
  24. Katunin V I, Savelsbergh A, Rodnina M V and Wintermeyer W 2002 Coupling of GTP hydrolysis by elongation factor G to translocation and factor recycling on the ribosome;Biochemistry 41 12806–12812PubMedCrossRefGoogle Scholar
  25. Kiel M C, Raj V S, Kaji H and Kaji A 2003 Release of ribosome-bound ribosome recycling factor by elongation factor G;J. Biol. Chem. 278 48041–48050PubMedCrossRefGoogle Scholar
  26. Kim K K, Min K and Suh S W 2000 Crystal structure of the ribosome recycling factor fromEscherichia coli;EMBO J. 19 2362–2370PubMedCrossRefGoogle Scholar
  27. Kozak M 1983 Comparison of initiation of protein synthesis in prokaryotes, eukaryotes, and organelles;Microbiol. Rev. 47 1–45PubMedGoogle Scholar
  28. Lancaster L, Kiel M C, Kaji A and Noller H F 2002 Orientation of ribosome recycling factor in the ribosome from directed hydroxyl radical probing;Cell 111 129–140PubMedCrossRefGoogle Scholar
  29. Moazed D, Samaha R R, Gualerzi C and Noller H F 1995 Specific protection of 16 S rRNA by translational initiation factors;J. Mol. Biol. 248 207–210PubMedGoogle Scholar
  30. Moll I, Hirokawa G, Kiel M C, Kaji A and Blasi U 2004 Translation initiation with 70S ribosomes: an alternative pathway for leaderless mRNAs;Nucleic Acids Res. 32 3354–3363PubMedCrossRefGoogle Scholar
  31. Nakano H, Yoshida T, Uchiyama S, Kawachi M, Matsuo H, Kato T, Ohshima A, Yamaichi Y, Honda T, Kato H, Yamagata Y, Ohkubo T and Kobayashi Y 2003 Structure and binding mode of a ribosome recycling factor (RRF) from mesophilic bacterium;J. Biol. Chem. 278 3427–3436PubMedCrossRefGoogle Scholar
  32. O’Donnell S M and Janssen G R 2002 Leaderless mRNAs bind 70S ribosomes more strongly than 30S ribosomal subunits inEscherichia coli;J. Bacteriol. 184 6730–6733PubMedCrossRefGoogle Scholar
  33. Pavlov M Y, Freistroffer D V, MacDougall J, Buckingham R H and Ehrenberg M 1997a Fast recycling ofEscherichia coli ribosomes requires both ribosome recycling factor (RRF) and release factor RF3;EMBO J. 16 4134–4141PubMedCrossRefGoogle Scholar
  34. Pavlov M Y, Freistroffer D V, Heurgue-Hamard V, Buckingham R H and Ehrenberg M 1997b Release factor RF3 abolishes competition between release factor RF1 and ribosome recycling factor (RRF) for a ribosome binding site;J. Mol. Biol. 273 389–401PubMedCrossRefGoogle Scholar
  35. Peske F, Rodnina M V and Wintermeyer W 2005 Sequence of steps in ribosome recycling as defined by kinetic analysis;Mol. Cell 18 403–412PubMedCrossRefGoogle Scholar
  36. Raj V S, Kaji H and Kaji A 2005 Interaction of RRF and EF-G fromE. coli andT. thermophilus with ribosomes from both origins-insight into the mechanism of the ribosome recycling step;RNA 11 275–284PubMedCrossRefGoogle Scholar
  37. Rao A R and Varshney U 2001 Specific interaction between the ribosome recycling factor and the elongation factor G fromMycobacterium tuberculosis mediates peptidyl-tRNA release and ribosome recycling inEscherichia coli;EMBO J. 20 2977–2986PubMedCrossRefGoogle Scholar
  38. Remme J, Margus T, Villems R and Nierhaus K H 1989 The third ribosomal tRNA-binding site, the E site, is occupied in native polysomes;Eur. J. Biochem. 183 281–284PubMedCrossRefGoogle Scholar
  39. Rodnina M V, Savelsbergh A, Katunin V I and Wintermeyer W 1997 Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome;Nature (London) 385 37–41CrossRefGoogle Scholar
  40. Rodnina M V, Savelsbergh A, Matassova N B, Katunin V I, Semenkov Y P and Wintermeyer W 1999 Thiostrepton inhibits the turnover but not the GTPase of elongation factor G on the ribosome;Proc. Natl. Acad. Sci. USA 96 9586–9590PubMedCrossRefGoogle Scholar
  41. Saikrishnan K, Kalapala S K, Varshney U and Vijayan M 2005 X-ray structural studies ofMycobacterium tuberculosis RRF and a comparative study of RRFs of known structure. Molecular plasticity and biological implications;J. Mol. Biol. 345 29–38PubMedCrossRefGoogle Scholar
  42. Savelsbergh A, Katunin V I, Mohr D, Peske F, Rodnina M V and Wintermeyer W 2003 An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation;Mol. Cell 11 1517–1523PubMedCrossRefGoogle Scholar
  43. Selmer M, Al-Karadaghi S, Hirokawa Q Kaji A and Liljas A 1999 Crystal structure ofThermotoga maritima ribosome recycling factor: a tRNA mimic;Science 286 2349–2352PubMedCrossRefGoogle Scholar
  44. Seo H S, Kiel M, Pan D, Raj V S, Kaji A and Cooperman B S 2004 Kinetics and thermodynamics of RRF, EF-G, and thiostrepton interaction on theEscherichia coli ribosome;Biochemistry 43 12728–12740PubMedCrossRefGoogle Scholar
  45. Singh N S, Das G, Seshadri A, Sangeetha R and Varshney U 2005 Evidence for a role of initiation factor 3 in recycling of ribosomal complexes stalled on mRNAs inEscherichia coli;Nucleic Acids Res. 33 5591–5601PubMedCrossRefGoogle Scholar
  46. Toyoda T, Tin O F, Ito K, Fujiwara T, Kumasaka T, Yamamoto M, Garber M B and Nakamura Y 2000 Crystal structure combined with genetic analysis of theThermus thermophilus ribosome recycling factor shows that a flexible hinge may act as a functional switch;RNA 6 1432–1444PubMedCrossRefGoogle Scholar
  47. Udagawa T, Shimizu Y and Ueda T 2004 Evidence for the translation initiation of leaderless mRNAs by the intact 70 S ribosome without its dissociation into subunits in eubacteria;J. Biol. Chem. 279 8539–8546PubMedCrossRefGoogle Scholar
  48. Umekage S and Ueda T 2006 Spermidine inhibits transient and stable ribosome subunit dissociation;FEBS Lett. 580 1222–1226PubMedCrossRefGoogle Scholar
  49. Wilson D N, Schluenzen F, Harms J M, Yoshida T, Ohkubo T, Albrecht R, Buerger J, Kobayashi Y and Fucini P 2005 X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit;EMBO J. 24 251–260PubMedCrossRefGoogle Scholar
  50. Yoshida T, Uchiyama S, Nakano H, Kashimori H, Kijima H, Ohshima T, Saihara Y, Ishino T, Shimahara H, Yokose K, Ohkubo T, Kaji A and Kobayashi Y 2001 Solution structure of the ribosome recycling factor fromAquifex aeolicus;Biochemistry 40 2387–2396PubMedCrossRefGoogle Scholar
  51. Yusupov M M, Yusupova G Z, Baucom A, Lieberman K, Earnest T N, Cate J H and Noller H F 2001 Crystal structure of the ribosome at 5.5 å resolution;Science 292 883–896PubMedCrossRefGoogle Scholar
  52. Zavialov A V, Buckingham R H and Ehrenberg M 2001 A posttermination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor RF3;Cell 107 115–124PubMedCrossRefGoogle Scholar
  53. Zavialov A V, Mora L, Buckingham R H and Ehrenberg M 2002 Release of peptide promoted by the GGQ motif of class 1 release factors regulates the GTPase activity of RF3;Mol. Cell 10 789–798PubMedCrossRefGoogle Scholar
  54. Zavialov A V, Hauryliuk V V and Ehrenberg M 2005a Splitting of the posttermination ribosome into subunits by the concerted action of RRF and EF-G;Mol. Cell 18 675–686PubMedCrossRefGoogle Scholar
  55. Zavialov A V, Hauryliuk V V and Ehrenberg M 2005b Guaninenucleotide exchange on ribosome-bound elongation factor G initiates the translocation of tRNAs;J. Biol. 4 9–27PubMedCrossRefGoogle Scholar

Copyright information

© Indian Academy of Sciences 2006

Authors and Affiliations

  1. 1.Department of Microbiology and Cell BiologyIndian Institute of ScienceBangaloreIndia

Personalised recommendations