smpB

Summary

Gene Symbol: smpB
Description: tmRNA-binding trans-translation protein
Alias: ECK2616, JW2601, smqB
Species: Escherichia coli str. K-12 substr. MG1655

Top Publications

  1. Holberger L, Hayes C. Ribosomal protein S12 and aminoglycoside antibiotics modulate A-site mRNA cleavage and transfer-messenger RNA activity in Escherichia coli. J Biol Chem. 2009;284:32188-200 pubmed publisher
    ..A-site mRNA cleavage is thought to facilitate transfer-messenger RNA (tmRNA).SmpB- mediated recycling of stalled ribosome complexes...
  2. Karzai A, Susskind M, Sauer R. SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA). EMBO J. 1999;18:3793-9 pubmed
    ..The SsrA-tagged protein is then degraded by C-terminal-specific proteases. SmpB, a unique RNA-binding protein that is conserved throughout the bacterial kingdom, is shown here to be an essential ..
  3. Hallier M, Ivanova N, Rametti A, Pavlov M, Ehrenberg M, Felden B. Pre-binding of small protein B to a stalled ribosome triggers trans-translation. J Biol Chem. 2004;279:25978-85 pubmed
    ..With the help of small protein B (SmpB), tmRNA restarts protein synthesis and adds by the trans-translation mechanism a peptide tag to the stalled protein ..
  4. Shimizu Y, Ueda T. The role of SmpB protein in trans-translation. FEBS Lett. 2002;514:74-7 pubmed
    The function of SmpB protein in the trans-translation system was evaluated using the well-defined cell-free translation system consisting of purified ribosome, alanyl-tRNA synthetase and elongation factors...
  5. Withey J, Friedman D. A salvage pathway for protein structures: tmRNA and trans-translation. Annu Rev Microbiol. 2003;57:101-23 pubmed
    ..Proteins known to be associated with tmRNA include SmpB, ribosomal protein S1, RNase R, and phosphoribosyl pyrophosphate...
  6. Valle M, Gillet R, Kaur S, Henne A, Ramakrishnan V, Frank J. Visualizing tmRNA entry into a stalled ribosome. Science. 2003;300:127-30 pubmed publisher
    ..The structure reveals how tmRNA could move through the ribosome despite its complicated topology and also suggests roles for proteins S1 and SmpB in the function of tmRNA.
  7. Komine Y, Kitabatake M, Yokogawa T, Nishikawa K, Inokuchi H. A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli. Proc Natl Acad Sci U S A. 1994;91:9223-7 pubmed
    ..A pair could be overcome by the introduction of a gene encoding alanyl-tRNA synthetase (alaS) on a multicopy plasmid. The evidence suggests that the proposed structural features of 10Sa RNA are indeed manifested in vivo...
  8. Dulebohn D, Cho H, Karzai A. Role of conserved surface amino acids in binding of SmpB protein to SsrA RNA. J Biol Chem. 2006;281:28536-45 pubmed
    Bacteria possess a unique salvage mechanism for rescuing ribosomes stalled on aberrant mRNAs. A complex of SmpB protein and SsrA RNA orchestrates this salvage process...
  9. Andersen E, Rosenblad M, Larsen N, Westergaard J, Burks J, Wower I, et al. The tmRDB and SRPDB resources. Nucleic Acids Res. 2006;34:D163-8 pubmed publisher
    ..Also shown are alignments of the tmRNA-associated proteins SmpB, ribosomal protein S1, alanyl-tRNA synthetase and Elongation Factor Tu, as well as the SRP proteins SRP9, SRP14, ..

More Information

Publications49

  1. Ivanova N, Pavlov M, Bouakaz E, Ehrenberg M, Schiavone L. Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA. Nucleic Acids Res. 2005;33:3529-39 pubmed
    In trans-translation transfer messenger RNA (tmRNA) and small protein B (SmpB) rescue ribosomes stalled on truncated or in other ways problematic mRNAs...
  2. Sundermeier T, Dulebohn D, Cho H, Karzai A. A previously uncharacterized role for small protein B (SmpB) in transfer messenger RNA-mediated trans-translation. Proc Natl Acad Sci U S A. 2005;102:2316-21 pubmed
    ..Small protein B (SmpB) is required for all known activities of SsrA...
  3. Jacob Y, Sharkady S, Bhardwaj K, Sanda A, Williams K. Function of the SmpB tail in transfer-messenger RNA translation revealed by a nucleus-encoded form. J Biol Chem. 2005;280:5503-9 pubmed
    ..This process requires the tmRNA-binding and ribosome-binding cofactor SmpB, a beta-barrel protein with a protruding C-terminal tail of unresolved structure...
  4. Takahashi T, Konno T, Muto A, Himeno H. Various effects of paromomycin on tmRNA-directed trans-translation. J Biol Chem. 2003;278:27672-80 pubmed
    ..Paromomycin bound at G332/G333 inhibited aminoacylation, and the inhibition was suppressed by the addition of SmpB, a tmRNA-binding protein...
  5. Wower J, Zwieb C, Hoffman D, Wower I. SmpB: a protein that binds to double-stranded segments in tmRNA and tRNA. Biochemistry. 2002;41:8826-36 pubmed
    Binding of the SmpB protein to tmRNA is essential for trans-translation, a process that facilitates peptide tagging of incompletely synthesized proteins. We have used three experimental approaches to study these interactions in vitro...
  6. Hanawa Suetsugu K, Takagi M, Inokuchi H, Himeno H, Muto A. SmpB functions in various steps of trans-translation. Nucleic Acids Res. 2002;30:1620-9 pubmed
    ..b>SmpB is a tmRNA binding protein that has been identified to be essential for trans-translation in vivo...
  7. Barends S, Björk K, Gultyaev A, de Smit M, Pleij C, Kraal B. Functional evidence for D- and T-loop interactions in tmRNA. FEBS Lett. 2002;514:78-83 pubmed
    ..Strikingly, this in evolution conserved interaction is not primarily important for tmRNA alanylation and for binding to elongation factor Tu, but especially for a proper functioning of SmpB.
  8. Barends S, Karzai A, Sauer R, Wower J, Kraal B. Simultaneous and functional binding of SmpB and EF-Tu-TP to the alanyl acceptor arm of tmRNA. J Mol Biol. 2001;314:9-21 pubmed
    ..In other studies, protein SmpB and ribosomal protein S1 appeared to bind directly to tmRNA and to be indispensable for trans-translation...
  9. Karzai A, Roche E, Sauer R. The SsrA-SmpB system for protein tagging, directed degradation and ribosome rescue. Nat Struct Biol. 2000;7:449-55 pubmed
    ..tags to their C-termini in a reaction that is mediated by ribosome-bound SsrA RNA and an associated protein factor, SmpB. This system plays a key role in intracellular protein quality control and also provides a mechanism to clear ..
  10. Choy J, Aung L, Karzai A. Lon protease degrades transfer-messenger RNA-tagged proteins. J Bacteriol. 2007;189:6564-71 pubmed
    ..Small protein B (SmpB) and transfer-messenger RNA (tmRNA) are the two known factors required for and dedicated to trans translation...
  11. Corvaisier S, Bordeau V, Felden B. Inhibition of transfer messenger RNA aminoacylation and trans-translation by aminoglycoside antibiotics. J Biol Chem. 2003;278:14788-97 pubmed
    ..b>SmpB and elongation factor Tu have RNA chaperone activities, ensuring that tmRNA adopts an optimal conformation during ..
  12. Watts T, Cazier D, Healey D, Buskirk A. SmpB contributes to reading frame selection in the translation of transfer-messenger RNA. J Mol Biol. 2009;391:275-81 pubmed publisher
    ..Together with its protein partner, SmpB (small protein B), tmRNA enters stalled ribosomes and transfers an Ala residue to the growing polypeptide chain...
  13. Dulebohn D, Choy J, Sundermeier T, Okan N, Karzai A. Trans-translation: the tmRNA-mediated surveillance mechanism for ribosome rescue, directed protein degradation, and nonstop mRNA decay. Biochemistry. 2007;46:4681-93 pubmed
    ..This review will focus on recent advances in our understanding of the structural properties, mechanistic details, and physiological significance of this unique RNA and its principal protein partners. ..
  14. Richards J, Mehta P, Karzai A. RNase R degrades non-stop mRNAs selectively in an SmpB-tmRNA-dependent manner. Mol Microbiol. 2006;62:1700-12 pubmed
    The SmpB-tmRNA-mediated trans-translation system has two well-established activities: rescuing ribosomes stalled on aberrant mRNAs and marking the associated protein fragments for proteolysis...
  15. Miller M, Liu Z, Cazier D, Gebhard G, Herron S, Zaher H, et al. The role of SmpB and the ribosomal decoding center in licensing tmRNA entry into stalled ribosomes. RNA. 2011;17:1727-36 pubmed publisher
    ..Instead, tmRNA entry is licensed by the binding of its protein partner, SmpB, to the ribosomal decoding center...
  16. Wower I, Zwieb C, Wower J. Contributions of pseudoknots and protein SmpB to the structure and function of tmRNA in trans-translation. J Biol Chem. 2004;279:54202-9 pubmed
    ..Protein SmpB enhanced tmRNA processing, suggesting a new role for SmpB in trans-translation...
  17. Li J, Ji L, Shi W, Xie J, Zhang Y. Trans-translation mediates tolerance to multiple antibiotics and stresses in Escherichia coli. J Antimicrob Chemother. 2013;68:2477-81 pubmed publisher
    Trans-translation mediated by SsrA (tmRNA) and its associated protein SmpB plays an important role in rescuing stalled ribosomes and detoxifying toxic protein products under stress conditions...
  18. Cheng K, Ivanova N, Scheres S, Pavlov M, Carazo J, Hebert H, et al. tmRNA.SmpB complex mimics native aminoacyl-tRNAs in the A site of stalled ribosomes. J Struct Biol. 2010;169:342-8 pubmed publisher
    ..We used single-particle cryo-electron microscopy to visualize tmRNA together with its helper protein SmpB on the 70S Escherichia coli ribosome in states subsequent to GTP hydrolysis on elongation factor Tu (EF-Tu)...
  19. Daher M, Rueda D. Fluorescence characterization of the transfer RNA-like domain of transfer messenger RNA in complex with small binding protein B. Biochemistry. 2012;51:3531-8 pubmed publisher
    Transfer messenger RNA (tmRNA) and small binding protein B (SmpB) are the main components of the trans-translation rescue machinery that releases stalled ribosomes from defective mRNAs...
  20. Liang W, Deutscher M. Transfer-messenger RNA-SmpB protein regulates ribonuclease R turnover by promoting binding of HslUV and Lon proteases. J Biol Chem. 2012;287:33472-9 pubmed publisher
    ..RNase R instability results from acetylation which promotes binding of tmRNA-SmpB, two trans-translation factors, to its C-terminal region...
  21. Janssen B, Hayes C. Kinetics of paused ribosome recycling in Escherichia coli. J Mol Biol. 2009;394:251-67 pubmed publisher
    The bacterial tmRNA.SmpB system recycles stalled translation complexes in a process termed 'ribosome rescue.' tmRNA...
  22. Konno T, Kurita D, Takada K, Muto A, Himeno H. A functional interaction of SmpB with tmRNA for determination of the resuming point of trans-translation. RNA. 2007;13:1723-31 pubmed
    ..possessing a dual function as a tRNA and an mRNA, relieves a stalled translation on the ribosome with the help of SmpB. Here, we established an in vitro system using Escherichia coli translation and trans-translation factors to ..
  23. Nonin Lecomte S, Germain Amiot N, Gillet R, Hallier M, Ponchon L, Dardel F, et al. Ribosome hijacking: a role for small protein B during trans-translation. EMBO Rep. 2009;10:160-5 pubmed publisher
    ..In eubacteria, translational surveillance and ribosome rescue are performed by the 'tmRNA-SmpB' system (transfer messenger RNA-small protein B)...
  24. Wower J, Wower I, Kraal B, Zwieb C. Quality control of the elongation step of protein synthesis by tmRNP. J Nutr. 2001;131:2978S-82S pubmed
    ..demonstrated that tmRNA functions as a ribonucleoprotein (RNP) complex with elongation factor Tu (EF-Tu), protein SmpB and ribosomal protein S1...
  25. Roche E, Sauer R. Identification of endogenous SsrA-tagged proteins reveals tagging at positions corresponding to stop codons. J Biol Chem. 2001;276:28509-15 pubmed
    The SsrA.SmpB quality control system adds a C-terminal degradation peptide (AANDENYALAA) to nascent chains on stalled ribosomes, thereby freeing the ribosome and ensuring proteolysis of the tagged protein...
  26. Karzai A, Sauer R. Protein factors associated with the SsrA.SmpB tagging and ribosome rescue complex. Proc Natl Acad Sci U S A. 2001;98:3040-4 pubmed
    ..are marked for degradation by addition of peptide tags to their C termini in a reaction mediated by SsrA RNA and SmpB, a specific SsrA-RNA binding protein...
  27. Moore S, Sauer R. Ribosome rescue: tmRNA tagging activity and capacity in Escherichia coli. Mol Microbiol. 2005;58:456-66 pubmed
    ..of tagging was not significantly increased in cells expressing very high levels of tmRNA and its binding protein SmpB, suggesting that recognition of 'stalled' ribosomes does not involve competition between tmRNA and other ..
  28. Miczak A, Chauhan A, Apirion D. Two new genes located between 2758 and 2761 kilobase pairs on the Escherichia coli genome. J Bacteriol. 1991;173:3271-2 pubmed
  29. Kurita D, Konno T, Takada K, Muto A, Himeno H. Molecular mechanism of trans-translation. Nucleic Acids Symp Ser (Oxf). 2007;:43-4 pubmed
    ..this process, tmRNA enters the ribosomal A-site without a codonanticodon interaction, but with a protein factor SmpB. Here, we established in vitro trans-translation system, which is able to evaluate peptidyl transfer to alanyltmRNA ..
  30. Ramrath D, Yamamoto H, Rother K, Wittek D, Pech M, Mielke T, et al. The complex of tmRNA-SmpB and EF-G on translocating ribosomes. Nature. 2012;485:526-9 pubmed publisher
    ..The SmpB protein forms a complex with the tmRNA, and the transfer-RNA-like domain (TLD) of the tmRNA then enters the A site ..
  31. Liang W, Deutscher M. A novel mechanism for ribonuclease regulation: transfer-messenger RNA (tmRNA) and its associated protein SmpB regulate the stability of RNase R. J Biol Chem. 2010;285:29054-8 pubmed publisher
    ..Here we identify two components of the trans-translation machinery, transfer-messenger RNA (tmRNA) and SmpB, that are responsible for the short half-life of RNase R in exponential phase cells...
  32. Kurita D, Muto A, Himeno H. Role of the C-terminal tail of SmpB in the early stage of trans-translation. RNA. 2010;16:980-90 pubmed publisher
    ..relieves a stalled translation on the bacterial ribosome by transfer-messenger RNA (tmRNA) with the help of SmpB, an essential cofactor of tmRNA...
  33. Ross J, Eady E, Cove J, Baumberg S. Identification of a chromosomally encoded ABC-transport system with which the staphylococcal erythromycin exporter MsrA may interact. Gene. 1995;153:93-8 pubmed
    ..Sequences highly similar to stpA and smpA (stpB and smpB) were also found adjacent to a chromosomal copy of msrA in S. hominis...
  34. Bugaeva E, Shpanchenko O, Felden B, Isaksson L, Dontsova O. One SmpB molecule accompanies tmRNA during its passage through the ribosomes. FEBS Lett. 2008;582:1532-6 pubmed publisher
    tmRNA and SmpB are the main participants of trans-translation, a process which rescues the ribosome blocked during translation of non-stop mRNA...
  35. Kurita D, Sasaki R, Muto A, Himeno H. Interaction of SmpB with ribosome from directed hydroxyl radical probing. Nucleic Acids Res. 2007;35:7248-55 pubmed
    ..enters the vacant A-site of the stalled ribosome without a codon-anticodon interaction, but with a protein factor SmpB. Here, we studied the sites and modes of binding of SmpB to the ribosome by directed hydroxyl radical probing from ..
  36. Ivanova N, Lindell M, Pavlov M, Holmberg Schiavone L, Wagner E, Ehrenberg M. Structure probing of tmRNA in distinct stages of trans-translation. RNA. 2007;13:713-22 pubmed
    ..mRNAs in bacterial cells can be rescued by transfer-messenger RNA (tmRNA), its helper protein (small protein B, SmpB), and elongation factor Tu (EF-Tu) through a mechanism called trans-translation...
  37. Gillet R, Felden B. [Lost in translation]. Med Sci (Paris). 2007;23:633-9 pubmed
    ..tmRNA (transfer messenger RNA) and SmpB (small protein B) are the main components of that process...
  38. Sundermeier T, Ge Z, Richards J, Dulebohn D, Karzai A. Studying tmRNA-mediated surveillance and nonstop mRNA decay. Methods Enzymol. 2008;447:329-58 pubmed publisher
    ..or defective mRNAs are rescued by the action of a specialized ribonucleoprotein complex composed of tmRNA and SmpB protein in a process known as trans-translation; for recent reviews see Dulebohn et al...
  39. Sundermeier T, Karzai A. Functional SmpB-ribosome interactions require tmRNA. J Biol Chem. 2007;282:34779-86 pubmed
    Small protein B (SmpB) is a requisite component of the transfer messenger RNA (tmRNA)-mediated bacterial translational quality control system known as trans-translation...
  40. Mu X, Huan H, Xu H, Gao Q, Xiong L, Gao R, et al. The transfer-messenger RNA-small protein B system plays a role in avian pathogenic Escherichia coli pathogenicity. J Bacteriol. 2013;195:5064-71 pubmed publisher
    ..coli (APEC) is a member of the ExPEC group and causes avian colibacillosis. Transfer-mRNA-small protein B (tmRNA-SmpB)-mediated trans-translation is a bacterial translational control system that directs the modification and ..