Requirements for resuming translation in chimeric transfer-messenger RNAs of Escherichia coli and Mycobacterium tuberculosis

BMC Molecular Biology

Jacek Wower²  Christian Zwieb¹  Iwona K Wower² 

[1] Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA;Department of Animal Sciences, Auburn University, Auburn, AL 36849, USA

关键词: Protein tagging;    Trans-translation;    SmpB;    Chimeric tmRNA;   

Others  :  1227873
DOI  :  10.1186/1471-2199-15-19

 received in 2014-03-27, accepted in 2014-06-18,  发布年份 2014

【 摘 要 】

Background

Trans-translation is catalyzed by ribonucleprotein complexes composed of SmpB protein and transfer-messenger RNA. They release stalled ribosomes from truncated mRNAs and tag defective proteins for proteolytic degradation. Comparative sequence analysis of bacterial tmRNAs provides considerable insights into their secondary structures in which a tRNA-like domain and an mRNA-like region are connected by a variable number of pseudoknots. Progress toward understanding the molecular mechanism of trans-translation is hampered by our limited knowledge about the structure of tmRNA:SmpB complexes.

Results

Complexes consisting of M. tuberculosis tmRNA and E. coli SmpB tag truncated proteins poorly in E. coli. In contrast, the tagging activity of E. coli tmRNA is well supported by M. tuberculosis SmpB that is expressed in E. coli. To investigate this incompatibility, we constructed 12 chimeric tmRNA molecules composed of structural features derived from both E. coli and M. tuberculosis. Our studies demonstrate that replacing the hp5-pk2-pk3-pk4 segment of E. coli tmRNA with the equivalent segment of M. tuberculosis tmRNA has no significant effect on the tagging efficiency of chimeric tmRNAs in the presence of E. coli SmpB. Replacing either helices 2b-2d, the single-stranded part of the ORF, pk1, or residues 79–89 of E. coli tmRNA with the equivalent features of M. tuberculosis tmRNA yields chimeric tmRNAs that are tagged at 68 to 88 percent of what is observed with E. coli tmRNA. Exchanging segments composed of either pk1 and the single-stranded segment upstream of the ORF or helices 2b-2d and pk1 results in markedly impaired tagging activity.

Conclusion

Our observations demonstrate the existence of functionally important but as yet uncharacterized structural constraints in the segment of tmRNA that connects its TLD to the ORF used for resuming translation. As trans-translation is important for the survival of M. tuberculosis, our work provides a new target for pharmacological intervention against multidrug-resistant tuberculosis.

【 授权许可】

   
2014 Wower et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

Figure 7.

【 参考文献 】

• [1]Moore SD, Sauer RT: The tmRNA system for translational surveillance and ribosome rescue. Annu Rev Biochem 2007, 76:101-124.
• [2]Keiler KC: Biology of trans-translation. Annu Rev Microbiol 2008, 62:133-151.
• [3]Felden B, Himeno H, Muto A, Atkins JF, Gesteland RF: Structural organization of Escherichia coli tmRNA. Biochimie 1996, 78:979-983.
• [4]Williams KP, Bartel DP: The tmRNA Website. Nucleic Acids Res 1998, 26:163-165.
• [5]Knudsen B, Wower J, Zwieb C, Gorodkin J: tmRDB (tmRNA database). Nucleic Acids Res 2001, 29:171-172.
• [6]Bessho Y, Shibata R, Sekine S, Murayama K, Higashijima K, Hori-Takemoto C, Shirouzu M, Kuramitsu S, Yokoyama S: Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA. Proc Natl Acad Sci USA 2007, 2007(104):8293-8298.
• [7]Rudinger-Thirion J, Giege R, Felden B: Aminoacylated tmRNA from Escherichia coli interacts with prokaryotic elongation factor Tu. RNA 1999, 5:989-992.
• [8]Barends S, Karzai AW, Sauer RT, 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.
• [9]Wower IK, Jahan N, Zwieb C, Wower J: Ribosomal Protein S1: An Important Trans-Translation Factor. Biochemistry & Physiology 2013, S2:1-7.
• [10]Wower IK, Zwieb CW, Guven SA, Wower J: Binding and cross-linking of tmRNA to ribosomal protein S1, on and off the Escherichia coli ribosome. EMBO J 2000, 19:6612-6621.
• [11]Shi W, Zhang X, Jiang X, Yuan H, Lee JS, Barry CE, Wang H, Zhang W, Zhang Y: Pyrazinamide inhibits trans-translation in Mycobacterium tuberculosis. Science 2011, 333:1630-1632.
• [12]Saguy M, Gillet R, Skorski P, Hermann-Le Denmat S, Felden B: Ribosomal protein S1 influences trans-translation in vitro and in vivo. Nucleic Acids Res. 2007, 35:2368-2376.
• [13]Qi H, Shimizu Y, Ueda T: Ribosomal protein S1 is not essential for the trans-translation machinery. J. Mol. Biol. 2007, 368:845-852.
• [14]Takada K, Takemoto C, Kawazoe M, Konno T, Hanawa-Suetsugu K, Lee S, Shirouzu M, Yokoyama S, Muto A, Himeno H: In vitro trans-translation of Thermus thermophilus: ribosomal protein S1 is not required for the early stage of trans-translation. RNA 2007, 13:503-510.
• [15]Valle M, Gillet R, Kaur S, Henne A, Ramakrishnan V, Frank J: Visualizing tmRNA entry into a stalled ribosome. Science 2003, 300:127-130.
• [16]Kaur S, Gillet R, Li W, Gursky R, Frank J: Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome. Proc Natl Acad Sci USA 2006, 103:16484-16489.
• [17]Cheng K, Ivanova N, Scheres SH, Pavlov MY, Carazo JM, Hebert H, Ehrenberg M, Lindahl M: tmRNA-SmpB complex mimics native aminoacyl-tRNAs in the A site of stalled ribosomes. J Struct Biol 2010, 169:342-348.
• [18]Fu J, Hashem Y, Wower I, Lei J, Liao HY, Zwieb C, Wower J, Frank J: Visualizing the transfer-messenger RNA as the ribosome resumes translation. EMBO J. 2010, 29:3819-3825.
• [19]Weis F, Bron P, Giudice E, Rolland JP, Thomas D, Felden B, Gillet R: tmRNA-SmpB: a journey to the centre of the bacterial ribosome. EMBO J 2010, 29:3810-3818.
• [20]Ramrath DJ, Yamamoto H, Rother K, Wittek D, Pech M, Mielke T, Loerke J, Scheerer P, Ivanov P, Teraoka Y, Shpanchenko O, Nierhaus KH, Spahn CM: The complex of tmRNA-SmpB and EF-G on translocating ribosomes. Nature 2012, 485:526-529.
• [21]Fu J, Hashem Y, Wower J: Frank J: tmRNA on its way through the ribosome. RNA Biology 2011, 8:586-590.
• [22]Wower IK, Zwieb C, Wower J: Escherichia coli tmRNA lacking pseudoknot 1 tags truncated proteins in vivo and in vitro. RNA 2009, 15:128-137.
• [23]Miller MR, Healey DW, Robison SG, Dewey JD, Buskirk AR: The role of upstream sequences in selecting the reading frame on tmRNA. BMC Biol 2008, 6:1-10. BioMed Central Full Text
• [24]Wower IK, Zwieb C, Wower J: Contributions of pseudoknots and protein SmpB to the structure and function of tmRNA in trans-translation. J Biol Chem 2004, 279:54202-54209.
• [25]Nameki N, Tadaki T, Himeno H, Muto A: Three of four pseudoknots in tmRNA are interchangeable and are substitutable with single-stranded RNAs. FEBS Lett 2000, 470:345-349.
• [26]Zucker M: Mfold web server for nucleic acid folding and hybridization. Nucleic Acids Res 2003, 31:3406-3415.
• [27]Mattice WL, Riser JM, Clark DS: Conformational properties of the complexes formed by proteins and sodium dodecyl sulfate. Biochemistry 1976, 15:4264-4272.
• [28]Rath A, Glibowicka M, Nadeau VG, Chen G, Deber CM: Detergent binding explains anomalous SDS-PAGE migration of membrane proteins. Proc Natl Acad Sci USA 2009, 106:1760-1765.
• [29]Tanner DR, Dewey JD, Miller MR, Buskirk AR: Genetic analysis of the structure and function of transfer messenger RNA pseudoknot 1. J Biol Chem 2006, 281:10561-10566.
• [30]Kapoor S, Samhita L, Varshney U: Functional significance of an evolutionarily conserved alanine (GCA) resume codon in tmRNA in Escherichia coli. J Bacteriol 2011, 193:3569-3576.
• [31]Wower J, Wower IK, Zwieb C: Making the jump: new insights into the mechanism of trans-translation. J Biol 2008, 7:1-4. BioMed Central Full Text
• [32]Gueneau de Novoa P, Williams KP: The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts. Nucleic Acids Res 2004, 32:D104-D108.
• [33]Andersen ES, Rosenblad MA, Larsen N, Westergaard JC, Burks J, Wower IK, Wower J, Gorodkin J, Samuelsson T, Zwieb C: The tmRDB and SRPDB resources. Nucleic Acids Res 2006, 34:D163-D168.
• [34]Keiler KC, Shapiro L, Williams KP: tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter. Proc Natl Acad Sci USA 2000, 97:7778-7783.
• [35]Williams KP: Descent of a split RNA. Nucleic Acids Res 2002, 30:2025-2030.
• [36]Zwieb C, Wower I, Wower J: Comparative sequence analysis of tmRNA. Nucleic Acids Res 1999, 27:2063-2071.
• [37]Roche ED, Sauer RT: SsrA-mediated peptide tagging caused by rare codons and tRNA scarcity. EMBO J 1999, 18:4579-4589.
• [38]Dong H, Nilsson L, Kurland CG: Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J Mol Biol 1996, 260:649-663.
• [39]O’Connor M: Minimal translation of the tmRNA tag-coding region is required for ribosome release. Biochem Biophys Res Commun 2007, 357:276-281.
• [40]Thibonnier M, Aubert S, Ecobichon C, De Reuse H: Study of the functionality of the Helicobacter pylori trans-translation components SmpB and SsrA in an heterologous system. BMC Microbiol 2010, 10:1-11. BioMed Central Full Text
• [41]Williams KP, Martindale KA, Bartel DP: Resuming translation on tmRNA: a unique mode of determining a reading frame. EMBO J 1999, 18:5423-5433.
• [42]Lee S, Ishii M, Tadaki T, Muto A, Himeno H: Determinants on tmRNA for initiating efficient and precise trans-translation: some mutations upstream of the tag-encoding sequence of Escherichia coli tmRNA shift the initiation point of trans-translation in vitro. RNA 2001, 7:999-1012.
• [43]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, 13:1723-1731.
• [44]Wower J, Zwieb CW, Hoffman DW, Wower IK: SmpB: a protein that binds to double-stranded segments in tmRNA and tRNA. Biochemistry 2002, 2002(41):8826-8836.
• [45]Gillet R, Kaur S, Li W, Hallier M, Felden B, Frank J: Scaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1. J Biol Chem 2007, 282:6356-6363.
• [46]Ivanov PV, Zvereva MI, Shpanchenko OV, Dontsova OA, Bogdanov AA, Aglyamova GV, Lim VI, Teraoka Y, Nierhaus KH: How does tmRNA move through the ribosome? FEBS Lett 2002, 514:55-59.
• [47]Personne Y, Parish T: Mycobacterium tuberculosis posseses an unusual tmRNA rescue system. Tuberculosis 2014, 94:34-42.
• [48]Wower IK, Wower J, Zimmermann RA: Ribosomal protein L27 participates in both 50S subunit assembly and the peptidyl transferase reaction. J Biol Chem 1998, 273:19847-19852.
• [49]Chen GJ, Qiu N, Karrer C, Caspers P, Page MG: Restriction site-free insertion of PCR products directionally into vectors. Biotechniques 2000, 28:498-500. 504-505