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Journal articles on the topic 'SmpB'

Author: Grafiati

Published: 4 June 2021

Last updated: 10 February 2022

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1

Okan, Nihal A., Patricio Mena, Jorge L. Benach, James B. Bliska, and A. Wali Karzai. "The smpB-ssrA Mutant of Yersinia pestis Functions as a Live Attenuated Vaccine To Protect Mice against Pulmonary Plague Infection." Infection and Immunity 78, no. 3 (January 11, 2010): 1284–93. http://dx.doi.org/10.1128/iai.00976-09.

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ABSTRACT The bacterial SmpB-SsrA system is a highly conserved translational quality control mechanism that helps maintain the translational machinery at full capacity. Here we present evidence to demonstrate that the smpB-ssrA genes are required for pathogenesis of Yersinia pestis, the causative agent of plague. We found that disruption of the smpB-ssrA genes leads to reduction in secretion of the type III secretion-related proteins YopB, YopD, and LcrV, which are essential for virulence. Consistent with these observations, the smpB-ssrA mutant of Y. pestis was severely attenuated in a mouse model of infection via both the intranasal and intravenous routes. Most significantly, intranasal vaccination of mice with the smpB-ssrA mutant strain of Y. pestis induced a strong antibody response. The vaccinated animals were well protected against subsequent lethal intranasal challenges with virulent Y. pestis. Taken together, our results indicate that the smpB-ssrA mutant of Y. pestis possesses the desired qualities for a live attenuated cell-based vaccine against pneumonic plague.

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2

Rae, Christopher D., Yuliya Gordiyenko, and V. Ramakrishnan. "How a circularized tmRNA moves through the ribosome." Science 363, no. 6428 (February 14, 2019): 740–44. http://dx.doi.org/10.1126/science.aav9370.

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During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used cryo–electron microscopy to determine the structures of three key states of the tmRNA-SmpB-ribosome complex during trans translation at resolutions of 3.7 to 4.4 angstroms. The results show how tmRNA and SmpB act specifically on stalled ribosomes and how the circularized complex moves through the ribosome, enabling translation to switch from the old defective message to the reading frame on tmRNA.

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3

Une, M., D. Kurita, A. Muto, and H. Himeno. "Trans-translation by tmRNA and SmpB." Nucleic Acids Symposium Series 53, no. 1 (September 1, 2009): 305–6. http://dx.doi.org/10.1093/nass/nrp153.

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4

Sundermeier, Thomas R., and A. Wali Karzai. "Functional SmpB-Ribosome Interactions Require tmRNA." Journal of Biological Chemistry 282, no. 48 (October 2, 2007): 34779–86. http://dx.doi.org/10.1074/jbc.m707256200.

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5

Shin, Ji-Hyun, and Chester W. Price. "The SsrA-SmpB Ribosome Rescue System Is Important for Growth of Bacillus subtilis at Low and High Temperatures." Journal of Bacteriology 189, no. 10 (March 16, 2007): 3729–37. http://dx.doi.org/10.1128/jb.00062-07.

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ABSTRACT Bacillus subtilis has multiple stress response systems whose integrated action promotes growth and survival under unfavorable conditions. Here we address the function and transcriptional organization of a five-gene cluster containing ssrA, previously known to be important for growth at high temperature because of the role of its tmRNA product in rescuing stalled ribosomes. Reverse transcription-PCR experiments detected a single message for the secG-yvaK-rnr-smpB-ssrA cluster, suggesting that it constitutes an operon. However, rapid amplification of cDNA ends-PCR and lacZ fusion experiments indicated that operon transcription is complex, with at least five promoters controlling different segments of the cluster. One σA-like promoter preceded secG (P1), and internal σA-like promoters were found in both the rnr-smpB (P2) and smpB-ssrA intervals (P3 and PHS). Another internal promoter lay in the secG-yvaK intercistronic region, and this activity (PB) was dependent on the general stress factor σB. Null mutations in the four genes downstream from PB were tested for their effects on growth. Loss of yvaK (carboxylesterase E) or rnr (RNase R) caused no obvious phenotype. By contrast, smpB was required for growth at high temperature (52°C), as anticipated if its product (a small ribosomal binding protein) is essential for tmRNA (ssrA) function. Notably, smpB and ssrA were also required for growth at low temperature (16°C), a phenotype not previously associated with tmRNA activity. These results extend the known high-temperature role of ssrA and indicate that the ribosome rescue system is important at both extremes of the B. subtilis temperature range.

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6

Shimizu, Yoshihiro, and Takuya Ueda. "The role of SmpB protein intrans-translation." FEBS Letters 514, no. 1 (February 1, 2002): 74–77. http://dx.doi.org/10.1016/s0014-5793(02)02333-5.

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7

Kurita, Daisuke, Akira Muto, and Hyouta Himeno. "tRNA/mRNA Mimicry by tmRNA and SmpB inTrans-Translation." Journal of Nucleic Acids 2011 (2011): 1–9. http://dx.doi.org/10.4061/2011/130581.

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Since accurate translation from mRNA to protein is critical to survival, cells have developed translational quality control systems. Bacterial ribosomes stalled on truncated mRNA are rescued by a system involving tmRNA and SmpB referred to astrans-translation. Here, we review current understanding of the mechanism oftrans-translation. Based on results obtained by using directed hydroxyl radical probing, we propose a new type of molecular mimicry duringtrans-translation. Besides such chemical approaches, biochemical and cryo-EM studies have revealed the structural and functional aspects of multiple stages oftrans-translation. These intensive works provide a basis for studying the dynamics of tmRNA/SmpB in the ribosome.

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8

Hanawa-Suetsugu, K. "SmpB functions in various steps of trans-translation." Nucleic Acids Research 30, no. 7 (April 1, 2002): 1620–29. http://dx.doi.org/10.1093/nar/30.7.1620.

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9

Kovács, L., Klára Megyeri, Anna Juhász, Anikó Zaja, and A. Miczák. "Cloning, expression and purification of smpb fromMycobacterium tuberculosis." Acta Microbiologica et Immunologica Hungarica 51, no. 3 (November 2004): 297–302. http://dx.doi.org/10.1556/amicr.51.2004.3.7.

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10

Zhang, Yidong, Zebin Liu, Yanqiong Tang, Xiang Ma, Hongqian Tang, Hong Li, and Zhu Liu. "Cbl upregulates cysH for hydrogen sulfide production in Aeromonas veronii." PeerJ 9 (September 9, 2021): e12058. http://dx.doi.org/10.7717/peerj.12058.

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Endogenous hydrogen sulfide (H2S) is generated in many metabolism pathways, and has been recognized as a second messenger against antibiotics and reactive oxygen species (ROS). In Aeromonas veronii, Small Protein B (SmpB) plays an important role in resisting stress. The absence of smpB could trigger sulfate assimilation pathway to adapt the nutrient deficiency, of which was mediated by up-regulation of cbl and cys genes and followed with enhancing H2S production. To figure out the mutual regulations of cbl and cys genes, a series of experiments were performed. Compared with the wild type, cysH was down-regulated significantly in cbl deletion by qRT-PCR. The fluorescence analysis further manifested that Cbl had a positive regulatory effect on the promoter of cysJIH. Bacterial one-hybrid analysis and electrophoretic mobility shift assay (EMSA) verified that Cbl bound with the promoter of cysJIH. Collectively, the tolerance to adversity could be maintained by the production of H2S when SmpB was malfunctioned, of which the activity of cysJIH promoter was positively regulated by upstream Cbl protein. The outcomes also suggested the enormous potentials of Aeromonas veronii in environmental adaptability.

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11

Felden, Brice, and Reynald Gillet. "SmpB as the handyman of tmRNA during trans-translation." RNA Biology 8, no. 3 (May 2011): 440–49. http://dx.doi.org/10.4161/rna.8.3.15387.

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12

Nameki, Nobukazu, Tatsuhiko Someya, Satoshi Okano, Reiko Suemasa, Michiko Kimoto, Kyoko Hanawa-Suetsugu, Takaho Terada, et al. "Interaction Analysis between tmRNA and SmpB from Thermus thermophilus." Journal of Biochemistry 138, no. 6 (December 1, 2005): 729–39. http://dx.doi.org/10.1093/jb/mvi180.

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13

Bäumler, Andreas J., and Fred Heffron. "Mosaic Structure of the smpB-nrdEIntergenic Region of Salmonella enterica." Journal of Bacteriology 180, no. 8 (April 15, 1998): 2220–23. http://dx.doi.org/10.1128/jb.180.8.2220-2223.1998.

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ABSTRACT The Salmonella enterica smpB-nrdE intergenic region contains about 45 kb of DNA that is not present in Escherichia coli. This DNA region was not introduced by a single horizontal transfer event, but was generated by multiple insertions and/or deletions that gave rise to a mosaic structure in this area of the chromosome.

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14

Kurita, Daisuke, Rumi Sasaki, Akira Muto, and Hyouta Himeno. "Interaction of SmpB with ribosome from directed hydroxyl radical probing." Nucleic Acids Research 35, no. 21 (October 24, 2007): 7248–55. http://dx.doi.org/10.1093/nar/gkm677.

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15

Someya, Tatsuhiko, Nobukazu Nameki, Haruko Hosoi, Sakura Suzuki, Hideki Hatanaka, Michiko Fujii, Takaho Terada, et al. "Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus." FEBS Letters 535, no. 1-3 (December 31, 2002): 94–100. http://dx.doi.org/10.1016/s0014-5793(02)03880-2.

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16

Ramrath, David J. F., Hiroshi Yamamoto, Kristian Rother, Daniela Wittek, Markus Pech, Thorsten Mielke, Justus Loerke, et al. "The complex of tmRNA–SmpB and EF-G on translocating ribosomes." Nature 485, no. 7399 (May 2012): 526–29. http://dx.doi.org/10.1038/nature11006.

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17

Weis, F., P. Bron, J. P. Rolland, D. Thomas, B. Felden, and R. Gillet. "Accommodation of tmRNA-SmpB into stalled ribosomes: A cryo-EM study." RNA 16, no. 2 (December 28, 2009): 299–306. http://dx.doi.org/10.1261/rna.1757410.

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18

Okan, Nihal A., James B. Bliska, and A. Wali Karzai. "A Role for the SmpB-SsrA System in Yersinia pseudotuberculosis Pathogenesis." PLoS Pathogens 2, no. 1 (January 27, 2006): e6. http://dx.doi.org/10.1371/journal.ppat.0020006.

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19

Weis, Félix, Patrick Bron, Emmanuel Giudice, Jean-Paul Rolland, Daniel Thomas, Brice Felden, and Reynald Gillet. "tmRNA–SmpB: a journey to the centre of the bacterial ribosome." EMBO Journal 29, no. 22 (October 15, 2010): 3810–18. http://dx.doi.org/10.1038/emboj.2010.252.

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20

Bugaeva, Elizaveta Y., Olga V. Shpanchenko, Brice Felden, Leif A. Isaksson, and Olga A. Dontsova. "One SmpB molecule accompanies tmRNA during its passage through the ribosomes." FEBS Letters 582, no. 10 (April 7, 2008): 1532–36. http://dx.doi.org/10.1016/j.febslet.2008.03.049.

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21

Holden, James, George Moutafis, Taghrid Istivan, Peter J. Coloe, and Peter M. Smooker. "SmpB: A novel outer membrane protein present in some Brachyspira hyodysenteriae strains." Veterinary Microbiology 113, no. 1-2 (March 2006): 109–16. http://dx.doi.org/10.1016/j.vetmic.2005.10.025.

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22

Ivanova, N. "Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA." Nucleic Acids Research 33, no. 11 (June 16, 2005): 3529–39. http://dx.doi.org/10.1093/nar/gki666.

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23

Karzai, A. W., and R. T. Sauer. "Protein factors associated with the SsrA*SmpB tagging and ribosome rescue complex." Proceedings of the National Academy of Sciences 98, no. 6 (February 27, 2001): 3040–44. http://dx.doi.org/10.1073/pnas.051628298.

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24

Yang, Juanjuan, Yindi Liu, Shuli Xu, Haiying Lin, Chun Meng, and Donghai Lin. "Expression, purification and characterization of the full-length SmpB protein from Mycobacterium tuberculosis." Protein Expression and Purification 151 (November 2018): 9–17. http://dx.doi.org/10.1016/j.pep.2018.05.014.

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25

Wower, Jacek, Christian W. Zwieb, David W. Hoffman, and Iwona K. Wower. "SmpB: A Protein that Binds to Double-Stranded Segments in tmRNA and tRNA†." Biochemistry 41, no. 28 (July 2002): 8826–36. http://dx.doi.org/10.1021/bi0201365.

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26

Ranaei-Siadat, Ehsan, Cécile Mérigoux, Bili Seijo, Luc Ponchon, Jean-Michel Saliou, Julie Bernauer, Sarah Sanglier-Cianférani, Fréderic Dardel, Patrice Vachette, and Sylvie Nonin-Lecomte. "In vivo tmRNA protection by SmpB and pre-ribosome binding conformation in solution." RNA 20, no. 10 (August 18, 2014): 1607–20. http://dx.doi.org/10.1261/rna.045674.114.

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27

Hong, Sue-Jean, Quyen-Anh Tran, and Kenneth C. Keiler. "Cell cycle-regulated degradation of tmRNA is controlled by RNase R and SmpB." Molecular Microbiology 57, no. 2 (June 9, 2005): 565–75. http://dx.doi.org/10.1111/j.1365-2958.2005.04709.x.

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28

Richards, Jamie, Preeti Mehta, and A. Wali Karzai. "RNase R degrades non-stop mRNAs selectively in an SmpB-tmRNA-dependent manner." Molecular Microbiology 62, no. 6 (December 2006): 1700–1712. http://dx.doi.org/10.1111/j.1365-2958.2006.05472.x.

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29

Watts, Talina, DeAnna Cazier, David Healey, and Allen Buskirk. "SmpB Contributes to Reading Frame Selection in the Translation of Transfer–Messenger RNA." Journal of Molecular Biology 391, no. 2 (August 2009): 275–81. http://dx.doi.org/10.1016/j.jmb.2009.06.037.

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30

Mraheil, Mobarak Abu, Renate Frantz, Lisa Teubner, Heiko Wendt, Uwe Linne, Jessica Wingerath, Thomas Wirth, and Trinad Chakraborty. "Requirement of the RNA-binding protein SmpB during intracellular growth of Listeria monocytogenes." International Journal of Medical Microbiology 307, no. 3 (April 2017): 166–73. http://dx.doi.org/10.1016/j.ijmm.2017.01.007.

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31

Koehl, Patrice, Frederic Poitevin, Henri Orland, and Marc Delarue. "Modified Poisson–Boltzmann equations for characterizing biomolecular solvation." Journal of Theoretical and Computational Chemistry 13, no. 03 (May 2014): 1440001. http://dx.doi.org/10.1142/s021963361440001x.

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Methods for computing electrostatic interactions often account implicitly for the solvent, due to the much smaller number of degrees of freedom involved. In the Poisson–Boltzmann (PB) approach the electrostatic potential is obtained by solving the Poisson–Boltzmann equation (PBE), where the solvent region is modeled as a homogeneous medium with a high dielectric constant. PB however is not exempt of problems. It does not take into account for example the sizes of the ions in the atmosphere surrounding the solute, nor does it take into account the inhomogeneous dielectric response of water due to the presence of a highly charged surface. In this paper we review two major modifications of PB that circumvent these problems, namely the size-modified PB (SMPB) equation and the Dipolar Poisson–Boltzmann Langevin (DPBL) model. In SMPB, steric effects between ions are accounted for with a lattice gas model. In DPBL, the solvent region is no longer modeled as a homogeneous dielectric media but rather as an assembly of self-orienting interacting dipoles of variable density. This model results in a dielectric profile that transits smoothly from the solute to the solvent region as well as in a variable solvent density that depends on the charges of the solute. We show successful applications of the DPBL formalism to computing the solvation free energies of isolated ions in water. Further developments of more accurately modified PB models are discussed.

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32

Sakai, Fusako, Risa Sugita, Jung-Wei Chang, Tetsuhiro Ogawa, Natsuko Tsumadori, Kazutoshi Takahashi, Makoto Hidaka, and Haruhiko Masaki. "Transfer-messenger RNA and SmpB mediate bacteriostasis in Escherichia coli cells against tRNA cleavage." Microbiology 161, no. 10 (October 1, 2015): 2019–28. http://dx.doi.org/10.1099/mic.0.000144.

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33

Holden, James, Peter J. Coloe, and Peter M. Smooker. "An evaluation of the immunogenicity and protective responses to Brachyspira hyodysenteriae recombinant SmpB vaccination." Veterinary Microbiology 128, no. 3-4 (April 2008): 354–63. http://dx.doi.org/10.1016/j.vetmic.2007.10.026.

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34

Yang, Chunzhong, and John R. Glover. "The SmpB-tmRNA Tagging System Plays Important Roles in Streptomyces coelicolor Growth and Development." PLoS ONE 4, no. 2 (February 12, 2009): e4459. http://dx.doi.org/10.1371/journal.pone.0004459.

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35

Dulebohn, Daniel P., Hye Jin Cho, and A. Wali Karzai. "Role of Conserved Surface Amino Acids in Binding of SmpB Protein to SsrA RNA." Journal of Biological Chemistry 281, no. 39 (July 24, 2006): 28536–45. http://dx.doi.org/10.1074/jbc.m605137200.

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36

Neubauer, C., R. Gillet, A. C. Kelley, and V. Ramakrishnan. "Decoding in the Absence of a Codon by tmRNA and SmpB in the Ribosome." Science 335, no. 6074 (March 15, 2012): 1366–69. http://dx.doi.org/10.1126/science.1217039.

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37

Gutmann, Sascha, Peter W. Haebel, Laurent Metzinger, Markus Sutter, Brice Felden, and Nenad Ban. "Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB." Nature 424, no. 6949 (August 2003): 699–703. http://dx.doi.org/10.1038/nature01831.

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38

Kurita, D., A. Muto, and H. Himeno. "Role of the C-terminal tail of SmpB in the early stage of trans-translation." RNA 16, no. 5 (March 26, 2010): 980–90. http://dx.doi.org/10.1261/rna.1916610.

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39

Wower, Iwona K., Christian Zwieb, and Jacek Wower. "Contributions of Pseudoknots and Protein SmpB to the Structure and Function of tmRNA intrans-Translation." Journal of Biological Chemistry 279, no. 52 (October 19, 2004): 54202–9. http://dx.doi.org/10.1074/jbc.m410488200.

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40

Karzai, A. W. "SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA)." EMBO Journal 18, no. 13 (July 1, 1999): 3793–99. http://dx.doi.org/10.1093/emboj/18.13.3793.

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41

Liu, Zebin, Kang Hu, Yanqiong Tang, Hong Li, Hongqian Tang, Xinwen Hu, Xiang Ma, and Zhu Liu. "SmpB down-regulates proton-motive force for the persister tolerance to aminoglycosides in Aeromonas veronii." Biochemical and Biophysical Research Communications 507, no. 1-4 (December 2018): 407–13. http://dx.doi.org/10.1016/j.bbrc.2018.11.052.

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42

Yang, Juanjuan, Yindi Liu, Zhao Liu, Chun Meng, and Donghai Lin. "Backbone and side-chain resonance assignments for the tmRNA-binding protein, SmpB, from Mycobacterium tuberculosis." Biomolecular NMR Assignments 11, no. 2 (March 4, 2017): 175–79. http://dx.doi.org/10.1007/s12104-017-9742-y.

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43

Sundermeier, T. R., D. P. Dulebohn, H. J. Cho, and A. W. Karzai. "A previously uncharacterized role for small protein B (SmpB) in transfer messenger RNA-mediated trans-translation." Proceedings of the National Academy of Sciences 102, no. 7 (February 7, 2005): 2316–21. http://dx.doi.org/10.1073/pnas.0409694102.

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44

Dong, G. "Structure of small protein B: the protein component of the tmRNA-SmpB system for ribosome rescue." EMBO Journal 21, no. 7 (April 1, 2002): 1845–54. http://dx.doi.org/10.1093/emboj/21.7.1845.

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45

Watts, Talina, David Healey, DeAnna Jones, and Allen Buskirk. "The role of tmRNA nucleotides and the SmpB protein in setting the translational frame on tmRNA." FASEB Journal 22, S2 (April 2008): 224. http://dx.doi.org/10.1096/fasebj.22.2_supplement.224.

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46

Miller, M. R., Z. Liu, D. J. Cazier, G. M. Gebhard, S. R. Herron, H. S. Zaher, R. Green, and A. R. Buskirk. "The role of SmpB and the ribosomal decoding center in licensing tmRNA entry into stalled ribosomes." RNA 17, no. 9 (July 27, 2011): 1727–36. http://dx.doi.org/10.1261/rna.2821711.

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47

Konno, T., D. Kurita, K. Takada, A. Muto, and H. Himeno. "A functional interaction of SmpB with tmRNA for determination of the resuming point of trans-translation." RNA 13, no. 10 (August 13, 2007): 1723–31. http://dx.doi.org/10.1261/rna.604907.

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48

Barends, Sharief, A. Wali Karzai, Robert T. Sauer, Jacek Wower, and Barend Kraal. "Simultaneous and functional binding of SmpB and EF-Tu·GTP to the alanyl acceptor arm of tmRNA." Journal of Molecular Biology 314, no. 1 (November 2001): 9–21. http://dx.doi.org/10.1006/jmbi.2001.5114.

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49

Jacob, Yannick, Stephen M. Sharkady, Kanchan Bhardwaj, Alina Sanda, and Kelly P. Williams. "Function of the SmpB Tail in Transfer-messenger RNA Translation Revealed by a Nucleus-encoded Form." Journal of Biological Chemistry 280, no. 7 (December 13, 2004): 5503–9. http://dx.doi.org/10.1074/jbc.m409277200.

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50

Liang, Wenxing, and Murray P. Deutscher. "Transfer-messenger RNA-SmpB Protein Regulates Ribonuclease R Turnover by Promoting Binding of HslUV and Lon Proteases." Journal of Biological Chemistry 287, no. 40 (August 9, 2012): 33472–79. http://dx.doi.org/10.1074/jbc.m112.375287.

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