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tmRDB Bibliography

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Lessner, F. H., Venters, B. J., and Keiler, K. C. (2007)
Proteolytic adaptor for transfer-messenger RNA-tagged proteins from alpha-proteobacteria,
J Bacteriol 189, 272-275

Garza-Sanchez, F., Janssen, B. D., and Hayes, C. S. (2006)
Prolyl-tRNAPro in the A site of SecM-arrested ribosomes inhibits the recruitment of tmRNA,
J Biol Chem, 189 272-275

Mehta, P., Richards, J., and Karzai, A. W. (2006)
tmRNA determinants required for facilitating nonstop mRNA decay,
RNA 12, 2187-2198;

Kaur, S., Gillet, R., Li, W., Gursky, R., and Frank, J. (2006)
Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome,
Proc Natl Acad Sci U S A 103, 16484-16489

Montero, C. I., Lewis, D. L., Johnson, M. R., Conners, S. B., Nance, E. A., Nichols, J. D., and Kelly, R. M. (2006)
Colocation of genes encoding a tRNA-mRNA hybrid and a putative signaling peptide on complementary strands in the genome of the hyperthermophilic bacterium Thermotoga maritima,
J Bacteriol 188, 6802-6807

Richards, J., Mehta, P., and Karzai, A. W. (2006)
RNase R degrades non-stop mRNAs selectively in an SmpB-tmRNA-dependent manner,
Mol Microbiol 62, 1700–1712

Garza-Sanchez, F., Janssen, B. D., and Hayes, C. S. (2006)
Prolyl-tRNA(Pro) in the A-site of SecM-arrested ribosomes inhibits the recruitment of transfer-messenger RNA,
J Biol Chem 281, 34258-34268

Shimizu, Y., and Ueda, T. (2006)
SmpB triggers GTP hydrolysis of elongation factor Tu on ribosomes by compensating for the lack of codon-anticodon interaction during trans-translation initiation,
J Biol Chem 281, 15987-15996

Iyer, L. M., Burroughs, M. A., and Aravind, L. (2006)
The prokaryotic antecedents of the Ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains,
Genome Biol 7, R60

Andersen, E. S., Rosenblad, M. A., Larsen, N., Westergaard, J. C., Burks, J., Wower, I. K., Wower, J., Gorodkin, J., Samuelsson, T., and Zwieb, C. (2006)
The tmRDB and SRPDB resources,
Nucleic Acids Res 34, D163-8

Tanner, D. R., Dewey, J. D., Miller, M. R., and Buskirk, A. R. (2006)
Genetic analysis of the structure and function of tmRNA Pseudoknot 1,
J Biol Chem 281, 10561-10566

Braud, S., Lavire, C., Bellier, A., and Mazodier, P. (2006)
Effect of SsrA (tmRNA) tagging system on translational regulation in Streptomyces,
Arch Microbiol 184, 343-352

Li, X., Hirano, R., Tagami, H., and Aiba, H. (2006)
Protein tagging at rare codons is caused by tmRNA action at the 3' end of nonstop mRNA generated in response to ribosome stalling,
RNA 12, 248-255

Mehta, P., Richards, J., and Karzai, A. W. (2006)
tmRNA determinants required for facilitating nonstop mRNA decay,
RNA 12, 2187-2198

Zhou, H. Y., Wu, Y. Y., Chen, J. H., Zeng, F. Y., and Tian, Y. (2006)
A model for trans-translation,

Tanner, D. R., Dewey, J. D., Miller, M. R., and Buskirk, A. R. (2006)
Genetic analysis of the structure and function of transfer messenger RNA pseudoknot 1,
J Biol Chem 281, 10561-10566

Hallier, M., Desreac, J., and Felden, B. (2006)
Small protein B interacts with the large and the small subunits of a stalled ribosome during trans-translation,
Nucleic Acids Res 34, 1935-1943

Nonin-Lecomte, S., Felden, B., and Dardel, F. (2006)
NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation,
Nucleic Acids Res 34, 1847-1853

Zappulla, D. C., and Cech, T. R. (2006)
RNA as a flexible scaffold for proteins: yeast telomerase and beyond,
Cold Spring Harb Symp Quant Biol 71, 217-224

Ou, H. Y., Chen, L. L., Lonnen, J., Chaudhuri, R. R., Thani, A. B., Smith, R., Garton, N. J., Hinton, J., Pallen, M., Barer, M. R., and Rajakumar, K. (2006)
A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria,
Nucleic Acids Res 34, e3

Pandey, D. P., and Gerdes, K. (2005)
Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes,
Nucleic Acids Res 33, 966-976

Metzinger, L., Hallier, M., and Felden, B. (2005)
Independent binding sites of small protein B onto transfer-messenger RNA during trans-translation,
Nucleic Acids Res 33, 2384-2394

Ivanova, N., Pavlov, M. Y., Bouakaz, E., Ehrenberg, M., and Schiavone, L. H. (2005)
Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA,
Nucleic Acids Res 33, 3529-3539

Oussenko, I. A., Abe, T., Ujiie, H., Muto, A., and Bechhofer, D. H. (2005)
Participation of 3'-to-5' Exoribonucleases in the Turnover of Bacillus subtilis mRNA,
J Bacteriol 187, 2758-2767

Shpanchenko, O. V., Zvereva, M. I., Ivanov, P. V., Bugaeva, E. Y., Rozov, A. S., Bogdanov, A. A., Kalkum, M., Isaksson, L. A., Nierhaus, K. H., and Dontsova, O. A. (2005)
Stepping tmRNA through the ribosome,
J Biol Chem

Jacob, Y., Sharkady, S. M., Bhardwaj, K., Sanda, A., and Williams, K. P. (2005)
Function of the SmpB Tail in Transfer-messenger RNA Translation Revealed by a Nucleus-encoded Form,
J Biol Chem 280, 5503-5509

Lim, V. I., and Garber, M. B. (2005)
Analysis of recognition of transfer-messenger RNA by the ribosomal decoding center,
J Mol Biol 346, 395-398

Butland, G., Peregrin-Alvarez, J. M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., Davey, M., Parkinson, J., Greenblatt, J., and Emili, A. (2005)
Interaction network containing conserved and essential protein complexes in Escherichia coli,
Nature 433, 531-537

Randau, L., Munch, R., Hohn, M. J., Jahn, D., and Soll, D. (2005)
Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves,
Nature 433, 537-541

Sundermeier, T. R., Dulebohn, D. P., Cho, H. J., and Karzai, A. W. (2005)
A previously uncharacterized role for small protein B (SmpB) in transfer messenger RNA-mediated trans-translation,
Proc Natl Acad Sci U S A

Hong, S. J., Tran, Q. A., and Keiler, K. C. (2005)
Cell cycle-regulated degradation of tmRNA is controlled by RNase R and SmpB,
Mol Microbiol 57, 565-575

Munavar, H., Zhou, Y., and Gottesman, S. (2005)
Analysis of the Escherichia coli Alp Phenotype: Heat Shock Induction in ssrA Mutants,
J Bacteriol 187, 4739-4751

Burks, J., Zwieb, C., Muller, F., Wower, I., and Wower, J. (2005)
Comparative 3-D Modeling of tmRNA,
BMC Mol Biol 6, 14

Ivanova, N., Pavlov, M. Y., and Ehrenberg, M. (2005)
tmRNA-induced Release of Messenger RNA from Stalled Ribosomes,
J Mol Biol

Wower, I. K., Zwieb, C., and Wower, J. (2005)
Transfer-messenger RNA unfolds as it transits the ribosome,
RNA 11, 668-673

Fouace, S., Gaudin, C., Picard, S., Corvaisier, S., Renault, J., Carboni, B., and Felden, B. (2004)
Polyamine derivatives as selective RNaseA mimics,
Nucleic Acids Res 32, 151-157

Konno, T., Takahashi, T., Kurita, D., Muto, A., and Himeno, H. (2004)
A minimum structure of aminoglycosides that causes an initiation shift of trans-translation,
Nucleic Acids Res 32, 4119-4126

Kovacs, L., Megyeri, K., Juhasz, A., Zaja, A., and Miczak, A. (2004)
Cloning, expression and purification of SmpB from Mycobacterium tuberculosis,
Acta Microbiol Immunol Hung 51, 297-302

Laslett, D., and Canback, B. (2004)
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences,
Nucleic Acids Res 32, 11-16

Sharkady, S. M., and Williams, K. P. (2004)
A third lineage with two-piece tmRNA,
Nucleic Acids Res 32, 4531-4538

Singh, N. S., and Varshney, U. (2004)
A physiological connection between tmRNA and peptidyl-tRNA hydrolase functions in Escherichia coli,
Nucleic Acids Res 32, 6028-6037

Jacob, Y., Seif, E., Paquet, P. O., and Lang, B. F. (2004)
Loss of the mRNA-like region in mitochondrial tmRNAs of jakobids,
RNA 10, 605-614

Leigh, J., and Lang, B. F. (2004)
Mitochondrial 3' tRNA editing in the jakobid Seculamonas ecuadoriensis: a novel mechanism and implications for tRNA processing,
RNA 10, 615-621

Williams, K. (2004)
Evolutionary resealing of a split RNA: Reversal of gene permutation,
RNA 10, 555-557

Ivanova, N., Pavlov, M. Y., Felden, B., and Ehrenberg, M. (2004)
Ribosome rescue by tmRNA requires truncated mRNAs,
J Mol Biol 338, 33-41

Hersch, G. L., Baker, T. A., and Sauer, R. T. (2004)
SspB delivery of substrates for ClpXP proteolysis probed by the design of improved degradation tags,
Proc Natl Acad Sci U S A 101, 12136-12141

Kim, N., Shiffeldrim, N., Gan, H. H., and Schlick, T. (2004)
Candidates for novel RNA topologies,
J Mol Biol 341, 1129-1144

Wower, I. K., Zwieb, C., and Wower, J. (2004)
Contributions of pseudoknots and protein SmpB to the structure and function of tmRNA in trans-translation,
J Biol Chem 279, 54202-54209

Haebel, P. W., Gutmann, S., and Ban, N. (2004)
Dial tm for rescue: tmRNA engages ribosomes stalled on defective mRNAs,
Curr Opin Struct Biol 14, 58-65

Kolkman, M. A., and Ferrari, E. (2004)
The fate of extracellular proteins tagged by the SsrA system of Bacillus subtilis,
Microbiology 150, 427-436

Gueneau de Novoa, P., and Williams, K. P. (2004)
The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts,
Nucleic Acids Res 32, D104-8

Sunohara, T., Jojima, K., Tagami, H., Inada, T., and Aiba, H. (2004)
Ribosome stalling during translation elongation induces cleavage of mRNA being translated in Escherichia coli,
J Biol Chem

Christensen, S. K., and Gerdes, K. (2004)
Delayed-relaxed response explained by hyperactivation of RelE,
Mol Microbiol 53, 587-597

Kim, C. C., and Falkow, S. (2004)
Delineation of upstream signaling events in the salmonella pathogenicity island 2 transcriptional activation pathway,
J Bacteriol 186, 4694-4704

Hallier, M., Ivanova, N., Rametti, A., Pavlov, M., Ehrenberg, M., and Felden, B. (2004)
Pre-binding of small protein B to a stalled ribosome triggers trans-translation,
J Biol Chem 279, 25978-25985

Sunohara, T., Jojima, K., Yamamoto, Y., Inada, T., and Aiba, H. (2004)
Nascent-peptide-mediated ribosome stalling at a stop codon induces mRNA cleavage resulting in nonstop mRNA that is recognized by tmRNA,
RNA 10, 378-386

Abo, T., Inada, T., and Aiba, H. (2004)
[When trans-translation occurs?],
Tanpakushitsu Kakusan Koso 49, 1067-1068

Himeno, H., and Muto, A. (2004)
[Trans-translation: co-translation protein quality control system],
Tanpakushitsu Kakusan Koso 49, 1062-1066

Tian, Y., Lu, X. Y., Yi, K., Tang, Y. J., and Chen, H. M. (2004)
[The structure and function of tmRNA.],
Yi Chuan 26, 409-413

Trimble, M. J., Minnicus, A., and Williams, K. P. (2004)
tRNA slippage at the tmRNA resume codon,
RNA 10, 805-812

Okada, T., Wower, I. K., Wower, J., Zwieb, C. W., and Kimura, M. (2004)
Contribution of the second OB fold of ribosomal protein S1 from Escherichia coli to the recognition of TmRNA,
Biosci Biotechnol Biochem 68, 2319-2325

Bolon, D. N., Grant, R. A., Baker, T. A., and Sauer, R. T. (2004)
Nucleotide-dependent substrate handoff from the SspB adaptor to the AAA+ ClpXP protease,
Mol Cell 16, 343-350

McGinness, K. E., and Sauer, R. T. (2004)
Ribosomal protein S1 binds mRNA and tmRNA similarly but plays distinct roles in translation of these molecules,
Proc Natl Acad Sci U S A 101, 13454-13459

Flynn, J. M., Levchenko, I., Sauer, R. T., and Baker, T. A. (2004)
Modulating substrate choice: the SspB adaptor delivers a regulator of the extracytoplasmic-stress response to the AAA+ protease ClpXP for degradation,
Genes Dev 18, 2292-2301

Shpachenko, O. V., Ivanov, P. V., Zverev, M. E., Bogdanov, A. A., and Dontsov, O. A. (2004)
[Trans-translation: main participants and role in the cell life],
Mol Biol (Mosk) 38, 914-925

Konno, T., Takahashi, T., Muto, A., and Himeno, H. (2003)
Various effects of paromomycin on tmRNA-mediated trans-translation,
Nucleic Acids Res Suppl 3, 235-236

Takada, K., Hori-Takemoto, C., Kawazoe, M., Lee, S., Shirouzu, M., Yokoyama, S., Muto, A., and Himeno, H. (2003)
In vitro analysis of the initial steps of trans-translation,
Nucleic Acids Res Suppl 3, 287-288

Withey, J. H., and Friedman, D. I. (2003)
A salvage pathway for protein structures: tmRNA and trans-translation,
Annu Rev Microbiol 57, 101-123

Yamamoto, Y., Sunohara, T., Jojima, K., Inada, T., and Aiba, H. (2003)
SsrA-mediated trans-translation plays a role in mRNA quality control by facilitating degradation of truncated mRNAs,
Rna 9, 408-418

Bisaglia, M., Laalami, S., Uzan, M., and Bontems, F. (2003)
Activation of the RegB Endoribonuclease by the S1 Ribosomal Protein Is Due to Cooperation between the S1 Four C-terminal Modules in a Substrate-dependant Manner,
J Biol Chem 278, 15261-15271

Corvaisier, S., Bordeau, V., and Felden, B. (2003)
Inhibition of transfer messenger RNA aminoacylation and trans-translation by aminoglycoside antibiotics,
J Biol Chem 278, 14788-14797

Moore, S. D., McGinness, K. E., and Sauer, R. T. (2003)
Structural biology. A glimpse into tmRNA-mediated ribosome rescue,
Science 300, 72-73

Valle, M., Gillet, R., Kaur, S., Henne, A., Ramakrishnan, V., and Frank, J. (2003)
Visualizing tmRNA entry into a stalled ribosome,
Science 300, 127-130

Dougan, D. A., Weber-Ban, E., and Bukau, B. (2003)
Targeted delivery of an ssrA-tagged substrate by the adaptor protein SspB to its cognate AAA+ protein ClpX,
Mol Cell 12, 373-380

Levchenko, I., Grant, R. A., Wah, D. A., Sauer, R. T., and Baker, T. A. (2003)
Structure of a delivery protein for an AAA+ protease in complex with a peptide degradation tag,
Mol Cell 12, 365-372

Wah, D. A., Levchenko, I., Rieckhof, G. E., Bolon, D. N., Baker, T. A., and Sauer, R. T. (2003)
Flexible linkers leash the substrate binding domain of SspB to a peptide module that stabilizes delivery complexes with the AAA+ ClpXP protease,
Mol Cell 12, 355-363

Gutmann, S., Haebel, P. W., Metzinger, L., Sutter, M., Felden, B., and Ban, N. (2003)
Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB,
Nature 424, 699-703

Gaudin, C., Nonin-Lecomte, S., Tisne, C., Corvaisier, S., Bordeau, V., Dardel, F., and Felden, B. (2003)
The tRNA-like Domains of E.coli and A.aeolicus Transfer-Messenger RNA: Structural and Functional Studies,
J Mol Biol 331, 457-471

Slavcev, R. A., and Hayes, S. (2003)
Blocking the T4 lysis inhibition phenotype,
Gene 321, 163-171

Plant, E. P., Jacobs, K. L., Harger, J. W., Meskauskas, A., Jacobs, J. L., Baxter, J. L., Petrov, A. N., and Dinman, J. D. (2003)
The 9-A solution: How mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting,
RNA 9, 168-174

Stepanov, V. G., and Nyborg, J. (2003)
tmRNA from Thermus thermophilus. Interaction with alanyl-tRNA synthetase and elongation factor Tu,
Eur J Biochem 270, 463-475

Williams, K. P. (2003)
Traffic at the tmRNA gene,
J Bacteriol 185, 1059-1070

Keiler, K. C., and Shapiro, L. (2003)
TmRNA is required for correct timing of DNA replication in Caulobacter crescentus,
J Bacteriol 185, 573-580

Zwieb, C., Gorodkin, J., Knudsen, B., Burks, J., and Wower, J. (2003)
tmRDB (tmRNA database),
Nucleic Acids Res 31, 446-447

Pedersen, K., Zavialov, A. V., Pavlov, M. Y., Elf, J., Gerdes, K., and Ehrenberg, M. (2003)
The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site,
Cell 112, 131-140

Rawat, U. B., Zavialov, A. V., Sengupta, J., Valle, M., Grassucci, R. A., Linde, J., Vestergaard, B., Ehrenberg, M., and Frank, J. (2003)
A cryo-electron microscopic study of ribosome-bound termination factor RF2,
Nature 421, 87-90

Vioque, A., and de la Cruz, J. (2003)
Trans-translation and protein synthesis inhibitors,
FEMS Microbiol Lett 218, 9-14

Someya, T., Nameki, N., Hosoi, H., Suzuki, S., Hatanaka, H., Fujii, M., Terada, T., Shirouzu, M., Inoue, Y., Shibata, T., Kuramitsu, S., Yokoyama, S., and Kawai, G. (2003)
Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus,
FEBS Lett 535, 94-100

Song, H. K., and Eck, M. J. (2003)
Structural basis of degradation signal recognition by SspB, a specificity-enhancing factor for the ClpXP proteolytic machine,
Mol Cell 12, 75-86

Takahashi, T., Konno, T., Muto, A., and Himeno, H. (2003)
Various effects of paromomycin on tmRNA-directed trans-translation,
J Biol Chem 278, 27672-27680

Christensen, S. K., and Gerdes, K. (2003)
RelE toxins from bacteria and Archaea cleave mRNAs on translating ribosomes, which are rescued by tmRNA,
Mol Microbiol 48, 1389-1400

Elf, J., Nilsson, D., Tenson, T., and Ehrenberg, M. (2003)
Selective charging of tRNA isoacceptors explains patterns of codon usage,
Science 300, 1718-1722

Herman, C., Prakash, S., Lu, C. Z., Matouschek, A., and Gross, C. A. (2003)
Lack of a robust unfoldase activity confers a unique level of substrate specificity to the universal AAA protease FtsH,
Mol Cell 11, 659-669

Keiler, K. C., and Shapiro, L. (2003)
TmRNA in Caulobacter crescentus is cell cycle regulated by temporally controlled transcription and RNA degradation,
J Bacteriol 185, 1825-1830

Muto, A., and Himeno, H. (2003)
[Molecular mechanism and physiological roles of trans-translation mediated by tmRNA],
Tanpakushitsu Kakusan Koso 48, 346-356

Grzymski, E. C. (2003)
tmRNA to the rescue,
Nat Struct Biol 10, 321

Cairrao, F., Cruz, A., Mori, H., and Arraiano, C. M. (2003)
Cold shock induction of RNase R and its role in the maturation of the quality control mediator SsrA/tmRNA,
Mol Microbiol 50, 1349-1360

Di Giulio, M. (2003)
The early phases of genetic code origin: conjectures on the evolution of coded catalysis,
Orig Life Evol Biosph 33, 479-489

Hayes, C. S., and Sauer, R. T. (2003)
Cleavage of the A site mRNA codon during ribosome pausing provides a mechanism for translational quality control,
Mol Cell 12, 903-911

Pelludat, C., Mirold, S., and Hardt, W. D. (2003)
The SopEPhi phage integrates into the ssrA gene of Salmonella enterica serovar Typhimurium A36 and is closely related to the Fels-2 prophage,
J Bacteriol 185, 5182-5191

Christensen, S. K., Pedersen, K., Hansen, F. G., and Gerdes, K. (2003)
Toxin-antitoxin loci as stress-response-elements: ChpAK/MazF and ChpBK cleave translated RNAs and are counteracted by tmRNA,
J Mol Biol 332, 809-819

Withey, J. H., and Friedman, D. I. (2002)
The biological roles of trans-translation,
Curr Opin Microbiol 5, 154-159

Lindell, M., Romby, P., and Wagner, E. G. (2002)
Lead(II) as a probe for investigating RNA structure in vivo,
RNA 8, 534-541

Hanawa-Suetsugu, K., Takagi, M., Inokuchi, H., Himeno, H., and Muto, A. (2002)
SmpB functions in various steps of trans-translation,
Nucleic Acids Res 30, 1620-1629

Ito, K., Tadaki, T., Lee, S., Takada, K., Muto, A., and Himeno, H. (2002)
Trans-translation mediated by Bacillus subtilis tmRNA,
FEBS Lett 516, 245-252

Dong, G., Nowakowski, J., and Hoffman, D. W. (2002)
Structure of small protein B: the protein component of the tmRNA-SmpB system for ribosome rescue,
Embo J 21, 1845-1854

Bordeau, V., and Felden, B. (2002)
Ribosomal protein S1 induces a conformational change of tmRNA; more than one protein S1 per molecule of tmRNA,
Biochimie 84, 723-729

Laslett, D., Canback, B., and Andersson, S. (2002)
BRUCE: a program for the detection of transfer-messenger RNA genes in nucleotide sequences,
Nucleic Acids Res 30, 3449-3453

Kapust, R. B., Routzahn, K. M., and Waugh, D. S. (2002)
Processive degradation of nascent polypeptides, triggered by tandem AGA codons, limits the accumulation of recombinant tobacco etch virus protease in Escherichia coli BL21(DE3),
Protein Expr Purif 24, 61-70

Williams, K. P. (2002)
Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies,
Nucleic Acids Res 30, 866-875

Williams, K. P. (2002)
The tmRNA Website: invasion by an intron,
Nucleic Acids Res 30, 179-182

Abo, T., Ueda, K., Sunohara, T., Ogawa, K., and Aiba, H. (2002)
SsrA-mediated protein tagging in the presence of miscoding drugs and its physiological role in Escherichia coli,
Genes Cells 7, 629-638

Wower, J., Zwieb, C. W., Hoffman, D. W., and Wower, I. K. (2002)
SmpB: a protein that binds to double-stranded segments in tmRNA and tRNA,
Biochemistry 41, 8826-8836

Fujihara, A., Tomatsu, H., Inagaki, S., Tadaki, T., Ushida, C., Himeno, H., and Muto, A. (2002)
Detection of tmRNA-mediated trans-translation products in Bacillus subtilis,
Genes Cells 7, 343-350

Dougan, D. A., Reid, B. G., Horwich, A. L., and Bukau, B. (2002)
ClpS, a substrate modulator of the ClpAP machine,
Mol Cell 9, 673-683

Miao, E. A., Freeman, J. A., and Miller, S. I. (2002)
Transcription of the SsrAB regulon is repressed by alkaline pH and is independent of PhoPQ and magnesium concentration,
J Bacteriol 184, 1493-1497

Li, Z., Reimers, S., Pandit, S., and Deutscher, M. P. (2002)
RNA quality control: degradation of defective transfer RNA,
EMBO J 21, 1132-1138

Ivanov, P. V., Zvereva, M. I., Shpanchenko, O. V., Dontsova, O. A., Bogdanov, A. A., Aglyamova, G. V., Lim, V. I., Teraoka, Y., and Nierhaus, K. H. (2002)
How does tmRNA move through the ribosome?,
FEBS Lett 514, 55-59

Barends, S., Bjork, K., Gultyaev, A. P., de Smit, M. H., Pleij, C. W., and Kraal, B. (2002)
Functional evidence for D- and T-loop interactions in tmRNA,
FEBS Lett 514, 78-83

Shimizu, Y., and Ueda, T. (2002)
The role of SmpB protein in trans-translation,
FEBS Lett 514, 74-77

Gaudin, C., Zhou, X., Williams, K. P., and Felden, B. (2002)
Two-piece tmRNA in cyanobacteria and its structural analysis,
Nucleic Acids Res 30, 2018-2024

Williams, K. P. (2002)
Descent of a split RNA,
Nucleic Acids Res 30, 2025-2030

Sunohara, T., Abo, T., Inada, T., and Aiba, H. (2002)
The C-terminal amino acid sequence of nascent peptide is a major determinant of SsrA tagging at all three stop codons,
Rna 8, 1416-1427

Wernegreen, J. J. (2002)
Genome evolution in bacterial endosymbionts of insects,
Nat Rev Genet 3, 850-861

Dougan, D. A., Mogk, A., and Bukau, B. (2002)
Protein folding and degradation in bacteria: to degrade or not to degrade? That is the question,
Cell Mol Life Sci 59, 1607-1616

Komarova, A. V., Tchufistova, L. S., Supina, E. V., and Boni, I. V. (2002)
Protein S1 counteracts the inhibitory effect of the extended Shine-Dalgarno sequence on translation,
Rna 8, 1137-1147

Hayes, C. S., Bose, B., and Sauer, R. T. (2002)
Proline residues at the C terminus of nascent chains induce SsrA tagging during translation termination,
J Biol Chem 277, 33825-33832

Atkins, J. F., Baranov, P. V., Fayet, O., Herr, A. J., Howard, M. T., Ivanov, I. P., Matsufuji, S., Miller, W. A., Moore, B., Prere, M. F., Wills, N. M., Zhou, J., and Gesteland, R. F. (2001)
Overriding standard decoding: implications of recoding for ribosome function and enrichment of gene expression,
Cold Spring Harb Symp Quant Biol 66, 217-232

Felden, B., Massire, C., Westhof, E., Atkins, J. F., and Gesteland, R. F. (2001)
Phylogenetic analysis of tmRNA genes within a bacterial subgroup reveals a specific structural signature,
Nucleic Acids Res 29, 1602-1607

Nissen, P., Ippolito, J. A., Ban, N., Moore, P. B., and Steitz, T. A. (2001)
RNA tertiary interactions in the large ribosomal subunit: the A-minor motif,
Proc Natl Acad Sci U S A 98, 4899-4903

Zwieb, C., Guven, S. A., Wower, I. K., and Wower, J. (2001)
Three-dimensional folding of the tRNA-like domain of Escherichia coli tmRNA,
Biochemistry 40, 9587-9595

Herr, A. J., Wills, N. M., Nelson, C. C., Gesteland, R. F., and Atkins, J. F. (2001)
Drop-off during ribosome hopping,
J Mol Biol 311, 445-452

Ranquet, C., Geiselmann, J., and Toussaint, A. (2001)
The tRNA function of SsrA contributes to controlling repression of bacteriophage Mu prophage,
Proc Natl Acad Sci U S A 98, 10220-10225

Tous, C., Vega-Palas, M. A., and Vioque, A. (2001)
Conditional expression of RNase P in the cyanobacterium Synechocystis sp. PCC6803 allows detection of precursor RNAs. Insight in the in vivo maturation pathway of transfer and other stable RNAs,
J Biol Chem 276, 29059-29066

de la Cruz, J., and Vioque, A. (2001)
Increased sensitivity to protein synthesis inhibitors in cells lacking tmRNA,
RNA 7, 1708-1716

Steiner, K., and Malke, H. (2001)
relA-Independent amino acid starvation response network of Streptococcus pyogenes,
J Bacteriol 183, 7354-7364

Zvereva, M. I., Ivanov, P. V., Teraoka, Y., Topilina, N. I., Dontsova, O. A., Bogdanov, A. A., Kalkum, M., Nierhaus, K. H., and Shpanchenko, O. V. (2001)
Complex of transfer-messenger RNA and elongation factor Tu. Unexpected modes of interaction,
J Biol Chem 276, 47702-47708

Knudsen, B., Wower, J., Zwieb, C., and Gorodkin, J. (2001)
tmRDB (tmRNA database),
Nucleic Acids Res 29, 171-172

Lee, S., Ishii, M., Tadaki, T., Muto, A., and Himeno, H. (2001)
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 7, 999-1012

Wiegert, T., and Schumann, W. (2001)
SsrA-mediated tagging in Bacillus subtilis,
J Bacteriol 183, 3885-3889

Roche, E. D., and Sauer, R. T. (2001)
Identification of endogenous SsrA-tagged proteins reveals tagging at positions corresponding to stop codons,
J Biol Chem 276, 28509-28515

Nakano, H., Goto, S., Nakayashiki, T., and Inokuchi, H. (2001)
Temperature-sensitive mutations in various genes of Escherichia coli K12 can be suppressed by the ssrA gene for 10Sa RNA (tmRNA),
Mol Genet Genomics 265, 615-621

Gillet, R., and Felden, B. (2001)
Transfer RNA(Ala) recognizes transfer-messenger RNA with specificity; a functional complex prior to entering the ribosome?,
Embo J 20, 2966-2976

Burton, R. E., Siddiqui, S. M., Kim, Y. I., Baker, T. A., and Sauer, R. T. (2001)
Effects of protein stability and structure on substrate processing by the ClpXP unfolding and degradation machine,
EMBO J 20, 3092-3100

Stagg, S. M., Frazer-Abel, A. A., Hagerman, P. J., and Harvey, S. C. (2001)
Structural studies of the tRNA domain of tmRNA,
J Mol Biol 309, 727-735

Meli, M., Albert-Fournier, B., and Maurel, M. C. (2001)
Recent findings in the modern RNA world,
Int Microbiol 4, 5-11

Karzai, A. W., and Sauer, R. T. (2001)
Protein factors associated with the SsrA.SmpB tagging and ribosome rescue complex,
Proc Natl Acad Sci U S A 98, 3040-3044

Reid, B. G., Fenton, W. A., Horwich, A. L., and Weber-Ban, E. U. (2001)
ClpA mediates directional translocation of substrate proteins into the ClpP protease,
Proc Natl Acad Sci U S A 98, 3768-3772

Gillet, R., and Felden, B. (2001)
Emerging views on tmRNA-mediated protein tagging and ribosome rescue,
Mol Microbiol 42, 879-885

Ofengand, J., Del Campo, M., and Kaya, Y. (2001)
Mapping pseudouridines in RNA molecules,
Methods 25, 365-373

Paget, M. S., Molle, V., Cohen, G., Aharonowitz, Y., and Buttner, M. J. (2001)
Defining the disulphide stress response in Streptomyces coelicolor A3(2): identification of the sigmaR regulon,
Mol Microbiol 42, 1007-1020

Hanawa-Suetsugu, K., Bordeau, V., Himeno, H., Muto, A., and Felden, B. (2001)
Importance of the conserved nucleotides around the tRNA-like structure of Escherichia coli transfer-messenger RNA for protein tagging,
Nucleic Acids Res 29, 4663-4673

Barends, S., Karzai, A. W., Sauer, R. T., Wower, J., and Kraal, B. (2001)
Simultaneous and functional binding of SmpB and EF-Tu-TP to the alanyl acceptor arm of tmRNA,
J Mol Biol 314, 9-21

Gimple, O., and Schon, A. (2001)
In vitro and in vivo processing of cyanelle tmRNA by RNase P,
Biol Chem 382, 1421-1429

Sengupta, J., Agrawal, R. K., and Frank, J. (2001)
Visualization of protein S1 within the 30S ribosomal subunit and its interaction with messenger RNA,
Proc Natl Acad Sci U S A 98, 11991-11996

Flynn, J. M., Levchenko, I., Seidel, M., Wickner, S. H., Sauer, R. T., and Baker, T. A. (2001)
Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis,
Proc Natl Acad Sci U S A 98, 10584-10589

Schönhuber, W., Le Bourhis, G., Tremblay, J., Amann, R., and Kulakauskas, S. (2001)
Utilization of tmRNA sequences for bacterial identification,
BMC Microbiol 1, 20

de Macario, E. C., and Macario, A. J. (2000)
Stressors, stress and survival: overview,
Front Biosci 5, D780-6. [Abstract]

Karzai, A. W., Roche, E. D., and Sauer, R. T. (2000)
The SsrA-SmpB system for protein tagging, directed degradation and ribosome rescue,
Nat Struct Biol 7, 449-455

Wower, J., Zwieb, C. and Wower, I. (2000)
tmRNA: A Case of Structural and Functional Mimicry on and off the Ribosome?, (Garrett, R. A., Ed.) pp 397-405, ASM Press, Washington, D.C.

Zwieb, C., and Wower, J. (2000)
tmRDB (tmRNA database),
Nucleic Acids Research 28, 169-170

Herr, A. J., Atkins, J. F., and Gesteland, R. F. (2000)
Coupling of open reading frames by translational bypassing,
Annu Rev Biochem 69, 343-372

Muto, A., Fujihara, A., Ito, K. I., Matsuno, J., Ushida, C., and Himeno, H. (2000)
Requirement of transfer-messenger RNA for the growth of Bacillus subtilis under stresses,
Genes Cells 5, 627-635

Singh, S. K., Grimaud, R., Hoskins, J. R., Wickner, S., and Maurizi, M. R. (2000)
Unfolding and internalization of proteins by the ATP-dependent proteases ClpXP and ClpAP,
Proc Natl Acad Sci U S A 97, 8898-8903

Hoskins, J. R., Singh, S. K., Maurizi, M. R., and Wickner, S. (2000)
Protein binding and unfolding by the chaperone ClpA and degradation by the protease ClpAP,
Proc Natl Acad Sci U S A 97, 8892-8897

Wower, I. K., Zwieb, C. W., Guven, S. A., and Wower, J. (2000)
Binding and cross-linking of tmRNA to ribosomal protein S1, on and off the Escherichia coli ribosome,
EMBO J 19, 6612-6621

Lee, A. K., Detweiler, C. S., and Falkow, S. (2000)
OmpR regulates the two-component system SsrA-ssrB in Salmonella pathogenicity island 2,
J Bacteriol 182, 771-781

RajBhandary, U. L. (2000)
More surprises in translation: initiation without the initiator tRNA,
Proc Natl Acad Sci U S A 97, 1325-1327

Nishikawa, F., and Nishikawa, S. (2000)
Requirement for canonical base pairing in the short pseudoknot structure of genomic hepatitis delta virus ribozyme,
Nucleic Acids Res 28, 925-931

Williams, K. P. (2000)
The tmRNA website,
Nucleic Acids Res 28, 168

Mohr, S., Wanner, L. A., Bertrand, H., and Lambowitz, A. M. (2000)
Characterization of an unusual tRNA-like sequence found inserted in a Neurospora retroplasmid,
Nucleic Acids Res 28, 1514-1524

Abo, T., Inada, T., Ogawa, K., and Aiba, H. (2000)
SsrA-mediated tagging and proteolysis of LacI and its role in the regulation of lac operon,
EMBO J 19, 3762-3769

Keiler, K. C., Shapiro, L., and Williams, K. P. (2000)
tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter,
Proc Natl Acad Sci U S A 97, 7778-7783

Julio, S. M., Heithoff, D. M., and Mahan, M. J. (2000)
ssrA (tmRNA) plays a role in Salmonella enterica serovar Typhimurium pathogenesis,
J Bacteriol 182, 1558-1563

Huang, C., Wolfgang, M. C., Withey, J., Koomey, M., and Friedman, D. I. (2000)
Charged tmRNA but not tmRNA-mediated proteolysis is essential for Neisseria gonorrhoeae viability,
EMBO J 19, 1098-1107

Barends, S., Wower, J., and Kraal, B. (2000)
Kinetic parameters for tmRNA binding to alanyl-tRNA synthetase and elongation factor Tu from Escherichia coli,
Biochemistry 39, 2652-2658

Nameki, N., Tadaki, T., Himeno, H., and Muto, A. (2000)
Three of four pseudoknots in tmRNA are interchangeable and are substitutable with single-stranded RNAs,
FEBS Lett 470, 345-349

Zvereva, M. E., Shpanchenko, O. V., Dontsova, O. A., and Bogdanov, A. A. (2000)
[Structure and function of tmRNA (10Sa RNK)],
Mol Biol (Mosk) 34, 1081-1089

Molnos, J., Lange, R., and Amrein, K. E. (2000)
An improved vector system for insertional gene inactivation inspired by the tmRNA-tagging system of S. pneumoniae,
J Microbiol Methods 42, 197-201

Juan, V., and Wilson, C. (1999)
RNA secondary structure prediction based on free energy and phylogenetic analysis,
J Mol Biol 289, 935-947

Macario, A. J., Lange, M., Ahring, B. K., and De Macario, E. C. (1999)
Stress genes and proteins in the archaea,
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Wower, J., Wower, I. K., and Zwieb, C. (1999)
An extended hybrid model for translocation of tRNA and the structure of peptidyl transferase of the Escherichia coli ribosome,
Nucleic Acids Symposium Series 41, 187-191

Wower, J., and Zwieb, C. (1999)
The tmRNA database (tmRDB),
Nucleic Acids Research 27, 167

Zwieb, C., Muller, F., and Wower, J. (1999)
Comparative three-dimensional modeling of tmRNA,
Nucleic Acids Synposium Series 41, 200-204

Zwieb, C., Wower, I., and Wower, J. (1999)
Comparative Sequence Analysis of tmRNA,
Nucleic Acids Research 27, 2063-2071

Nishikawa, F., Shirai, M., and Nishikawa, S. (1999)
Importance of short pseudoknot base pairs between two single-stranded regions of HDV ribozyme,
Nucleic Acids Symp Ser 287-288

Withey, J., and Friedman, D. (1999)
Analysis of the role of trans-translation in the requirement of tmRNA for lambdaimmP22 growth in Escherichia coli,
J Bacteriol 181, 2148-2157

Rozenski, J., and McCloskey, J. A. (1999)
Determination of nearest neighbors in nucleic acids by mass spectrometry,
Anal Chem 71, 1454-1459

Deiwick, J., and Hensel, M. (1999)
Regulation of virulence genes by environmental signals in Salmonella typhimurium,
Electrophoresis 20, 813-817

Rudinger-Thirion, J., Giege, R., and Felden, B. (1999)
Aminoacylated tmRNA from Escherichia coli interacts with prokaryotic elongation factor Tu,
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Roche, E. D., and Sauer, R. T. (1999)
SsrA-mediated peptide tagging caused by rare codons and tRNA scarcity,
EMBO J 18, 4579-4589

Nameki, N., Felden, B., Atkins, J. F., Gesteland, R. F., Himeno, H., and Muto, A. (1999)
Functional and structural analysis of a pseudoknot upstream of the tag-encoded sequence in E. coli tmRNA,
J Mol Biol 286, 733-744

Williams, K. P. (1999)
The tmRNA website,
Nucleic Acids Res 27, 165-166

Rozenski, J., Crain, P. F., and McCloskey, J. A. (1999)
The RNA Modification Database: 1999 update,
Nucleic Acids Res 27, 196-197

Karzai, A. W., Susskind, M. M., and Sauer, R. T. (1999)
SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA),
Embo J 18, 3793-3799

Felden, B., Gesteland, R. F., and Atkins, J. F. (1999)
Eubacterial tmRNAs: everywhere except the alpha-proteobacteria?,
Biochim Biophys Acta 1446, 145-148

McCloskey, J. A., Whitehill, A. B., Rozenski, J., Qiu, F., and Crain, P. F. (1999)
New techniques for the rapid characterization of oligonucleotides by mass spectrometry,
Nucleosides Nucleotides 18, 1549-1553

Nameki, N., Tadaki, T., Muto, A., and Himeno, H. (1999)
Amino acid acceptor identity switch of Escherichia coli tmRNA from alanine to histidine in vitro,
J Mol Biol 289, 1-7

Bouthinon, D., and Soldano, H. (1999)
A new method to predict the consensus secondary structure of a set of unaligned RNA sequences,
Bioinformatics 15, 785-798

Williams, K. P., Martindale, K. A., and Bartel, D. P. (1999)
Resuming translation on tmRNA: a unique mode of determining a reading frame,
Embo J 18, 5423-5433

Himeno, H. (1999)
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Nameki, N., Chattopadhyay, P., Himeno, H., Muto, A., and Kawai, G. (1999)
An NMR and mutational analysis of an RNA pseudoknot of Escherichia coli tmRNA involved in trans-translation,
Nucleic Acids Res 27, 3667-3675

Ibba, M., Sever, S., Praetorius-Ibba, M., and Soll, D. (1999)
Transfer RNA identity contributes to transition state stabilization during aminoacyl-tRNA synthesis,
Nucleic Acids Res 27, 3631-3637

Zwieb, C., Larsen, N., and Wower, J. (1998)
The tmRNA database,
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Avota, E., Berzins, V., Grens, E., Vishnevsky, Y., Luce, R., and Biebricher, C. K. (1998)
The natural 6 S RNA found in Q beta-infected cells is derived from host and phage RNA,
J Mol Biol 276, 7-17

Bourdeau, V., Steinberg, S. V., Ferbeyre, G., Emond, R., Cermakian, N., and Cedergren, R. (1998)
Amber suppression in Escherichia coli by unusual mitochondria-like transfer RNAs,
Proc Natl Acad Sci U S A 95, 1375-1380

Muto, A., Ushida, C., and Himeno, H. (1998)
A bacterial RNA that functions as both a tRNA and an mRNA,
Trends Biochem Sci 23, 25-29

Williams, K. P., and Bartel, D. P. (1998)
The tmRNA Website,
Nucleic Acids Res 26, 163-165

Felden, B., Hanawa, K., Atkins, J. F., Himeno, H., Muto, A., Gesteland, R. F., McCloskey, J. A., and Crain, P. F. (1998)
Presence and location of modified nucleotides in Escherichia coli tmRNA: structural mimicry with tRNA acceptor branches,
EMBO J 17, 3188-3196

Hickerson, R. P., Watkins-Sims, C. D., Burrows, C. J., Atkins, J. F., Gesteland, R. F., and Felden, B. (1998)
A nickel complex cleaves uridine in folded RNA structures: application to E. coli tmRNA and related engineered molecules,
J Mol Biol 279, 577-587

Op De Bekke, A., Kiefmann, M., Kremerskothen, J., Vornlocher, H. P., Sprinzl, M., and Brosius, J. (1998)
The 10Sa RNA gene of Thermus thermophilus,
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Li, Z., Pandit, S., and Deutscher, M. P. (1998)
3' exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli,
Proc Natl Acad Sci U S A 95, 2856-2861

Karaolis, D. K., Johnson, J. A., Bailey, C. C., Boedeker, E. C., Kaper, J. B., and Reeves, P. R. (1998)
A Vibrio cholerae pathogenicity island associated with epidemic and pandemic strains,
Proc Natl Acad Sci U S A 95, 3134-3139

Watanabe, T., Sugita, M., and Sugiura, M. (1998)
Identification of 10Sa RNA (tmRNA) homologues from the cyanobacterium Synechococcus sp. strain PCC6301 and related organisms,
Biochim Biophys Acta 1396, 97-104

Gottesman, S., Roche, E., Zhou, Y., and Sauer, R. T. (1998)
The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system,
Genes Dev 12, 1338-1347

Herman, C., Thevenet, D., Bouloc, P., Walker, G. C., and D'Ari, R. (1998)
Degradation of carboxy-terminal-tagged cytoplasmic proteins by the Escherichia coli protease HflB (FtsH),
Genes Dev 12, 1348-1355

Li, Z., Pandit, S., and Deutscher, M. P. (1998)
Polyadenylation of stable RNA precursors in vivo,
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Bycroft, M., Hubbard, T. J., Proctor, M., Freund, S. M., and Murzin, A. G. (1997)
The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold,
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Macario, A. J., and Conway de Macario, E. (1997)
Mini-Review; Stress Genes: An Introductory Overview,
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Himeno, H., Nameki, N., Tadaki, T., Sato, M., Hanawa, K., Fukushima, M., Ishii, M., Ushida, C., and Muto, A. (1997)
Escherichia coli tmRNA (10Sa RNA) in trans-translation,
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Ushida, C., Sasamura, S., and Muto, A. (1997)
Probing the secondary structure of MCS4 RNA of Mycoplasma capricolum,
J Biochem (Tokyo) 122, 1202-1207

Matveeva, O., Felden, B., Audlin, S., Gesteland, R. F., and Atkins, J. F. (1997)
A rapid in vitro method for obtaining RNA accessibility patterns for complementary DNA probes: correlation with an intracellular pattern and known RNA structures,
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Felden, B., Himeno, H., Muto, A., McCutcheon, J. P., Atkins, J. F., and Gesteland, R. F. (1997)
Probing the structure of the Escherichia coli 10Sa RNA (tmRNA),
Rna 3, 89-103

Hanes, J., and Pluckthun, A. (1997)
In vitro selection and evolution of functional proteins by using ribosome display,
Proc Natl Acad Sci U S A 94, 4937-4942

Himeno, H., Sato, M., Tadaki, T., Fukushima, M., Ushida, C., and Muto, A. (1997)
In vitro trans translation mediated by alanine-charged 10Sa RNA,
J Mol Biol 268, 803-808

Poole, E. S., Brimacombe, R., and Tate, W. P. (1997)
Decoding the translational termination signal: the polypeptide chain release factor in Escherichia coli crosslinks to the base following the stop codon,
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Felden, B., Himeno, H., Muto, A., Atkins, J. F., and Gesteland, R. F. (1996)
Structural organization of Escherichia coli tmRNA,
Biochimie 78, 979-983

Muto, A., Sato, M., Tadaki, T., Fukushima, M., Ushida, C., and Himeno, H. (1996)
Structure and function of 10Sa RNA: trans-translation system,
Biochimie 78, 985-991

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, 959-969

Janosi, L., Hara, H., Zhang, S., and Kaji, A. (1996)
Ribosome recycling by ribosome recycling factor (RRF)--an important but overlooked step of protein biosynthesis,
Adv Biophys 32, 121-201

Williams, K. P., and Bartel, D. P. (1996)
Phylogenetic analysis of tmRNA secondary structure,
RNA 2, 1306-1310

Tadaki, T., Fukushima, M., Ushida, C., Himeno, H., and Muto, A. (1996)
Interaction of 10Sa RNA with ribosomes in Escherichia coli,
FEBS Lett 399, 223-226

Ando, H., Kitabatake, M., and Inokuchi, H. (1996)
10Sa RNA complements the temperature-sensitive phenotype caused by a mutation in the phosphoribosyl pyrophosphate synthetase (prs) gene in Escherichia coli,
Genes Genet Syst 71, 47-50

Keiler, K. C., Waller, P. R., and Sauer, R. T. (1996)
Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA,
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Jentsch, S. (1996)
When proteins receive deadly messages at birth,
Science 271, 955-956

Keiler, K. C., and Sauer, R. T. (1996)
Sequence determinants of C-terminal substrate recognition by the Tsp protease,
J Biol Chem 271, 2589-2593

Atkins, J. F., and Gesteland, R. F. (1996)
A case for trans translation,
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Felden, B., Atkins, J. F., and Gesteland, R. F. (1996)
tRNA and mRNA both in the same molecule,
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Komine, Y., Kitabatake, M., and Inokuchi, H. (1996)
10Sa RNA is associated with 70S ribosome particles in Escherichia coli,
J Biochem (Tokyo) 119, 463-467

Ringquist, S., Jones, T., Snyder, E. E., Gibson, T., Boni, I., and Gold, L. (1995)
High-affinity RNA ligands to Escherichia coli ribosomes and ribosomal protein S1: comparison of natural and unnatural binding sites,
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Tu, G. F., Reid, G. E., Zhang, J. G., Moritz, R. L., and Simpson, R. J. (1995)
C-terminal extension of truncated recombinant proteins in Escherichia coli with a 10Sa RNA decapeptide,
J Biol Chem 270, 9322-9326

Keiler, K. C., Silber, K. R., Downard, K. M., Papayannopoulos, I. A., Biemann, K., and Sauer, R. T. (1995)
C-terminal specific protein degradation: activity and substrate specificity of the Tsp protease,
Protein Sci 4, 1507-1515

Keiler, K. C., and Sauer, R. T. (1995)
Identification of active site residues of the Tsp protease,
J Biol Chem 270, 28864-28868

Seibert, F. S., Tabcharani, J. A., Chang, X. B., Dulhanty, A. M., Mathews, C., Hanrahan, J. W., and Riordan, J. R. (1995)
cAMP-dependent protein kinase-mediated phosphorylation of cystic fibrosis transmembrane conductance regulator residue Ser-753 and its role in channel activation,
J Biol Chem 270, 2158-2162

Retallack, D. M., and Friedman, D. I. (1995)
A role for a small stable RNA in modulating the activity of DNA-binding proteins,
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Ushida, C., and Muto, A. (1995)
Novel small stable RNAs of Mycoplasma capricolum,
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Haring, V., Billington, S. J., Wright, C. L., Huggins, A. S., Katz, M. E., and Rood, J. I. (1995)
Delineation of the virulence-related locus (vrl) of Dichelobacter nodosus,
Microbiology 141, 2081-2089

Ushida, C., Izawa, D., and Muto, A. (1995)
RNase P RNA of Mycoplasma capricolum,
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Retallack, D. M., Johnson, L. L., and Friedman, D. I. (1994)
Role for 10Sa RNA in the growth of lambda-P22 hybrid phage,
J Bacteriol 176, 2082-2089

Kirby, J. E., Trempy, J. E., and Gottesman, S. (1994)
Excision of a P4-like cryptic prophage leads to Alp protease expression in Escherichia coli,
J Bacteriol 176, 2068-2081

Trempy, J. E., Kirby, J. E., and Gottesman, S. (1994)
Alp suppression of Lon: dependence on the slpA gene,
J Bacteriol 176, 2061-2067

Ushida, C., Himeno, H., Watanabe, T., and Muto, A. (1994)
tRNA-like structures in 10Sa RNAs of Mycoplasma capricolum and Bacillus subtilis,
Nucleic Acids Res 22, 3392-3396

Komine, Y., Kitabatake, M., Yokogawa, T., Nishikawa, K., and Inokuchi, H. (1994)
A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli,
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Taha, M. K., Larribe, M., Dupuy, B., Giorgini, D., and Marchal, C. (1992)
Role of pilA, an essential regulatory gene of Neisseria gonorrhoeae, in the stress response,
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Tyagi, J. S., and Kinger, A. K. (1992)
Identification of the 10Sa RNA structural gene of Mycobacterium tuberculosis,
Nucleic Acids Res 20, 138

Srivastava, R. A., Srivastava, N., and Apirion, D. (1992)
Characterization of the RNA processing enzyme RNase III from wild type and overexpressing Escherichia coli cells in processing natural RNA substrates,
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Ebeling, S., Kundig, C., and Hennecke, H. (1991)
Discovery of a rhizobial RNA that is essential for symbiotic root nodule development,
J Bacteriol 173, 6373-6382

Oh, B. K., and Apirion, D. (1991)
10Sa RNA, a small stable RNA of Escherichia coli, is functional,
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Srivastava, R. A., Srivastava, N., and Apirion, D. (1991)
RNA processing enzymes RNase III, E and P in Escherichia coli are not ribosomal enzymes,
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Location of a gene (ssrA) for a small, stable RNA (10Sa RNA) in the Escherichia coli chromosome,
J Bacteriol 172, 4708-4709

Grubman, M. J., Zellner, M., and Samal, S. (1990)
Nucleotide and deduced amino acid sequence of the nonstructural phosphoprotein, NS2, of bluetongue virus serotype 17: comparison to two isolates of serotype 10,
Virus Res 15, 243-250

Brown, J. W., Hunt, D. A., and Pace, N. R. (1990)
Nucleotide sequence of the 10Sa RNA gene of the beta-purple eubacterium Alcaligenes eutrophus,
Nucleic Acids Res 18, 2820

Subbarao, M. N., and Apirion, D. (1989)
A precursor for a small stable RNA (10Sa RNA) of Escherichia coli,
Mol Gen Genet 217, 499-504

Chauhan, A. K., and Apirion, D. (1989)
The gene for a small stable RNA (10Sa RNA) of Escherichia coli,
Mol Microbiol 3, 1481-1485

Lee, S. Y., Bailey, S. C., and Apirion, D. (1978)
Small stable RNAs from Escherichia coli: evidence for the existence of new molecules and for a new ribonucleoprotein particle containing 6S RNA,
J Bacteriol 133, 1015-1023

Tam Lennette, E., Meyhack, B., and Apirion, D. (1972)
A mutation affecting degradation of stable RNA in Escherichia coli,
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