Cloaked dagger: tRNA slicing by an unlikely culprit

References

• Pandey DP, Gerdes K. Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res 2005; 33:966-76; PMID:15718296; http://dx.doi.org/10.1093/nar/gki201
   PubMed Web of Science ®Google Scholar
• Sala A, Bordes P, Genevaux P. Multiple toxin-antitoxin systems in Mycobacterium tuberculosis. Toxins 2014; 6:1002-20; PMID:24662523; http://dx.doi.org/10.3390/toxins6031002
   PubMed Web of Science ®Google Scholar
• Albrethsen J, Agner J, Piersma SR, Hojrup P, Pham TV, Weldingh K, Jimenez CR, Andersen P, Rosenkrands I. Proteomic profiling of Mycobacterium tuberculosis identifies nutrient-starvation-responsive toxin-antitoxin systems. Mol Cell Proteomics 2013; 12:1180-91; PMID:23345537; http://dx.doi.org/10.1074/mcp.M112.018846
   PubMed Web of Science ®Google Scholar
• Betts JC, Lukey PT, Robb LC, McAdam RA, Duncan K. Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol Microbiol 2002; 43:717-31; PMID:11929527; http://dx.doi.org/10.1046/j.1365-2958.2002.02779.x
   PubMed Web of Science ®Google Scholar
• Cortes T, Schubert OT, Rose G, Arnvig KB, Comas I, Aebersold R, Young DB. Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis. Cell Rep 2013; 5:1121-31; PMID:24268774; http://dx.doi.org/10.1016/j.celrep.2013.10.031
   PubMed Web of Science ®Google Scholar
• Tiwari P, Arora G, Singh M, Kidwai S, Narayan OP, Singh R. MazF ribonucleases promote Mycobacterium tuberculosis drug tolerance and virulence in guinea pigs. Nat Commun 2015; 6:6059; PMID:25608501; http://dx.doi.org/10.1038/ncomms7059
   PubMed Web of Science ®Google Scholar
• Ramage HR, Connolly LE, Cox JS. Comprehensive functional analysis of Mycobacterium tuberculosis toxin-antitoxin systems: implications for pathogenesis, stress responses, and evolution. PLoS genetics 2009; 5:e1000767; PMID:20011113; http://dx.doi.org/10.1371/journal.pgen.1000767
   PubMedGoogle Scholar
• Rustad TR, Harrell MI, Liao R, Sherman DR. The enduring hypoxic response of Mycobacterium tuberculosis. PloS one 2008; 3:e1502; PMID:18231589; http://dx.doi.org/10.1371/journal.pone.0001502
   PubMed Web of Science ®Google Scholar
• Cappelli G, Volpe E, Grassi M, Liseo B, Colizzi V, Mariani F. Profiling of Mycobacterium tuberculosis gene expression during human macrophage infection: upregulation of the alternative sigma factor G, a group of transcriptional regulators, and proteins with unknown function. Res Microbiol 2006; 157:445-55; PMID:16483748; http://dx.doi.org/10.1016/j.resmic.2005.10.007
   PubMed Web of Science ®Google Scholar
• Fontan P, Aris V, Ghanny S, Soteropoulos P, Smith I. Global transcriptional profile of Mycobacterium tuberculosis during THP-1 human macrophage infection. Infect Immun 2008; 76:717-25; PMID:18070897; http://dx.doi.org/10.1128/IAI.00974-07
   PubMed Web of Science ®Google Scholar
• Korch SB, Contreras H, Clark-Curtiss JE. Three Mycobacterium tuberculosis Rel toxin-antitoxin modules inhibit mycobacterial growth and are expressed in infected human macrophages. J Bacteriol 2009; 191:1618-30; PMID:19114484; http://dx.doi.org/10.1128/JB.01318-08
   PubMed Web of Science ®Google Scholar
• Denkin S, Byrne S, Jie C, Zhang Y. Gene expression profiling analysis of Mycobacterium tuberculosis genes in response to salicylate. Arch Microbiol 2005; 184:152-7; PMID:16175359; http://dx.doi.org/10.1007/s00203-005-0037-9
   PubMed Web of Science ®Google Scholar
• Provvedi R, Boldrin F, Falciani F, Palu G, Manganelli R. Global transcriptional response to vancomycin in Mycobacterium tuberculosis. Microbiology 2009; 155:1093-102; PMID:19332811; http://dx.doi.org/10.1099/mic.0.024802-0
   PubMed Web of Science ®Google Scholar
• Singh R, Barry CE, 3rd, Boshoff HI. The three RelE homologs of Mycobacterium tuberculosis have individual, drug-specific effects on bacterial antibiotic tolerance. J Bacteriol 2010; 192:1279-91; PMID:20061486; http://dx.doi.org/10.1128/JB.01285-09
   PubMed Web of Science ®Google Scholar
• Han JS, Lee JJ, Anandan T, Zeng M, Sripathi S, Jahng WJ, Lee SH, Suh JW, Kang CM. Characterization of a chromosomal toxin-antitoxin, Rv1102c-Rv1103c system in Mycobacterium tuberculosis. Biochem Biophys Res Commun 2010; 400:293-8; PMID:20705052; http://dx.doi.org/10.1016/j.bbrc.2010.08.023
   PubMed Web of Science ®Google Scholar
• Rothenbacher FP, Suzuki M, Hurley JM, Montville TJ, Kirn TJ, Ouyang M, Woychik NA. Clostridium difficile MazF Toxin Exhibits Selective, Not Global, mRNA Cleavage. J Bacteriol 2012; 194:3464-74; PMID:22544268; http://dx.doi.org/10.1128/JB.00217-12
   PubMed Web of Science ®Google Scholar
• Yamaguchi Y, Nariya H, Park JH, Inouye M. Inhibition of specific gene expressions by protein-mediated mRNA interference. Nat Commun 2012; 3:607; PMID:22215082; http://dx.doi.org/10.1038/ncomms1621
   PubMed Web of Science ®Google Scholar
• Zhang J, Zhang Y, Zhu L, Suzuki M, Inouye M. Interference of mRNA function by sequence-specific endoribonuclease PemK. J Biol Chem 2004; 279:20678-84; PMID:15024022; http://dx.doi.org/10.1074/jbc.M314284200
   PubMed Web of Science ®Google Scholar
• Zhang Y, Zhang J, Hara H, Kato I, Inouye M. Insights into the mRNA cleavage mechanism by MazF, an mRNA interferase. J Biol Chem 2005; 280:3143-50; PMID:15537630; http://dx.doi.org/10.1074/jbc.M411811200
   PubMed Web of Science ®Google Scholar
• Zhang Y, Zhang J, Hoeflich KP, Ikura M, Qing G, Inouye M. MazF cleaves cellular mRNAs specifically at ACA to block protein synthesis in Escherichia coli. Mol Cell 2003; 12:913-23; PMID:14580342; http://dx.doi.org/10.1016/S1097-2765(03)00402-7
   PubMed Web of Science ®Google Scholar
• Zhu L, Inoue K, Yoshizumi S, Kobayashi H, Zhang Y, Ouyang M, Kato F, Sugai M, Inouye M. Staphylococcus aureus MazF specifically cleaves a pentad sequence, UACAU, which is unusually abundant in the mRNA for pathogenic adhesive factor SraP. J Bacteriol 2009; 191:3248-55; PMID:19251861; http://dx.doi.org/10.1128/JB.01815-08
   PubMed Web of Science ®Google Scholar
• Zhu L, Phadtare S, Nariya H, Ouyang M, Husson RN, Inouye M. The mRNA interferases, MazF-mt3 and MazF-mt7 from Mycobacterium tuberculosis target unique pentad sequences in single-stranded RNA. Mol Microbiol 2008; 69:559-69; PMID:18485066; http://dx.doi.org/10.1111/j.1365-2958.2008.06284.x
   PubMed Web of Science ®Google Scholar
• Schifano JM, Cruz JW, Vvedenskaya IO, Edifor R, Ouyang M, Husson RN, Nickels BE, Woychik NA. tRNA is a new target for cleavage by a MazF toxin. Nucleic Acids Res 2016; 44:1256-70; PMID:26740583; http://dx.doi.org/10.1093/nar/gkv1370
   PubMed Web of Science ®Google Scholar
• Schifano JM, Edifor R, Sharp JD, Ouyang M, Konkimalla A, Husson RN, Woychik NA. Mycobacterial toxin MazF-mt6 inhibits translation through cleavage of 23S rRNA at the ribosomal A site. Proc Natl Acad Sci U S A 2013; 110:8501-6; PMID:23650345; http://dx.doi.org/10.1073/pnas.1222031110
   PubMed Web of Science ®Google Scholar
• Schifano JM, Vvedenskaya IO, Knoblauch JG, Ouyang M, Nickels BE, Woychik NA. An RNA-seq method for defining endoribonuclease cleavage specificity identifies dual rRNA substrates for toxin MazF-mt3. Nat Commun 2014; 5:3538; PMID:24709835; http://dx.doi.org/10.1038/ncomms4538
   PubMed Web of Science ®Google Scholar
• Zhu L, Zhang Y, Teh JS, Zhang J, Connell N, Rubin H, Inouye M. Characterization of mRNA interferases from Mycobacterium tuberculosis. J Biol Chem 2006; 281:18638-43; PMID:16611633; http://dx.doi.org/10.1074/jbc.M512693200
   PubMed Web of Science ®Google Scholar
• Vesper O, Amitai S, Belitsky M, Byrgazov K, Kaberdina AC, Engelberg-Kulka H, Moll I. Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli. Cell 2011; 147:147-57; PMID:21944167; http://dx.doi.org/10.1016/j.cell.2011.07.047
   PubMed Web of Science ®Google Scholar
• Winther K, Tree JJ, Tollervey D, Gerdes K. VapCs of Mycobacterium tuberculosis cleave RNAs essential for translation. Nucleic Acids Res 2016.
   Google Scholar
• Winther KS, Gerdes K. Enteric virulence associated protein VapC inhibits translation by cleavage of initiator tRNA. Proc Natl Acad Sci U S A 2011; 108:7403-7; PMID:21502523; http://dx.doi.org/10.1073/pnas.1019587108
   PubMed Web of Science ®Google Scholar
• Cruz JW, Sharp JD, Hoffer ED, Maehigashi T, Vvedenskaya IO, Konkimalla A, Husson RN, Nickels BE, Dunham CM, Woychik NA. Growth-regulating Mycobacterium tuberculosis VapC-mt4 toxin is an isoacceptor-specific tRNase. Nat Commun 2015; 6:7480; PMID:26158745; http://dx.doi.org/10.1038/ncomms8480
   PubMed Web of Science ®Google Scholar
• Arcus VL, McKenzie JL, Robson J, Cook GM. The PIN-domain ribonucleases and the prokaryotic VapBC toxin-antitoxin array. Protein Eng Des Sel 2011; 24:33-40; PMID:21036780; http://dx.doi.org/10.1093/protein/gzq081
   PubMed Web of Science ®Google Scholar
• Dienemann C, Boggild A, Winther KS, Gerdes K, Brodersen DE. Crystal structure of the VapBC toxin-antitoxin complex from Shigella flexneri reveals a hetero-octameric DNA-binding assembly. Journal of molecular biology 2011; 414:713-22; PMID:22037005; http://dx.doi.org/10.1016/j.jmb.2011.10.024
   PubMed Web of Science ®Google Scholar
• Kamada K, Hanaoka F, Burley SK. Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition. Mol Cell 2003; 11:875-84; PMID:12718874; http://dx.doi.org/10.1016/S1097-2765(03)00097-2
   PubMed Web of Science ®Google Scholar
• Mattison K, Wilbur JS, So M, Brennan RG. Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin-antitoxin heterodimers containing pin domains and ribbon-helix-helix motifs. J Biol Chem 2006; 281:37942-51; PMID:16982615; http://dx.doi.org/10.1074/jbc.M605198200
   PubMed Web of Science ®Google Scholar
• Miallau L, Faller M, Chiang J, Arbing M, Guo F, Cascio D, Eisenberg D. Structure and proposed activity of a member of the VapBC family of toxin-antitoxin systems. VapBC-5 from Mycobacterium tuberculosis. J Biol Chem 2009; 284:276-83; PMID:18952600; http://dx.doi.org/10.1074/jbc.M805061200
   PubMed Web of Science ®Google Scholar
• Min AB, Miallau L, Sawaya MR, Habel J, Cascio D, Eisenberg D. The crystal structure of the Rv0301-Rv0300 VapBC-3 toxin-antitoxin complex from M. tuberculosis reveals a Mg(2)(+) ion in the active site and a putative RNA-binding site. Protein Sci 2012; 21:1754-67; PMID:23011806; http://dx.doi.org/10.1002/pro.2161
   PubMed Web of Science ®Google Scholar
• Simanshu DK, Yamaguchi Y, Park JH, Inouye M, Patel DJ. Structural basis of mRNA recognition and cleavage by toxin MazF and its regulation by antitoxin MazE in Bacillus subtilis. Mol Cell 2013; 52:447-58; PMID:24120662; http://dx.doi.org/10.1016/j.molcel.2013.09.006
   PubMed Web of Science ®Google Scholar
• Zorzini V, Mernik A, Lah J, Sterckx YG, De Jonge N, Garcia-Pino A, De Greve H, Versées W, Loris R. Substrate Recognition and Activity Regulation of the Escherichia coli mRNA Endonuclease MazF. J Biol Chem 2016; 291:10950-60; PMID:27026704; http://dx.doi.org/10.1074/jbc.M116.715912
   PubMed Web of Science ®Google Scholar
• Miyamoto T, Kato Y, Sekiguchi Y, Tsuneda S, Noda N. Characterization of MazF-Mediated Sequence-Specific RNA Cleavage in Pseudomonas putida Using Massive Parallel Sequencing. PloS one 2016; 11:e0149494; PMID:26885644; http://dx.doi.org/10.1371/journal.pone.0149494
   PubMedGoogle Scholar
• Munoz-Gomez AJ, Santos-Sierra S, Berzal-Herranz A, Lemonnier M, Diaz-Orejas R. Insights into the specificity of RNA cleavage by the Escherichia coli MazF toxin. FEBS Lett 2004; 567:316-20; PMID:15178344; http://dx.doi.org/10.1016/j.febslet.2004.05.005
   PubMed Web of Science ®Google Scholar
• Park JH, Yamaguchi Y, Inouye M. Bacillus subtilis MazF-bs (EndoA) is a UACAU-specific mRNA interferase. FEBS letters 2011; 585:2526-32; PMID:21763692; http://dx.doi.org/10.1016/j.febslet.2011.07.008
   PubMed Web of Science ®Google Scholar
• Pellegrini O, Mathy N, Gogos A, Shapiro L, Condon C. The Bacillus subtilis ydcDE operon encodes an endoribonuclease of the MazF/PemK family and its inhibitor. Mol Microbiol 2005; 56:1139-48; PMID:15882409; http://dx.doi.org/10.1111/j.1365-2958.2005.04606.x
   PubMed Web of Science ®Google Scholar
• Fu Z, Donegan NP, Memmi G, Cheung AL. Characterization of MazFSa, an endoribonuclease from Staphylococcus aureus. J Bacteriol 2007; 189:8871-9; PMID:17933891; http://dx.doi.org/10.1128/JB.01272-07
   PubMed Web of Science ®Google Scholar
• Schuster CF, Park JH, Prax M, Herbig A, Nieselt K, Rosenstein R, Inouye M, Bertram R. Characterization of a mazEF toxin-antitoxin homologue from Staphylococcus equorum. J Bacteriol 2013; 195:115-25; PMID:23104807; http://dx.doi.org/10.1128/JB.00400-12
   PubMed Web of Science ®Google Scholar
• Miyamoto T, Yokota A, Tsuneda S, Noda N. AAU-Specific RNA Cleavage Mediated by MazF Toxin Endoribonuclease Conserved in Nitrosomonas europaea. Toxins 2016; 8; PMID:27271670; http://dx.doi.org/10.3390/toxins8060174
   PubMed Web of Science ®Google Scholar