Novel essential gene involved in 16S rRNA processing in escherichia coli

Journal of Molecular Biology

Volumn 427, Issue 4, 2015, Pages 955-965

  Kurata, Tatsuaki ^a   Nakanishi, Shinobu ^a   Hashimoto, Masayuki ^b   Taoka, Masato ^a   Yamazaki, Yukiko ^c   Isobe, Toshiaki ^a   Kato, Jun Ichi ^a  

^a TOKYO METROPOLITAN UNIVERSITY   (Japan)

^b NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

^c NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

16S rRNA; E. coli; essential gene; rRNA processing; YqgF

Indexed keywords

ESCHERICHIA COLI PROTEIN; PROTEIN UVC; PROTEIN YQGF; PROTEOME; RIBONUCLEASE H; RNA 16S; UNCLASSIFIED DRUG; BACTERIAL RNA; DEOXYRIBONUCLEASE; RIBOSOME PROTEIN; YQGF PROTEIN, E COLI;

ARTICLE; BACTERIAL CELL; BACTERIUM CULTURE; BACTERIUM MUTANT; CONTROLLED STUDY; ENZYME ACTIVITY; ESCHERICHIA COLI; ESSENTIAL GENE; GENE EXPRESSION; IN VITRO STUDY; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN MOTIF; RIBOSOME SUBUNIT; RNA PROCESSING; TEMPERATURE; WILD TYPE; ENZYMOLOGY; GENETICS; METABOLISM; MUTATION; PROTEIN PROCESSING; RIBOSOME;

ESCHERICHIA COLI;

ENDODEOXYRIBONUCLEASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENES, ESSENTIAL; MUTATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; RIBOSOMAL PROTEINS; RIBOSOMES; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S;

EID: 84922259838     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2014.12.013     Document Type: Article

References (46)

1. T. Baba, T. Ara, M. Hasegawa, Y. Takai, Y. Okumura, and M. Baba Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection Mol Syst Biol 2 2006 2006.0008
2. C. Freiberg, B. Wieland, F. Spaltmann, K. Ehlert, H. Brötz, and H. Labischinski Identification of novel essential Escherichia coli genes conserved among pathogenic bacteria J Mol Microbiol Biotechnol 3 2001 483 489
3. S.Y. Gerdes, M.D. Scholle, J.W. Campbell, G. Balázsi, E. Ravasz, and M.D. Daugherty Experimental determination and system level analysis of essential genes in Escherichia coli MG1655 J Bacteriol 185 2003 5673 5684
4. J. Kato, and M. Hashimoto Construction of consecutive deletions of the Escherichia coli chromosome Mol Syst Biol 3 2007 132
5. L. Aravind, K.S. Makarova, and E.V. Koonin Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories Nucleic Acids Res 28 2000 3417 3432
6. D. Liu, Y.S. Wang, and D.F. Wyss Solution structure of the hypothetical protein YqgF from Escherichia coli reveals an RNAse H fold J Biomol NMR 27 2003 389 392
7. C.P. Ponting Novel domains and orthologues of eukaryotic transcription elongation factors Nucleic Acids Res 30 2002 3643 3652
8. A. Iwamoto, A. Osawa, M. Kawai, H. Honda, S. Yoshida, and N. Furuya Mutations in the essential Escherichia coli gene, yqgF, and their effects on transcription J Mol Microbiol Biotechnol 22 2012 17 23
9. J.M. Peters, R.A. Mooney, P.F. Kuan, J.L. Rowland, S. Keles, and R. Landick Rho directs widespread termination of intragenic and stable RNA transcription Proc Natl Acad Sci U S A 106 2009 15406 15411
10. S. Adhya, and M. Gottesman Control of transcription termination Annu Rev Biochem 47 1978 967 996
11. T. Platt, and D.G. Bear Role of RNA polymerase, ρ factor, and ribosomes in transcription termination J. Beckwith, J. Davies, J.A. Gallant, Gene function in prokaryotes 1983 Cold Spring Harbor Laboratory Press New York, NY 123 161
12. B.M. Burmann, K. Schweimer, X. Luo, M.C. Wahl, B.L. Stitt, and M.E. Gottesman A NusE:NusG complex links transcription and translation Science 328 2010 501 504
13. S. Proshkin, A.R. Rahmouni, A. Mironov, and E. Nudler Cooperation between translating ribosomes and RNA polymerase in transcription elongation Science 328 2010 504 508
14. J.W. Roberts Syntheses that stay together Science 328 2010 436 437
15. N. Ban, P. Nissen, J. Hansen, P.B. Moore, and T.A. Steitz The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution Science 289 2000 905 920
16. J. Harms, F. Schluenzen, R. Zarivach, A. Bashan, S. Gat, and I. Agmon High resolution structure of the large ribosomal subunit from a mesophilic eubacterium Cell 107 2001 679 688
17. B.T. Wimberly, D.E. Brodersen, W.M. Clemons, R.J. Morgan-Warren, A.P. Carter, and C. Vonrhein Structure of the 30S ribosomal subunit Nature 407 2000 327 339
18. M.M. Yusupov, G.Z. Yusupova, A. Baucom, K. Lieberman, T.N. Earnest, and J.H. Cate Crystal structure of the ribosome at 5.5 Å resolution Science 292 2001 883 896
19. K.H. Nierhaus The assembly of prokaryotic ribosomes Biochimie 73 1991 739 755
20. H.F. Noller, and M. Nomura Ribosomes F. Neidhardt, J.L. Ingraham, K.B. Low, B. Magasanik, N. Schaechter, H.E. Umbarger, Escherichia coli and Salmonella typhimurium Cellular and Molecular Biology 1987 American Society for Microbiology Press Washington, DC 1527 1542
21. B.T. Lewicki, T. Margus, J. Remme, and K.H. Nierhaus Coupling of rRNA transcription and ribosomal assembly in vivo J Mol Biol 231 1993 581 593
22. J.H. Alix, and M.F. Guérin Mutant DnaK chaperones cause ribosome assembly defects in Escherichia coli Proc Natl Acad Sci U S A 90 1993 9725 9729
23. J. Charollais, M. Dreyfus, and I. Iost CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit Nucleic Acids Res 32 2004 2751 2759
24. J.A. Maki, D.J. Schnobrich, and G.M. Culver The DnaK chaperone system facilitates 30S ribosomal subunit assembly Mol Cell 10 2002 129 138
25. K. Nishi, F. Morel-Deville, J.W. Hershey, T. Leighton, and J. Schnier An eIF-4A-like protein is a suppressor of an Escherichia coli mutant defective in 50S ribosomal subunit assembly Nature 336 1988 496 498
26. M. Kaczanowska, and M. Rydén-Aulin Ribosome biogenesis and the translation process in Escherichia coli Microbiol Mol Biol Rev 71 2007 477 494
27. R.J. Bram, R.A. Young, and J.A. Steitz The ribonuclease III site flanking 23S sequences in the 30S ribosomal precursor RNA of E. coli Cell 19 1980 393 401
28. A. Liiv, and J. Remme Importance of transient structures during post-transcriptional refolding of the pre-23S rRNA and ribosomal large subunit assembly J Mol Biol 342 2004 725 741
29. R.A. Young, and J.A. Steitz Complementary sequences 1,700 nucleotides apart form a ribonuclease III cleavage site in Escherichia coli ribosomal precursor RNA Proc Natl Acad Sci U S A 75 1978 3593 3597
30. D.K. Jemiolo Processing of prokaryotic ribosomal RNA R.A. Zimmermann, A.E. Dahlberg, Ribosomal RNA, structure, evolution, processing, and function 1996 CRC Press New York, NY 453 468
31. Z. Li, S. Pandit, and M.P. Deutscher RNase G (CafA protein) and RNase E are both required for the 5′ maturation of 16S ribosomal RNA EMBO J 18 1999 2878 2885
32. M. Wachi, G. Umitsuki, M. Shimizu, A. Takada, and K. Nagai Escherichia coli cafA gene encodes a novel RNase, designated as RNase G, involved in processing of the 5′ end of 16S rRNA Biochem Biophys Res Commun 259 1999 483 488
33. S. Sulthana, and M.P. Deutscher Multiple exoribonucleases catalyze maturation of the 3′ terminus of 16S ribosomal RNA (rRNA) J Biol Chem 288 2013 12574 12579
34. A.I. Jacob, C. Köhrer, B.W. Davies, U.L. RajBhandary, and G.C. Walker Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation Mol Cell 49 2013 427 438
35. G. Mangiarotti, E. Turco, A. Ponzetto, and F. Altruda Precursor 16S RNA in active 30S ribosomes Nature 247 1974 147 148
36. G.W. Li, E. Oh, and J.S. Weissman The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria Nature 484 2012 538 541
37. B. Roy-Chaudhuri, N. Kirthi, and G.M. Culver Appropriate maturation and folding of 16S rRNA during 30S subunit biogenesis are critical for translational fidelity Proc Natl Acad Sci U S A 107 2010 4567 4572
38. M. Bubunenko, A. Korepanov, D.L. Court, I. Jagannathan, D. Dickinson, and B.R. Chaudhuri 30S ribosomal subunits can be assembled in vivo without primary binding ribosomal protein S15 RNA 12 2006 1229 1239
39. G.O. Bylund, L.C. Wipemo, L.A. Lundberg, and P.M. Wikström RimM and RbfA are essential for efficient processing of 16S rRNA in Escherichia coli J Bacteriol 180 1998 73 82
40. K. Connolly, J.P. Rife, and G. Culver Mechanistic insight into the ribosome biogenesis functions of the ancient protein KsgA Mol Microbiol 70 2008 1062 1075
41. A.J. Callaghan, J.P. Aurikko, L.L. Ilag, J. Günter Grossmann, V. Chandran, and K. Kühnel Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E J Mol Biol 340 2004 965 979
42. M. Lehnik-Habrink, J. Newman, F.M. Rothe, A.S. Solovyova, C. Rodrigues, and C. Herzberg RNase Y in Bacillus subtilis: a natively disordered protein that is the functional equivalent of RNase E from Escherichia coli J Bacteriol 193 2011 5431 5441
43. A.C. Chang, and S.N. Cohen Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid J Bacteriol 134 1978 1141 1156
44. S.F. Clatterbuck Soper, R.P. Dator, P.A. Limbach, and S.A. Woodson In vivo X-ray footprinting of pre-30S ribosomes reveals chaperone-dependent remodeling of late assembly intermediates Mol Cell 52 2013 506 516
45. M. Taoka, Y. Yamauchi, T. Shinkawa, H. Kaji, W. Motohashi, and H. Nakayama Only a small subset of the horizontally transferred chromosomal genes in Escherichia coli are translated into proteins Mol Cell Proteomics 3 2004 780 787
46. M. Taoka, Y. Yamauchi, Y. Nobe, S. Masaki, H. Nakayama, and H. Ishikawa An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes Nucleic Acids Res 37 2009 [PMID:19740761]