Functional and molecular analysis of Escherichia coli strains lacking multiple DEAD-box helicases

RNA

Volumn 16, Issue 7, 2010, Pages 1386-1392

  Jagessar, Kevin L ^a   Jain, Chaitanya ^a  

^a UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

Author keywords

DEAD box proteins; Escherichia coli; Ribosome assembly; RNA processing

Indexed keywords

DEAD BOX PROTEIN; RNA HELICASE;

ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; CONTROLLED STUDY; DELETION MUTANT; ESCHERICHIA COLI; GENE DELETION; LOW TEMPERATURE; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; RIBOSOME; RNA ANALYSIS; RNA METABOLISM; CHEMISTRY; ENZYMOLOGY; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

DEAD-BOX RNA HELICASES; ESCHERICHIA COLI; RIBOSOMES; SEQUENCE DELETION;

EID: 77953628314     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2015610     Document Type: Article

References (30)

1. Aiba H, Adhya S, de Crombrugghe B. 1981. Evidence for two functional gal promoters in intact Escherichia coli cells. J Biol Chem 256: 11905-11910.
2. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection. Mol Syst Biol 2: 2006.0008. doi: 10.1038/msb4100050.
3. Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, et al. 1997. The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1474.
4. Charollais J, Pflieger D, Vinh J, Dreyfus M, Iost I. 2003. The DEAD-box RNA helicase SrmB is involved in the assembly of 50S ribosomal subunits in Escherichia coli. Mol Microbiol 48: 1253-1265.
5. Charollais J, Dreyfus M, Iost I. 2004. CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit. Nucleic Acids Res 32: 2751-2759.
6. Coburn GA, Miao X, Briant DJ, Mackie GA. 1999. Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3′ exonuclease and a DEAD-box RNA helicase. Genes Dev 13: 2594-2603.
7. Cordin O, Banroques J, Tanner NK, Linder P. 2006. The DEAD-box protein family of RNA helicases. Gene 367: 17-37.
8. Datsenko KA, Wanner BL. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci 97: 6640-6645.
9. Diges CM, Uhlenbeck OC. 2001. Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA. EMBO J 20: 5503-5512.
10. Fairman ME, Maroney PA, Wang W, Bowers HA, Gollnick P, Nilsen TW, Jankowsky E. 2004. Protein displacement by DExH/D 'RNA helicases' without duplex unwinding. Science 304: 730-734.
11. Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, Maruf M, Hutchison CA 3rd, Smith HO, Venter JC. 2006. Essential genes of a minimal bacterium. Proc Natl Acad Sci 103: 425-430.
12. Gorbalenya AE, Koonin EV, Donchenko AP, Blinov VM. 1989. Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res 17: 4713-4730.
13. Iost I, Dreyfus M. 2006. DEAD-box RNA helicases in Escherichia coli. Nucleic Acids Res 34: 4189-4197.
14. Jain C. 2008. The E. coli RhlE RNA helicase regulates the function of related RNA helicases during ribosome assembly. RNA 14: 381-389.
15. Jankowsky E, Gross CH, Shuman S, Pyle AM. 2001. Active disruption of an RNA-protein interaction by a DExH/D RNA helicase. Science 291: 121-125.
16. Kalman M, Murphy H, Cashel M. 1991. rhlB, a new Escherichia coli K-12 gene with an RNA helicase-like protein sequence motif, one of at least five such possible genes in a prokaryote. New Biol 3: 886-895.
17. Khemici V, Carpousis AJ. 2004. The RNA degradosome and poly(A) polymerase of Escherichia coli are required in vivo for the degradation of small mRNA decay intermediates containing REP-stabilizers. Mol Microbiol 51: 777-790.
18. Khemici V, Poljak L, Toesca I, Carpousis AJ. 2005. Evidence in vivo that the DEAD-box RNA helicase RhlB facilitates the degradation of ribosome-free mRNA by RNase E. Proc Natl Acad Sci 102: 6913-6918.
19. Linder P. 2006. Dead-box proteins: A family affair - active and passive players in RNP-remodeling. Nucleic Acids Res 34: 4168-4180.
20. Linder P, Gasteiger E, Bairoch A. 2000. A comprehensive web resource on RNA helicases from the baker's yeast Saccharomyces cerevisiae. Yeast 16: 507-509.
21. Mohr S, Stryker JM, Lambowitz AM. 2002. A DEAD-box protein functions as an ATP-dependent RNA chaperone in group I intron splicing. Cell 109: 769-779.
22. Noble SM, Guthrie C. 1996. Identification of novel genes required for yeast pre-mRNA splicing by means of cold-sensitive mutations. Genetics 143: 67-80. (Pubitemid 26136973)
23. Nomura M, Gourse R, Baughman G. 1984. Regulation of the synthesis of ribosomes and ribosomal components. Annu Rev Biochem 53: 75-117.
24. Peil L, Virumae K, Remme J. 2008. Ribosome assembly in Escherichia coli strains lacking the RNA helicase DeaD/CsdA or DbpA. FEBS J 275: 3772-3782.
25. Rajkowitsch L, Chen D, Stampfl S, Semrad K, Waldsich C, Mayer O, Jantsch MF, Konrat R, Blasi U, Schroeder R. 2007. RNA chaperones, RNA annealers and RNA helicases. RNA Biol 4: 118-130.
26. Rocak S, Linder P. 2004. DEAD-box proteins: The driving forces behind RNA metabolism. Nat Rev Mol Cell Biol 5: 232-241.
27. Slagter-Jäger JG, Puzis L, Gutgsell NS, Belfort M, Jain C. 2007. Functional defects in transfer RNAs lead to the accumulation of ribosomal RNA precursors. RNA 13: 597-605.
28. Srivastava AK, Schlessinger D. 1990. Mechanism and regulation of bacterial ribosomal RNA processing. Annu Rev Microbiol 44: 105-129. (Pubitemid 20337510)
29. Tanner NK, Linder P. 2001. DExD/H box RNA helicases: From generic motors to specific dissociation functions. Mol Cell 8: 251-262.
30. Yang Q, Jankowsky E. 2005. ATP- and ADP-dependent modulation of RNA unwinding and strand annealing activities by the DEAD-box protein DED1. Biochemistry 44: 13591-13601.