Polyadenylation of mRNA in bacteria

Microbiology

Volumn 142, Issue 11, 1996, Pages 3125-3133

  Sarkar, Nilima ^a,b  

^a BOSTON BIOMEDICAL RESEARCH INSTITUTE   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

3' exonucleases; pcnB; Poly(A) polymerase; RNA degradation; RNA synthesis

Indexed keywords

BACTERIAL RNA; MESSENGER RNA; POLYADENYLATED RNA; POLYNUCLEOTIDE ADENYLYLTRANSFERASE;

ESCHERICHIA COLI; NONHUMAN; POLYADENYLATION; PRIORITY JOURNAL; REVIEW; RNA ANALYSIS; RNA DEGRADATION; RNA STRUCTURE; RNA SYNTHESIS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0029854299     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/13500872-142-11-3125     Document Type: Review

References (80)

1. Arraiano, C. M., Yancey, S. D. & Kushner, S. R. (1988). Stabilization of discrete mRNA breakdown products in ams pnp rnb multiple mutants of Escherichia coli K-12. J Bacteriol 170, 4625-4633.
2. August J. T., Ortiz, P. J. & Hurwitz, J. (1962). Ribonucleic acid-dependent ribonucleotide incorporation. I. Purification and properties of the enzyme. J Biol Cbem 237, 3786-3793.
3. Brown, J. W. & Reeve, J. N. (1985). Polyadenylated, noncapped RNA from the archaebacterium Methanococcus vannielii. J Bacteriol 162, 909-917.
4. Cao, G.-j. & Sarkar, N. (1992a). Poly(A) RNA in Escherichia coli: nucleotide sequence at the junction of the lpp transcript and the polyadenylate moiety. Proc Natl Acad Sci USA 89, 7546-7550.
5. Cao, G.-j. & Sarkar, N. (1992b). Identification of the gene for an Escherichia coli poly(A) polymerase. Proc Natl Acad Sci USA 89, 10380-10384.
6. Cao, G.-j. & Sarkar, N. (1993). Poly(A) RNA in Bacillus subtilis: identification of the polyadenylylation site of flagellin mRNA. FEMS Microbiol Lett 108, 281-286.
7. Cao, G.-j., Pogliano, J. & Sarkar N. (1996). Identification of the coding region for a second poly(A) polymerise in Escherichia coli. Proc Natl Acad Sci USA 93 (in press).
8. Carpousis, A. J., Van Houwe, G., Ehretsmann, C. & Krisch, H. M. (1994). Copurification of E. coli RNase E and PNPase : evidence for a specific association between two enzymes important in RNA processing and degradation. Cell 76, 889-900.
9. Chaney, S. G. & Boyer, P. D. (1972). Incorporation of water oxygens into intracellular nucleotides and RNA. II. Predominantly hydrolytic RNA turnover in Escherichia coli. J Mol Biol 64, 581-591.
10. Coburn, G. A. & Mackie, G. A. (1996). Overexpression, purification, and properties of Escherichia coli ribonuclease II. J Biol Chem 271, 1048-1053.
11. Cohen, S. N. (1995). Surprises at the 3′ end of prokaryotic RNA. Cell 80, 829-832.
12. Darnell, J. E., Wall, R. & Tushinski, R. J. (1971). An adenylic acid-rich sequence in messenger RNA of HeLa cells and its possible relationship to reiterated sites in DNA. Proc Natl Acad Sci USA 68, 13321-13325,
13. Deutscher, M. P. & Reuven, N. B. (1991). Enzymatic basis for hydrolytic versus phosphorolytic mRNA degradation in Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci USA 88, 3277-3280.
14. Donovan, W. P. & Kushner, S. R. (1986). Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12. Proc Natl Acad Sci USA 83, 120-124.
15. Duffy, J. J., Chaney, S. G. & Boyer, P. D. (1972). Incorporation of water oxygens into intracellular nucleotides and RNA. I. Predominantly non-hydrolytic RNA turnover in Bacillus subtilis. J Mol Biol 64, 565-579.
16. Edmonds, M., Vaughan, M. H., Jr & Nakazato, H. (1971). Polyadenylic acid sequences in the heterogeneous nuclear RNA and rapidly labeled polyribosomal RNA of HeLa cells: possible evidence for a precursor relationship. Proc Natl Acad Sci USA 68, 1336-1340.
17. Ehretsmann, C. P., Carpousis, A. J. & Krisch, H. M. (1992). mRNA degradation in procaryotes. FASEB J 6, 3186-3192.
18. Heischmann, R. D., Adams, M. D., White, O. & 37 other authors. (1995). Whole genome random sequencing of Haemophilus influenzae Rd. Science 269, 496-512.
19. Fraser, C. M., Gocayne, J. D., White, O. & 26 other authors. (1995). The minimal gene complement of Mycoplasma genitalium. Science 270, 397-403.
20. Gershon, P. D., Ahn, B.-Y., Garfield, M. & Moss, B. (1991). Poly(A) polymerase and a dissociable polyadenylation stimulatory factor encoded by vaccinia virus. Cell 66, 1269-1278.
21. Gopalakrishna, Y. & Sarkar, N. (1981). Selective resistance of bacterial polyadenylate-containing RNA to hydrolysis by the guanosine 3′,5′-monophosphate-sensitive nuclease of Bacillus brevis. Biochem Biophys Res Commun 103, 454-460.
22. Gopalakrishna, Y. & Sarkar, N. (1982a). Characterization of polyadenylate-containing ribonucleic acid from Bacillus subtilis. Biochemistry 21, 2724-2729.
23. Gopalakrishna, Y. & Sarkar, N. (1982b). The synthesis of DNA complementary to polyadenylate-containing RNA from Bacillus subtilis. J Biol Chem 257, 2747-2750.
24. Gopalakrishna, Y. & Sarkar, N. (1983). Synthesis of polyadenylate-containing RNA in vitro in permeable cells of Escherichia coli B. Arch Biochem Biophys 224, 196-205.
25. Gopalakrishna, Y., Langley, D. & Sarkar, N. (1981). Detection of high levels of polyadenylate-containing RNA in bacteria by the use of a single-step RNA isolation procedure. Nucleic Acids Res 9, 3545-3554.
26. Guarneros, G. & Portier, C. (1990). Different specificities of ribonuclease II and polynucleotide phosphorylase in 3′ mRNA decay. Biochimie 72, 771-777.
27. Hajnsdorf, E., Steier, O., Coscoy, L., Teysset, L. & Régnier, P. (1994). Roles of RNase E, RNase II and PNPase in the degradation of the rpsO transcripts of Escherichia coli: stabilizing function of RNase II and evidence for efficient degradation in an ams pnp rnb mutant. EMBO J 13, 3368-3377.
28. Hajnsdorf, E., Braun, F., Haugel-Nielsen, J. & Régnier, P. (1995). Polyadenylylation destabilizes the rpsO mRNA of Escherichia coli. Proc Natl Acad Sci USA 92, 3973-3977.
29. He, L., Söderbom, F., Wagner, E. G. H., Binnie, U., Binns, N. & Masters, M. (1993). PcnB is required for the rapid degradation of RNAI, the antisense RNA that controls the copy number of ColE1-related plasmids. Mol Microbiol 9, 1131-1142.
30. Hussain, I., Tsukagoshi, N. & Udaka, S. (1982). Characterization of polyadenylated RNA in a protein-producing bacterium, Bacillus brevis 47. J Bacteriol 151, 1162-1170.
31. Kalapos, M. P., Cao, G.-j., Kushner, S. R. & Sarkar, N. (1994). Identification of a second poly(A) polymerase in Escherichia coli. Biochem Biophys Res Commun 198, 459-465.
32. Karnik, P., Gopalakrishna, Y. & Sarkar, N. (1986). Construction of a cDNA library from polyadenylated RNA of Bacillus subtilis and the determination of some 3′-terminal sequences. Gene 49, 161-165.
33. Karnik, P., Taljanidlsz, J., Sasvari-Szekely, M. & Sarkar, N. (1987). 3′-Terminal polyadenylate sequences of Escherichia coli tryptophan synthetase α-subunit messenger RNA. J Mol Biol 196, 347-354.
34. Kaufer, N., Altmann, M. & Döhren, H. v. (1981). Isolation of highly active polysomes with polyadenylated sequences from Bacillus brevis. FEMS Microbiol Lett 12, 71-75.
35. Kaur, S. & Jayaraman, K. (1979). Appearance of polyadenylated RNA species during sporulation in Bacillus polymyxa. Biochem Biophys Res Commun 86, 331-339.
36. Kelly, K. O. & Deutscher, M. P. (1992). The presence of only one of five exoribonucleases is sufficient to support the growth of Escherichia coli. J Bacteriol 174, 6682-6684.
37. Kerjan, P. & Szulmajster, J. (1976). Isolation and properties of a cyclic guanosine-monophosphate sensitive intracellular ribonuclease from Bacillus subtilis. Biochimie 58, 533-541.
38. Kerjan, P. & Szulmajster, J. (1980). Isolation and characterization of polyadenylated RNA species from sporulating cells of Bacillus subtilis. Biochem Biophys Res Commun 93, 201-208.
39. Lee, S. Y., Memdecki, J. & Brawerman, G. (1971). A polynucleotide segment rich in adenylic acid in the rapidly labeled polyribosomal RNA component of mouse sarcoma 180 ascites cells. Proc Natl Acad Sci USA 68, 1331-1335.
40. Lingner, J., Kellermann, J. & Keller, W. (1991). Cloning and expression of the essential gene for poly(A) polymerase from S. cerevisiae. Nature 354, 496-498.
41. Liu, J. & Parkinson, J. S. (1989). Genetics and sequence analysis of the pcnB locus, an Escherichia coli gene involved in plasmid copy number control. J Bacteriol 171, 1254-1261.
42. Liu, J. & Parkinson, J. S. (1991). Genetic evidence for interaction between the CheW and Tsr proteins during chemoreceptor signaling by Escherichia coli. J Bacteriol 173, 4941-4951.
43. Lopilato, J., Bortner, S. & Beckwith, J. (1986). Mutations in a new chromosomal gene of Escherichia coli K-12, pcnB, reduce plasmid copy number of pBR322 and its derivatives. Mol Gen Genet 205, 285-290.
44. McLaren, R. S., Newbury, S. F., Dance, G. S. C, Causton, H. C. & Higgins, C. F. (1991). mRNA degradation by processive 3′-5′ exoribonucleases in vitro and the implications for prokaryotic mRNA decay in vivo. J Mol Biol 221, 81-95.
45. McLaughlin, C. S., Warner, J. R., Edmonds, M., Nakazato, H. & Vaughan, M. H. (1973). Polyadenylic acid sequences in yeast messenger ribonucleic acid. J Biol Chem 248, 1466-1471.
46. Majumdar, P. K. & McFadden, B. A. (1984). Polyadenylated mRNA from the photosynthetic procaryote Rhodospirillum rubrum. J Bacteriol 157, 795-801.
47. Marzluff, W. F. & Pandey, N.B. (1988). Multiple levels of regulation of histone mRNA concentrations. Trends Biochem Sci 13, 49-52.
48. Masters, M., March, J. B., Oliver, I. R. & Collins, J. F. (1990). A possible role for the pcnB gene product of Escherichia coli in modulating RNA: RNA interactions. Mol Gen Genet 220, 341-344.
49. Masters, M., Colloms, M. D., Oliver, I. R., He, L., MacNaughton, E. J. & Charters, Y. (1993). The pcnB gene of Escherichia coli, which is required for ColE1 copy number maintenance, is dispensable. J Bacteriol 175, 4405-4413.
50. Nakamura, K., Pirtle, R. M., Pirtle, I. M., Takeishi, K. & Inouye, M. (1980). Messenger ribonucleic acid of the lipoprotein of the Escherichia coli outer membrane. J Biol Chem 255, 210-216.
51. Nakazato, H., Venkatesan, S. & Edmonds, M. (1975). Polyadenylic acid sequences in E. coli messenger RNA. Nature 256, 144-146.
52. O'Hara, E. B., Chekanova, J. A., Ingle, C. A., Kushner, Z. R., Peters, E. & Kushner, S. R. (1995). Polyadenylylation helps regulate mRNA decay in Escherichia coli. Proc Natl Acad Sci USA 92, 1807-1811.
53. Ohta, N., Sanders, M. & Newton, A. (1975). Poly(adenylic acid) sequences in the RNA of Caulobacter crescentus. Proc Natl Acad Sci USA 72, 2343-2346.
54. Ohta, N., Sanders, M. & Newton, A. (1978). Characterization of unstable poly(A)-RN A in Caulobacter crescentus. Biochim Biophys Acta 517, 65-75.
55. Ono, M. & Kuwano, M. (1979). A conditional lethal mutation in an Escherichia coli strain with a longer chemical lifetime of mRNA. J Mol Biol 129, 343-357.
56. Paulus, H. & Sarkar, N. (1974). Control of transcription in Bacillus brevis by small molecules. In Control of Transcription, pp. 21-34. Edited by B. B. Biswas, R. K. Mandal, A. Stevens & W. E. Cohn. New York: Plenum.
57. Pepe, C. M., Maslesa-Galic, S. & Simons, R. W. (1994). Decay of the IS10 antisense RN A by 3′ exoribonucleases : evidence that RNase II stabilizes RNA-OUT against PNPase attack. Mol Microbiol 13, 1133-1142.
58. Perry, R. P., Kelley, D. E. & La Torre, J. (1972). Lack of polyadenylic acid sequences in the messenger RNA of E. coli. Biochem Biophys Res Commun 48, 1593-1600.
59. Py, B., Causton, H., Mudd, E. A. & Higgins, C. F. (1994). A protein complex mediating mRNA degradation in Escherichia coli. Mol Microbiol 14, 717-729.
60. Py, B., Higgins, C. F. H., Krisch, H. M. & Carpoussis, A. J. (1996). A DEAD-box RNA helicase in the Escherichia coli degradosome. Nature 381, 169-172.
61. Raabe, T., Bollum, F. J. & Manley, J. L. (1991). Primary structure and expression of bovine poly(A) polymerase. Nature 353, 229-234.
62. -, pnp). J Biol Chem 251, 6274-6286.
63. Régnier, P. & Hajnsdorf, E. (1991). Decay of mRNA encoding ribosomal protein S15 of Escherichia coli is initiated by an RNase E-dependent endonucleolytic cleavage that removes the 3′ stabilizing stem and loop structure. J Mol Biol 217, 283-292.
64. Reuven, N. B. & Deutscher, M. P. (1993a). Multiple exoribonucleases are required for the 3′ processing of Escherichia coli tRNA precursors in vivo. FASEB J 7, 143-148.
65. Reuven, N. B. & Deutscher, M. P. (1993b). Substitution of the 3′ terminal adenosine residue of transfer RNA in vivo. Proc Natl Acad Sci USA 90, 4350-4353.
66. Sachs, A. (1990). The role of poly(A) in the translation and stability of mRNA. Curr Opin Cell Biol 2, 1092-1098.
67. Sachs, A. B. & Deardorff, J. A. (1992). Translation initiation requires the PAB-dependent poly(A) ribonuclease in yeast. Cell 70, 961-973.
68. Sarkar, N. & Paulus, H. (1975). A guanosine 3′,5′-monophosphate-sensitive nuclease from Bacillus brevis. J Biol Chem 250, 684-690.
69. Sarkar, N., Langley, D. & Paulus, H. (1978). Isolation and characterization of polyadenylate-containing RNA from Bacillus brevis. Biochemistry 17, 3468-3474.
70. Sarkar, N., Cao, G.-j. & Kalapos, M. P. (1995). Polyadenylation of mRNA in prokaryotes. In Abstracts of the Meeting on Molecular Genetics of Bacteria & Phages (August 1995), p. 251. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
71. Schafer, R., Zillig, W. & Priess, H. (1972). A novel RNA-primed polynucleotidepyrophosphorylase from E. coli. FEBS Lett 25, 87-90.
72. Schultz, G. A., Chaconas, G. & Moore, R. L (1978). Polyadenylic acid sequences in the RNA of Hyphomicrobium. J Bacteriol 133, 569-575.
73. Sippel, A. E. (1973). Purification and characterization of adenosine phosphate: ribonucleic acid adenyltransferase from Escherichia coli. Eur J Biochem 37, 31-40.
74. Srinivasan, P. R., Ramanarayanan, M. & Rabbani, E. (1975). Presence of polyriboadenylate sequences in pulse-labeled RNA of Escherichia coli. Proc Natl Acad Sci USA 72, 2910-2914.
75. Taljanidisz, J., Karnik, P. & Sarkar, N. (1987). Messenger ribonucleic acid for the lipoprotein of the Escherichia coli outer membrane is polyadenylated. J Mol Biol 193, 507-515.
76. Wahle, E. (1991). Purification and characterization of a mammalian polyadenylate polymerase involved in the 3′ end processing of messenger RNA precursors. J Biol Chem 266, 3131-3139.
77. Wahle, E., Martin, G., Schiltz, E. & Keller, W. (1991). Isolation and expression of cDNA clones encoding mammalian poly(A) polymerase. EMBO J 10, 4251-4257.
78. Wang, W. & Bechhofer, D. H. (1996). Properties of a Bacillus subtilis polynucleotide phosphorylase deletion strain. J Bacteriol 178, 2375-2382.
79. Xu, F. & Cohen, S. N. (1995). RNA degradation in Escherichia coli regulated by 3′ adenylation and 5′ phosphorylation. Nature 374, 180-183.
80. Xu, F., Lin-Chao, S. & Cohen, S. N. (1993). The Escherichia coli pcnB gene promotes adenylylation of antisense RNAI of ColE1-type plasmids in vivo and degradation of RNAI decay intermediates. Proc Natl Acad Sci USA 90, 6756-6760.