New insight into RNase P RNA structure from comparative analysis of the archaeal RNA

RNA

Volumn 7, Issue 2, 2001, Pages 220-232

  Harris, J Kirk ^a,b   Haas, Elizabeth S ^a   Williams, Daniel ^a   Frank, Daniel N ^b   Brown, James W ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF COLORADO   (United States)

Author keywords

Archaea; Archaebacteria; Ribonuclease P; Ribozyme; rnpB

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS);

ARCHAEAL RNA; BACTERIAL RNA; ESCHERICHIA COLI PROTEIN; PRIMER DNA; RIBONUCLEASE; RIBONUCLEASE P; RIBONUCLEASE P, E COLI; RIBOZYME;

ARTICLE; BACTERIAL GENE; CELL CULTURE; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; CONFORMATION; DNA SEQUENCE; ENZYMOLOGY; ESCHERICHIA COLI; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASMID; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT;

BASE SEQUENCE; CELLS, CULTURED; DNA PRIMERS; ENDORIBONUCLEASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; PLASMIDS; POLYMERASE CHAIN REACTION; RIBONUCLEASE P; RNA, ARCHAEAL; RNA, BACTERIAL; RNA, CATALYTIC; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 0035259427     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838201001777     Document Type: Article

References (60)

1. Abramovitz DL, Pyle AM. 1997. Remarkable morphological variability of a common RNA folding motif: The GNRA tetraloop-receptor interaction. J Mol Biol 266:493-506.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 275:403-410.
3. Barns SM, Fundyga RE, Jeffries MW, Pace NR. 1994. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc Natl Acad Sci USA 91:1609-1613.
4. Baross JA. 1995. Isolation, growth and maintenance of hyperthermophiles. In: Robb FT, Place AR, Sowers KR, Schreier HJ, DasSarma S, Fleischmann EM, eds. Archaea: A laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. pp 15-23.
5. Brown JW. 1991. Phylogenetic comparative analysis of RNA structure on Macintosh computers. Comput Appl Biosci 7:391-393.
6. Brown JW. 1999. The Ribonuclease P Database. Nucleic Acids Res 27:314
7. Brown JW, Haas ES. 1995-1996. Ribonuclease P structure and function in Archaea. Mol Biol Rep 22:131-134.
8. Brown JW, Haas ES, James BD, Hunt DA, Liu JS, Pace NR. 1991. Phylogenetic analysis and evolution of RNase P RNA in proteobacteria. J Bacterial 173:3855-3863.
9. Brown JW, Nolan JM, Haas ES, Rubio MA, Major F, Pace NR. 1996. Comparative analysis of ribonuclease P RNA using gene sequences from natural microbial populations reveals tertiary structural elements. Proc Natl Acad Sci USA 93:3001-3006.
10. Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, Kerlavage AR, Dougherty BA, Tomb JF, Adams MD, Reich CI, Overbeek R, Kirkness EF, Weinstock KG, Merrick JM, Glodek A, Scott JL, Geoghagen NSM, Venter JC. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058-1073.
11. Burgin AB, Pace NR. 1990. Mapping the active site of ribonuclease P RNA using a substrate containing a photoaffinity agent. EMBO J 9:4111-4118.
12. Chen J-L, Nolan JM, Harris ME, Pace NR. 1998. Comparative photocross-linking analysis of the tertiary structures of Escherichia coli and Bacillus subtilis RNase P RNAs. EMBO J 17:1515-1525.
13. Chen J-L, Pace NR. 1997. Identification of the universally conserved core of ribonuclease P RNA. RNA 3:557-560.
14. Christian EL, Kaye NM, Harris ME. 2000. Helix P4 is a divalent metal ion binding site in the conserved core of the ribonuclease P ribozyme. RNA 6:511-519.
15. Darr SC, Zito K, Smith D, Pace NR. 1992. Contributions of phylogenetically variable structural elements to the function of the ribozyme ribonuclease P. Biochemistry 31:328-333.
16. Easterwood TR, Harvey SC. 1997. Ribonuclease P RNA: Models of the 15/16 bulge from Escherichia coli and the P15 stem loop of Bacillus subtilis. RNA 3:577-585.
17. Felsenstein J. 1989. PHYLIP - Phytogeny Inference Package (Version 3.2). Cladistics 5:164-166.
18. Frank DN, Pace NR. 1998. Ribonuclease P: Unity and diversity in a tRNA processing ribozyme. Annu Rev Biochem 67:153-180.
19. Gautheret D, Konings D, Gutell RR. 1994. A major family of motifs involving G·A mismatches in ribosomal RNA. J Mol Biol 242:1-8.
20. Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S. 1983. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35:849-857.
21. Gupta RS. 1998. Protein phytogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 62:1435-1491.
22. Haas ES, Armbruster DW, Vucson BM, Daniels CJ, Brown JW. 1996. Comparative analysis of ribonuclease P RNA structure in Archaea. Nucleic Acids Res 24:1252-1259.
23. Haas ES, Brown JW. 1998. Evolutionary variation in bacterial RNase P RNAs. Nucleic Acids Res 26:4093-4099.
24. Haas ES, Brown JW, Pitulle C, Pace NR. 1994. Further perspective on the catalytic core and secondary structure of ribonuclease P RNA. Proc Natl Acad Sci USA 91:2527-2531.
25. Haas ES, Morse DP, Brown JW, Schmidt FJ, Pace NR. 1991. Longrange structure in ribonuclease P RNA. Science 254:853-856.
26. Hardt WD, Schlegl J, Erdmann VA, Hartmann RK. 1995. Kinetics and thermodynamics of the RNase P RNA cleavage reaction: Analysis of tRNA 3′-end variants. J Mol Biol 247:161-172.
27. Harris ME, Kazantsev AV, Chen J-L, Pace NR. 1997. Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by site-specific photoaffinity crosslinking. RNA 3:561-576.
28. Harris ME, Nolan JM, Malhotra A, Brown JW, Harvey SC, Pace NR. 1994. Use of photoaffinity crosslinking and molecular modeling to analyze the global architecture of ribonuclease P RNA. EMBO J 13:3953-3963.
29. Harris ME, Pace NR. 1995. Identification of phosphates involved in catalysis by the ribozyme RNase P RNA. RNA 1:210-218.
30. Herrmann B, Pettersson B, Everett KD, Mikkelsen NE, Kirsebom LA. 2000. Characterization of the rnpB gene and RNase P RNA in the order Chlamydiales. Int J Syst Evol Microbiol 50:149-158.
31. Herrmann B, Winqvist O, Mattsson JG, Kirsebom LA. 1996. Differentiation of Chlamydia spp. by sequence determination and restriction endonuclease cleavage of RNase P RNA genes. J Clin Microbiol 34:1897-1902.
32. Hook LA, Corder RE, Hamilton PT, Frea JI, Reeve JN. 1984. Development of a plating system for genetic exchange studies in methanogens using a modified ultra-low oxygen chamber. In: Strohl WR, Tuovinen OH, eds. Microbial chemoautotrophy. Columbus, OH: The Ohio State University Press.
33. Karwan R, Pluk H, van Venrooij WJ, eds. 1995-1996. Special Issue: RNase MRP/RNase P Systems. Mol Biol Rep. 22, Nos. 2/3.
34. Kawarabayasi Y, Hino Y, Horikawa H, Yamazaki S, Haikawa Y, Jin-no K, Takahashi M, Sekine M, Baba S, Ankai A, Kosugi H. Hosoyama A, Fukui S, Nagai Y, Nishijima K, Nakazawa H, Takamiya M, Masuda S, Funahashi T, Tanaka T, Kudoh Y, Yamazaki J, Kushida N, Oguchi A, Aoki K, Kubota K, Nakamura Y, Nomura N, Sako Y, Kikuchi H. 1999. Complete genome sequence of an aerobic hyperthermophiliccrenarchaeon, Aeropyrum pernix K1. DNA Res 6:83-101, 145-152.
35. Kawarabayasi Y, Sawada M, Horikawa H, Haikawa Y, Hino Y, Yamamoto S, Sekine M, Baba S, Kosugi H, Hosoyama A, Nagai Y, Sakai M, Ogura K, Otsuka R, Nakazawa H, Takamiya M, Ohfuku Y, Funahashi T, Tanaka T, Kudoh Y, Yamazaki J, Kushida N, Oguchi A, Aoki K, Kikuchi H. 1998. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res 5:55-76.
36. Kierzek R, Burkard ME, Turner DH. 1999. Thermodynamics of single mismatches in RNA duplexes. Biochemistry 38:14214-14223.
37. Kirsebom LA, Svärd SG. 1994. Base pairing between Escherichia coli RNase P RNA and its substrate. EMBO J 13:4870-4876.
38. Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, Richardson DL, Kerlavage AR, Graham DE, Kyrpides NC, Fleischmann RD, Quackenbush J, Lee NH, Sutton GG, Gill S, Kirkness EF, Dougherty BA, McKenney K, Adams MD, Loftus B, Peterson S, Reich CI, McNeil LK, Badger JH, Glodek A, Zhou L, Overbeek R, Gocayne JD, Weidman JF, McDonald L, Utterback T, Cotton MD, Spriggs T, Artiach P, Kaine BP, Sykes SM, Sadow PW, D'Andrea K, Bowman C, Fujii C, Garland SA, Mason TM, Olsen GJ, Fraser CM, Smith HO, Woese CR, Venter JC. 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364-370.
39. Kunkel TA. 1985. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci USA 82:488-492.
40. LaGrandeur TE, Darr SC, Haas ES, Pace NR. 1993. Characterization of the RNase P RNA of Sulfolobus acidocaldarius. J Bacteriol 175:5043-5048.
41. Maidak BL, Cole JR, Lilburn TG, Parker CT, Saxman PR, Stredwick JM, Garrity GM, Li B, Olsen GJ, Pramanik S, Schmidt TM, Tiedje JM. 2000. The RDP (Ribosomal Database Project) continues. Nucleic Acids Res 28:173-174.
42. Massire C, Jaeger L, Westhof E. 1997. Phylogenetic evidence for a new tertiary interaction in bacterial RNase P RNAs. RNA 3:553-556.
43. Massire C, Jaeger L, Westhof E. 1998. Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis. J Mol Biol 279:773-793.
44. Michel F, Westhof E. 1991. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol 216:585-610.
45. Nieuwlandt DT, Haas ES, Daniels CJ. 1991, The RNA component of RNase P from the archaebacterium Haloferax volcanii. J Biol Chem 266:5689-5695.
46. Nolan JM, Burke DH, Pace NR. 1993. Circularly permuted tRNAs as specific photoaffinity probes of ribonuclease P RNA structure. Science 261:762-765.
47. 2- ions by ribonuclease P. Biochemistry 37:7277-7283.
48. Oh B-K, Pace NR. 1994. Interaction of the 3′-end of tRNA with ribonuclease P RNA. Nucleic Acids Res 22:4087-4094.
49. Pace NR, Brown JW. 1995. Evolutionary perspective on the structure and function of ribonuclease P, a ribozyme. J Bacteriol 177:1919-1928.
50. Pannucci JA, Haas ES, Hall TA, Harris JK, Brown JW. 1999. RNase P RNAs from some Archaea are catalytically active. Proc Natl Acad Sci USA 96:7803-7808.
51. Reysenbach AL, Wickham GS, Pace NR. 1994. Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park. Appl Environ Microbiol 60: 2113-2119.
52. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: A laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
53. Siegel RW, Banta AB, Haas ES, Brown JW, Pace NR. 1996. Mycoplasma fermentans simplifies our view of the catalytic core of ribonuclease P RNA. RNA 2:452-462.
54. Smith DR, Doucette-Stamm LA, Deloughery C, Lee H, Dubois J, Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert K, Harrison D, Hoang L, Keagle P, Lumm W, Pothier B, Qiu D, Spadafora R, Vicaire R, Wang Y, Wierzbowski J, Gibson R, Jiwani N, Caruso A, Bush D, Safer H, Patwell D, Prabhakar S, McDougall S, Shimer G, Goyal A, Pietrokovski S, Church GM, Daniels CJ, Mao JI, Rice P, Nölling J, Reeve JN. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum ΔH: Functional analysis and comparative genomics. J Bacteriol 179:7135-7155.
55. Tallsjo A, Svärd SG, Küfel J, Kirsebom LA. 1993. A novel tertiary interaction in M1 RNA, the catalytic subunit of Escherichia coli RNase P. Nucleic Acids Res 21:3927-3933.
56. Thomas BC, Chamberlain J, Engelke DR, Gegenheimer P. 2000. Evidence for an RNA-based catalytic mechanism in eukaryotic nuclear ribonuclease P. RNA 6:554-562.
57. Vioque A. 1992. Analysis of the gene encoding the RNA subunit of ribonuclease P from cyanobacteria. Nucleic Acids Res 20:6331-6337.
58. Vioque A. 1997. The RNase P RNA from cyanobacteria: Short tandemly repeated repetitive (STRR) sequences are present within the RNase P RNA gene in heterocyst-forming cyanobacteria. Nucleic Acids Res 25:3471-3477.
59. Waugh DS, Green CJ, Pace NR. 1989. The design and catalytic properties of a simplified ribonuclease P RNA. Science 244:1569-1571.
60. Westhof E, Altman S. 1994. Three-dimensional working model of M1 RNA, the catalytic RNA subunit of ribonuclease P from Escherichia coli. Proc Natl Acad Sci USA 91:5133-5137.