Sequence and characterisation of a ribosomal RNA operon from Agrobacterium vitis

Molecular and General Genetics

Volumn 251, Issue 1, 1996, Pages 99-107

  Otten, Léon ^a   De Ruffray, Patrice ^a   De Lajudie, Philippe ^b   Michot, Bernard ^a  

^a CNRS   (France)

^b INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (Senegal)

Author keywords

23S rRNA; Agrobacterium; Evolution; Ribosomal genes

Indexed keywords

NUCLEOTIDE; RIBOSOME RNA; RNA;

ARTICLE; BRADYRHIZOBIUM JAPONICUM; GENE; GENE SEQUENCE; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RHIZOBIUM; RHODOBACTER SPHAEROIDES;

BASE SEQUENCE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OPERON; REPETITIVE SEQUENCES, NUCLEIC ACID; RHIZOBIACEAE; RHIZOBIUM; RHODOBACTER SPHAEROIDES; RNA, BACTERIAL; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 23S; RNA, TRANSFER, MET; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 0029991403     PISSN: 00268925     EISSN: None     Source Type: Journal    
DOI: 10.1007/s004380050145     Document Type: Article

References (45)

1. Branlant C, Korobo V, Ebel JP (1976) The binding site of protein L1 on 23 ribosomal RNA from E. coli. Eur J Biochem 70:471-482
2. Brimacombe R, Greuer B, Mitchell P, Osswald M, Rinke-Appel J, Schueller D, Katrin S (1990) Three-dimensional structure and function of Escherichia coli 16S and 23S rRNA as studied by cross-linking techniques. In: Hill WE, Dahlberg A, Garret RA, Moore PB, Schlessinger D, Warner JR (eds) The ribosome: structure, function and evolution. Amer Soc Microbiol, Washington DC, pp 93-106
3. Canaday J, Gérard JC, Crouzet P, Otten L (1992) Organization and functional analysis of three T-DNAs from the vitopine Ti plasmid pTiS4. Mol Gen Genet 235:292-303
4. Cole ST, Saint Girons I (1994) Bacterial genomics. FEMS Microbiol Rev 14:139-160
5. Corpet F, Michot B (1994) RNAlign program: alignment of RNA sequences using both primary and secondary structures. Comp Appl Biosci 10:389-399
6. De Rijk P, van de Peer Y, Chapelle S, de Wachter R (1994) Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res 22:3495-3501
7. Devereux JP, Haeberli P, Marquess P (1987) The program manual for sequence analysis software package of the Genetics Computer Group. Nucleic Acids Res 12:387-395
8. Dryden SC, Kaplan S (1990) Localization and structural analysis of the ribosomal RNA operons of Rhodobacter sphaeroides. Nucleic Acids Res 18:7267-7277
9. East AK, Thompson DE, Collins MD (1992) Analysis of operons encoding 23S rRNA of Clostridium botulinum type A. J Bacteriol 174:8158-8162
10. Fox GE, Wisotzkey JD, Jurtshuk P (1992) How close is close: 16S rRNA sequence may not be sufficient to guarantee species identity. Int J Syst Bact 42:166-170
11. Gérard JC, Canaday J, Szegedi E, de la Salle H, Otten L (1992) Physical map of the vitopine Ti plasmid pTiS4. Plasmid 28: 146-156
12. Gray MW, Schnare MN (1990) Evolution of the modular structure of rRNA. In: Hill WE, Dahlberg A, Garret RA, Moore PB, Schlessinger D, Warner JR (eds) The ribosome: structure, function and evolution. Amer Soc Microbiol, Washington DC, pp 589-597
13. Gutell RR, Gray MW, Schnare MN (1993) A compilation of large subunit (23S and 28S-like) ribosomal RNA structures. Nucleic Acids 21:3055-3074
14. Hassouna N, Michot B, Bachellerie JP (1984) The complete nucleotide sequence of mouse rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eucaryotes. Nucleic Acids Res 12:3563-3583
15. Honeycutt RJ, McClelland M, Sobral BW (1993) Physical map of the genome of Rhizobium meliloti 1021. J Bacteriol 175: 6945-6952
16. Hopfl P, Ludwig W, Schleifer KH (1988) Complete nucleotide sequence of a 23S ribosomal RNA gene from Rhodobacter capsulatus. Nucleic Acids Res. 16:2343
17. Itaya M (1993) Physical mapping of multiple homologous genes in the Bacillus subtilis 168 chromosome: identification of ten ribosomal RNA operon loci. Biosci Biotechnol Biochem 57: 1611-1614
18. Laguerre G, Allard M-R, Revoy F, Amarger N (1994) Rapid identification of Rhizobia by restriction fragment length polymorphism analysis of PCR-amplified 16 rRNA genes. Appl Environ Microbiol 60:56-63
19. Lindhal L, Zengel JM (1986) Ribosomal genes in Escherichia coli. Annu Rev Genet 20:297-326
20. Michot B, Bachellerie JP (1987) Comparisons of lirge rRNAs reveal some eucaryote-specific elements of secondary structure. Biochimie 69:11-23
21. Michot B, Qu LH, Bachellerie JP (1990) Evolution of large subunit rRNA structure. The diversification of divergent domain D3 among major phylogenetic groups. Eur J Biochem 188:219-229
22. Mitchell P, Osswald M, Schueler D, Brimacombe R (1990) Selective isolation and detailed analysis of intra-RNA cross-links induced in the large ribosomal subunit of E. coli: a model for the tertiary structure of the tRNA binding domain in 23S RNA. Nucleic Acids Res 18: 4325-4333
23. Ophel K, Kerr A (1990) Agrobacterium vitis sp. nov. for strains of Agrobacterium biovar 3 from grapevines. Im J Syst Bact 40: 236-241
24. Otten L, De Ruffray P (1994) Agrobacterium vitis nopaline Ti plasmid pTiAB4: relationship to other Ti plasmids and T-DNA analysis. Mol Gen Genet 245:493-505
25. Otten L, van Nuenen M (1993) Natural instability of octopine/ cucumopine Ti plasmids of clonal origin. Microbial Releases 2:91-96
26. Otten L, Canaday J, Gérard JC, Fournier P, Crouzet P, Paulus P (1992) Evolution of Agrobacteria and their Ti plasmids A review. Mol Plant-Microbe Interact 5:279-287
27. Pace NR, Burgin AB (1990) Processing and evolution of the tRNAs. In: Hill WE, Dahlberg A, Garret RA, Moore PB, Schlessinger D, Warner JR (eds) The ribosome: structure, function and evolution. American Soc Microbiol, Washington DC, pp 417-425
28. Paulus F, Ridé M, Otten L (1989) Distribution of two Agrobacterium tumefaciens insertion elements in natural isolates: evidence for stable association between Ti plasmids and their bacterial hosts. Mol Gen Genet 219:145-152
29. Perochon-Dorisse J, Chetouani F, Aurel S, Iscolo N, Michot B (1995) RNA_d2: a computer program for editing and display of RNA secondary structures. Comp Appl Biosci 11:101-109
30. Raue HA, Muster W, Rutgers CA, Riet JV, Planta RJ (1990) rRNA: from structure to function. In: Hill WE, Dahlberg A, Garret RA, Moore PB, Schlessinger D, Warner JR (eds) The ribosome: structure, function and evolution. Amer Soc Microbiol, Washington DC, pp 217-235
31. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual (2nd edn). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
32. Sanger F, Nicklen S, Coulson A (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74: 5463-5467
33. Sechi LA, Daneo-Moore L (1993) Characterization of intergenic spacers in two rrn operons of Enterococcus hirae ATCC9790. J Bacteriol 175:3213-3219
34. Springer N, Ludwig W, Hardarson G (1993) A 23S rRNA targeted specific hybridization probe for Bradyrhizobium japonicum. Syst Appl Microbiol 16:468-470
35. Sweeney R, Chen L, Yao MC (1994) An rRNA region has an evolutionary conserved essential role despite sequence divergence. Mol Cell Biol 14:4203-4215
36. Szegedi E (1985) Host range and specific L(+)-tartrate utilization of biotype 3 Agrobacterium tumefaciens. Acta Phytopath Acad Sci Hungary 20:17-22
37. Vander Horn PB, Backstrom AD, Stewart V, Begley TP (1993) Structural genes for thiamine biosynthetic enzymes (thiCEFGH) in Escherichia coli K-12. J Bact 175:982-992
38. Van Nuenen M, De Ruffray P, Otten L (1993) Rapid divergence of Agrobacterium vitis octopine/cucumopine Ti plasmids from a recent common ancestor. Mol Gen Genet 240:49-57
39. Vester B, Garrett RA (1984) Structure of a protein L23-RNA complex located at the A-site domain of the ribosomal peptidyltransferase centre. J Mol Biol 179:431-452
40. Willems A, Collins MD (1993) Phylogenetic analysis of Rhizobia and Agrobacteria based on 16S rRNA gene sequences. Int J Syst Bact 43:305-313
41. Xing Y, Draper DE (1995) Stabilization of a ribosomal RNA tertiary structure by ribosomal protein L11. J Mol Biol 249:319-331
42. Yanagi M, Yamasato K (1993) Phylogenetic analysis of the family Rhizobiaceae and related bacteria by sequencing of 16S rRNA gene using PCR and DNA sequencer. FEMS Microbiol Lett 107:115-120
43. Young JPW, Downer HL, Eardley BD (1991) Phylogency of the phototrophic Rhizobium strain BTAiI by polymerase chain reaction-based sequencing of a 16S rRNA gene segment. J Bacteriol 173:2271-2277
44. Zimmerman RA, Thomas CL, Wower J (1990) Structure and function of rRNA in the decoding domain and at the peptidyltransferase center. In: Hill WE, Dahlberg A, Garret RA, Moore PB, Schlessinger D, Warner JR (eds) The ribosome: structure, function and evolution. Amer Soc Microbiol, Washington DC, pp 331-347
45. Zuker M, Stiegler P (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 9:133-148