Abstract
One of the four ribosomal RNA operons (rrnA) from theAgrobacterium vitis vitopine strain S4 was sequenced.rrnA is most closely related to therrn operons ofBradyrhizobium japonicum andRhodobacter sphaeroides and carries an fMet-tRNA gene downstream of its 5S gene, as in the case ofR. sphaeroides. The 16S rRNA sequence of S4 differs from theA. vitis K309 type strain sequence by only one nucleotide, in spite of the fact that S4 and K309 have very different Ti plasmids. The predicted secondary structure of the S4 23S rRNA shows several features that are specific for the alpha proteobacteria, and an unusual branched structure in the universal B8 stem. The 3′ ends of the three otherrrn copies of S4 were also cloned and sequenced. Sequence comparison delimits the 3′ ends of the four repeats and defines two groups:rrnA/rrnB andrrnC/rrnD.
Similar content being viewed by others
References
Branlant C, Korobo V, Ebel JP (1976) The binding site of protein L1 on 23 ribosomal RNA fromE. coli. Eur J Biochem 70:471–482
Brimacombe R, Greuer B, Mitchell P, Osswald M, Rinke-Appel J, Schueller D, Katrin S (1990) Three-dimensional structure and function ofEscherichia 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
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
Cole ST, Saint Girons I (1994) Bacterial genomics. FEMS Microbiol Rev 14:139–160
Corpet F, Michot B (1994) RNAlign program: alignment of RNA sequences using both primary and secondary structures. Comp Appl Biosci 10:389–399
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
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
Dryden SC, Kaplan S (1990) Localization and structural analysis of the ribosomal RNA operons ofRhodobacter sphaeroides. Nucleic Acids Res 18:7267–7277
East AK, Thompson DE, Collins MD (1992) Analysis of operons encoding 23S rRNA ofClostridium botulinum type A. J Bacteriol 174:8158–8162
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
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
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
Gutell RR, Gray MW, Schnare MN (1993) A compilation of large subunit (23S and 28S-like) ribosomal RNA structures. Nucleic Acids 21:3055–3074
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
Honeycutt RJ, McClelland M, Sobral BW (1993) Physical map of the genome ofRhizobium meliloti 1021. J Bacteriol 175:6945–6952
Hopfl P, Ludwig W, Schleifer KH (1988) Complete nucleotide sequence of a 23S ribosomal RNA gene fromRhodobacter capsulatus. Nucleic Acids Res. 16:2343
Itaya M (1993) Physical mapping of multiple homologous genes in theBacillus subtilis 168 chromosome: identification of ten ribosomal RNA operon loci. Biosci Biotechnol Biochem 57:1611–1614
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
Lindhal L, Zengel JM (1986) Ribosomal genes inEscherichia coli. Annu Rev Genet 20:297–326
Michot B, Bachellerie JP (1987) Comparisons of large rRNAs reveal some eucaryote-specific elements of secondary structure. Biochimie 69:11–23
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
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 ofE. coli: a model for the tertiary structure of the tRNA binding domain in 23S RNA. Nucleic Acids Res 18: 4325–4333
Ophel K, Kerr A (1990)Agrobacterium vitis sp. nov. for strains ofAgrobacterium biovar 3 from grapevines. Int J Syst Bact 40:236–241
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
Otten L, van Nuenen M (1993) Natural instability of octopine/cucumopine Ti plasmids of clonal origin. Microbial Releases 2:91–96
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
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
Paulus F, Ridé M, Otten L (1989) Distribution of twoAgrobacterium tumefaciens insertion elements in natural isolates: evidence for stable association between Ti plasmids and their bacterial hosts. Mol Gen Genet 219:145–152
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
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
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual (2nd edn). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
Sanger F, Nicklen S, Coulson A (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467
Sechi LA, Daneo-Moore L (1993) Characterization of intergenic spacers in tworrn operons ofEnterococcus hirae ATCC9790. J Bacteriol 175:3213–3219
Springer N, Ludwig W, Hardarson G (1993) A 23S rRNA targeted specific hybridization probe forBradyrhizobium japonicum. Syst Appl Microbiol 16:468–470
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
Szegedi E (1985) Host range and specific L(+)-tartrate utilization of biotype 3Agrobacterium tumefaciens. Acta Phytopath Acad Sci Hungary 20:17–22
Vander Horn PB, Backstrom AD, Stewart V, Begley TP (1993) Structural genes for thiamine biosynthetic enzymes (thiCEFGH) inEscherichia coli K-12. J Bact 175:982–992
Van Nuenen M, De Ruffray P, Otten L (1993) Rapid divergence ofAgrobacterium vitis octopine/cucumopine Ti plasmids from a recent common ancestor. Mol Gen Genet 240:49–57
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
Willems A, Collins MD (1993) Phylogenetic analysis of Rhizobia and Agrobacteria based on 16S rRNA gene sequences. Int J Syst Bact 43:305–313
Xing Y, Draper DE (1995) Stabilization of a ribosomal RNA tertiary structure by ribosomal protein L11. J Mol Biol 249:319–331
Yanagi M, Yamasato K (1993) Phylogenetic analysis of the familyRhizobiaceae and related bacteria by sequencing of 16S rRNA gene using PCR and DNA sequencer. FEMS Microbiol Lett 107:115–120
Young JPW, Downer HL, Eardley BD (1991) Phylogency of the phototrophic Rhizobium strain BTAil by polymerase chain reaction-based sequencing of a 16S rRNA gene segment. J Bacteriol 173:2271–2277
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
Zuker M, Stiegler P (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 9:133–148
Author information
Authors and Affiliations
Additional information
Communicated by A. Kondorosi
Rights and permissions
About this article
Cite this article
Otten, L., De Ruffray, P., de Lajudie, P. et al. Sequence and characterisation of a ribosomal RNA operon fromAgrobacterium vitis . Molec. Gen. Genet. 251, 99–107 (1996). https://doi.org/10.1007/BF02174350
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF02174350