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Plasmids of the Rhizobiaceae and Their Role in Interbacterial and Transkingdom Interactions. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/978-3-642-14512-4_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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Sequence analysis of a DNA fragment fromSinorhizobium fredii USDA257 which extends the nitrogen fixation host range ofRhizobium species NGR234 to soybean,Glycine max (L.) Merr cultivar Peking. Symbiosis 2009. [DOI: 10.1007/bf03179990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Luyten E, Swinnen E, Vlassak K, Verreth C, Dombrecht B, Vanderleyden J. Analysis of a symbiosis-specific cytochrome P450 homolog in Rhizobium sp. BR816. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2001; 14:918-924. [PMID: 11437267 DOI: 10.1094/mpmi.2001.14.7.918] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Sequence analysis of the DNA region upstream of nodO in Rhizobium sp. BR816 revealed an open reading frame in which the deduced amino acid sequence shows homology with cytochrome P450. Because the BR816 P450 homolog shows 73% amino acid similarity with CYP127A1(Y4vG), which is identified on the symbiotic plasmid of Rhizobium sp. NGR234, it is named CYP127A2. Transcriptional analysis of CYP127A2 revealed high expression in bacteroids, whereas no or hardly any expression was observed under free-living conditions. Low-level, free-living expression, however was noticed when cells were grown microoxically at acid pH levels. A number of possible substrates that may induce P450 gene expression were analyzed, but only the addition of short-chain alcohols to cultures slightly increased CYP127A2 expression. High levels of CYP127A2 expression observed in bacteroids of a nifH mutant strain, which formed non-fixing nodules on bean, indicated that the genuine substrate for CYP127A2 is not a metabolite resulting from N2-fixation. Nevertheless, expression analysis pointed to a NifA- and sigma54-dependent transcription.
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Affiliation(s)
- E Luyten
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium
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Perret X, Parsons J, Viprey V, Reichwald K, Broughton WJ. Séquences répétées des génomes de Rhizobium sp. NGR234 et Sinorhizobium meliloti : une analyse comparative par séquençage aléatoire. Can J Microbiol 2001. [DOI: 10.1139/w01-031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Amongst prokaryotic genomes, those of nitrogen-fixing members of the Rhizobiaceae family are relatively large (69 Mb), often include mega-plasmids of 1.52 Mb, and contain numerous families of repeated DNA sequences. Although most essential nodulation and nitrogen fixation genes are well characterized, these represent only a small fraction of the DNA content. Little is known about the detailed structure of rhizobial genomes. With the development of sequencing techniques and new bio-informatic tools such studies become possible, however. Using the 2275 shot-gun sequences of ANU265 (a derivative of NGR234 cured of pNGR234a), we have identified numerous families of repeats. Amongst these, the 58-bp-long NGRREP-4 represents the third most abundant DNA sequence after the RIME1 and RIME2 repeats, all of which are also found in Sinorhizobium meliloti. Surprisingly, studies on the distribution of these elements showed that in proportion to its size, the chromosome of NGR234 carries many more RIME modules than pNGR234a or pNGR234b. Together with the presence in NGR234 and S. meliloti 1021 of an insertion sequence (IS) element more conserved than essential nodulation and nitrogen fixation genes, these results give new insights into the origin and evolution of rhizobial genomes.Key words: shot-gun, repeats, BIME.
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Viprey V, Rosenthal A, Broughton WJ, Perret X. Genetic snapshots of the Rhizobium species NGR234 genome. Genome Biol 2000; 1:RESEARCH0014. [PMID: 11178268 PMCID: PMC16145 DOI: 10.1186/gb-2000-1-6-research0014] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2000] [Revised: 10/25/2000] [Accepted: 10/31/2000] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND In nitrate-poor soils, many leguminous plants form nitrogen-fixing symbioses with members of the bacterial family Rhizobiaceae. We selected Rhizobium sp. NGR234 for its exceptionally broad host range, which includes more than I 12 genera of legumes. Unlike the genome of Bradyrhizobium japonicum, which is composed of a single 8.7 Mb chromosome, that of NGR234 is partitioned into three replicons: a chromosome of about 3.5 Mb, a megaplasmid of more than 2 Mb (pNGR234b) and pNGR234a, a 536,165 bp plasmid that carries most of the genes required for symbioses with legumes. Symbiotic loci represent only a small portion of all the genes coded by rhizobial genomes, however. To rapidly characterize the two largest replicons of NGR234, the genome of strain ANU265 (a derivative strain cured of pNGR234a) was analyzed by shotgun sequencing. RESULTS Homology searches of public databases with 2,275 random sequences of strain ANU265 resulted in the identification of 1,130 putative protein-coding sequences, of which 922 (41%) could be classified into functional groups. In contrast to the 18% of insertion-like sequences (ISs) found on the symbiotic plasmid pNGR234a, only 2.2% of the shotgun sequences represent known ISs, suggesting that pNGR234a is enriched in such elements. Hybridization data also indicate that the density of known transposable elements is higher in pNGR234b (the megaplasmid) than on the chromosome. Rhizobium-specific intergenic mosaic elements (RIMEs) were found in 35 shotgun sequences, 6 of which carry RIME2 repeats previously thought to be present only in Rhizobium meliloti. As non-overlapping shotgun sequences together represent approximately 10% of ANU265 genome, the chromosome and megaplasmid may carry a total of over 200 RIMEs. CONCLUSIONS 'Skimming' the genome of Rhizobium sp. NGR234 sheds new light on the fine structure and evolution of its replicons, as well as on the integration of symbiotic functions in the genome of a soil bacterium. Although most putative coding sequences could be distributed into functional classes similar to those in Bacillus subtilis, functions related to transposable elements were more abundant in NGR234. In contrast to ISs that accumulated in pNGR234a and pNGR234b, the hundreds of RIME elements seem mostly attributes of the chromosome.
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Affiliation(s)
- Virginie Viprey
- Laboratoire de Biologie Moléculaire des Plantes Supérieures, Université de Genève, chemin de l'Impératrice, 1292 Chambésy, Genève, Switzerland. E-mail:
- Current address: John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - André Rosenthal
- Institut für Molekulare Biotechnologie, Abteilung Genomanalyze, Beutenbergstrasse, 07745 Jena, Germany
| | - William J Broughton
- Laboratoire de Biologie Moléculaire des Plantes Supérieures, Université de Genève, chemin de l'Impératrice, 1292 Chambésy, Genève, Switzerland. E-mail:
| | - Xavier Perret
- Laboratoire de Biologie Moléculaire des Plantes Supérieures, Université de Genève, chemin de l'Impératrice, 1292 Chambésy, Genève, Switzerland. E-mail:
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Barrios H, Valderrama B, Morett E. Compilation and analysis of sigma(54)-dependent promoter sequences. Nucleic Acids Res 1999; 27:4305-13. [PMID: 10536136 PMCID: PMC148710 DOI: 10.1093/nar/27.22.4305] [Citation(s) in RCA: 294] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Promoters recognized by the RNA-polymerase with the alternative sigma factor sigma(54) (Esigma54) are unique in having conserved positions around -24 and -12 nucleotides upstream from the transcriptional start site, instead of the typical -35 and -10 boxes. Here we compile 186 -24/-12 promoter sequences reported in the literature and generate an updated and extended consensus sequence. The use of the extended consensus increases the probability of identifying genuine -24/-12 promoters. The effect of several reported mutations at the -24/-12 elements on RNA-polymerase binding and promoter strength is discussed in the light of the updated consensus.
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Affiliation(s)
- H Barrios
- Departamento de Reconocimiento Molecular y Bioestructura, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62271, México
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Baldermann C, Lupas A, Lubieniecki J, Engelhardt H. The regulated outer membrane protein Omp21 from Comamonas acidovorans is identified as a member of a new family of eight-stranded beta-sheet proteins by its sequence and properties. J Bacteriol 1998; 180:3741-9. [PMID: 9683466 PMCID: PMC107353 DOI: 10.1128/jb.180.15.3741-3749.1998] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Omp21, a minor outer membrane protein of the soil bacterium Comamonas acidovorans, was purified from a spontaneous mutant lacking a surface layer and long-chain lipopolysaccharide. Omp21 synthesis is enhanced by oxygen depletion, and the protein has a variable electrophoretic mobility in sodium dodecyl sulfate-polyacrylamide gel electrophoresis due to its heat-modifiable behavior. The structural gene omp21 encodes a precursor of 204 amino acids with a putative signal peptide of 21 amino acids. Mature Omp21 is a typical outer membrane protein with a high content of beta structure as determined by infrared spectroscopy. Sequence comparisons show that it belongs to a new outer membrane protein family, characterized by eight amphipathic beta strands, which includes virulence proteins, such as the neisserial opacity proteins, Salmonella typhimurium Rck, and Yersinia enterocolitica Ail, as well as the major outer membrane proteins OmpA from Escherichia coli and OprF from Pseudomonas aeruginosa.
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Affiliation(s)
- C Baldermann
- Max-Planck-Institut für Biochemie, Molekulare Strukturbiologie, D-82152 Martinsried, Germany
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Brunner NA, Brinkmann H, Siebers B, Hensel R. NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase from Thermoproteus tenax. The first identified archaeal member of the aldehyde dehydrogenase superfamily is a glycolytic enzyme with unusual regulatory properties. J Biol Chem 1998; 273:6149-56. [PMID: 9497334 DOI: 10.1074/jbc.273.11.6149] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hyperthermophilic archaeum Thermoproteus tenax possesses two glyceraldehyde-3-phosphate dehydrogenases differing in cosubstrate specificity and phosphate dependence of the catalyzed reaction. NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase catalyzes the phosphate-independent irreversible oxidation of D-glyceraldehyde 3-phosphate to 3-phosphoglycerate. The coding gene was cloned, sequenced, and expressed in Escherichia coli. Sequence comparisons showed no similarity to phosphorylating glyceraldehyde-3-phosphate dehydrogenases but revealed a relationship to aldehyde dehydrogenases, with the highest similarity to the subgroup of nonphosphorylating glyceraldehyde-3-phosphate dehydrogenases. The activity of the enzyme is affected by a series of metabolites. All effectors tested influence the affinity of the enzyme for its cosubstrate NAD+. Whereas NADP(H), NADH, and ATP reduce the affinity for the cosubstrate, AMP, ADP, glucose 1-phosphate, and fructose 6-phosphate increase the affinity for NAD+. Additionally, most of the effectors investigated induce cooperativity of NAD+ binding. The irreversible catabolic oxidation of glyceraldehyde 3-phosphate, the control of the enzyme by energy charge of the cell, and the regulation by intermediates of glycolysis and glucan degradation identify the NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase as an integral constituent of glycolysis in T. tenax. Its regulatory properties substitute for those lacking in the reversible nonregulated pyrophosphate-dependent phosphofructokinase in this variant of the Embden-Meyerhof-Parnas pathway.
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Affiliation(s)
- N A Brunner
- Department of Microbiology, FB 9, Universit¿t-GH Essen, Universit¿tsstrasse 5, 45117 Essen, Germany
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Perret X, Viprey V, Freiberg C, Broughton WJ. Structure and evolution of NGRRS-1, a complex, repeated element in the genome of Rhizobium sp. strain NGR234. J Bacteriol 1997; 179:7488-96. [PMID: 9393715 PMCID: PMC179701 DOI: 10.1128/jb.179.23.7488-7496.1997] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Much of the remarkable ability of Rhizobium sp. strain NGR234 to nodulate at least 110 genera of legumes, as well as the nonlegume Parasponia andersonii, stems from the more than 80 different Nod factors it secretes. Except for nodE, nodG, and nodPQ, which are on the chromosome, most Nod factor biosynthesis genes are dispersed over the 536,165-bp symbiotic plasmid, pNGR234a. Mosaic sequences and insertion sequences (ISs) comprise 18% of pNGR234a. Many of them are clustered, and these IS islands divide the replicon into large blocks of functionally related genes. At 6 kb, NGRRS-1 is a striking example: there is one copy on pNGR234a and three others on the chromosome. DNA sequence comparisons of two NGRRS-1 elements identified three types of IS, NGRIS-2, NGRIS-4, and NGRIS-10. Here we show that all four copies of NGRRS-1 probably originated from transposition of NGRIS-4 into a more ancient IS-like sequence, NGRIS-10. Remarkably, all nine copies of NGRIS-4 have transposed into other ISs. It is unclear whether the accumulation of potentially mutagenic sequences in large clusters is due to the nature of the IS involved or to some selection process. Nevertheless, a direct consequence of the preferential targeting of transposons into such IS islands is to minimize the likelihood of disrupting vital functions.
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Affiliation(s)
- X Perret
- Laboratoire de Biologie Moleculaire de Plantes Supérieures, University of Geneva, Switzerland
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Choudhary M, Mackenzie C, Nereng K, Sodergren E, Weinstock GM, Kaplan S. Low-resolution sequencing of Rhodobacter sphaeroides 2.4.1T: chromosome II is a true chromosome. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 10):3085-3099. [PMID: 9353914 DOI: 10.1099/00221287-143-10-3085] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The photosynthetic bacterium Rhodobacter sphaeroides 2.4.1T has two chromosomes, CI (approximately 3.0 Mb) and CII (approximately 0.9 Mb). In this study a low-redundancy sequencing strategy was adopted to analyse 23 out of 47 cosmids from an ordered CII library. The sum of the lengths of these 23 cosmid inserts was approximately 495 kb, which comprised approximately 417 kb of unique DNA. A total of 1145 sequencing runs was carried out, with each run generating 559 +/- 268 bases of sequence to give approximately 640 kb of total sequence. After editing, approximately 2.8% bases per run were estimated to be ambiguous. After the removal of vector and Escherichia coli sequences, the remaining approximately 565 kb of R. sphaeroides sequences were assembled, generating approximately 291 kb of unique sequences. BLASTX analysis of these unique sequences suggested that approximately 131 kb (45% of the unique sequence) had matches to either known genes, or database ORFs of hypothetical or unknown function (dORFs). A total of 144 strong matches to the database was found; 101 of these matches represented genes encoding a wide variety of functions, e.g. amino acid biosynthesis, photosynthesis, nutrient transport, and various regulatory functions. Two rRNA operons (rrnB and rrnC) and five tRNAs were also identified. The remaining 160 kb of DNA sequence which did not yield database matches was then analysed using CODONPREFERENCE from the GCG package. This analysis suggested that 122 kb (42% of the total unique DNA sequence) could encode putative ORFs (pORFs), with the remaining 38 kb (13%) possibly representing non-coding intergenic DNA. From the data so far obtained, CII does not appear to be specialized for encoding any particular metabolic function, physiological state or growth condition. These data suggest that CII contains genes which are functionally as diverse as those found on any other bacterial chromosome and also contains sequences (pORFs), which may prove to be unique to this organism.
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Affiliation(s)
- M Choudhary
- Department of Microbiology & The University of Texas Health Science Center, Houston, TX 77225, USA
| | - C Mackenzie
- Department of Microbiology & The University of Texas Health Science Center, Houston, TX 77225, USA
| | - K Nereng
- Department of Microbiology & The University of Texas Health Science Center, Houston, TX 77225, USA
| | - Erica Sodergren
- Molecular Geneticsand Department of Biochemistry & Molecular Biology The University of Texas Health Science Center, Houston, TX 77225, USA
| | - G M Weinstock
- Molecular Geneticsand Department of Biochemistry & Molecular Biology The University of Texas Health Science Center, Houston, TX 77225, USA
- Department of Microbiology & The University of Texas Health Science Center, Houston, TX 77225, USA
| | - S Kaplan
- Department of Microbiology & The University of Texas Health Science Center, Houston, TX 77225, USA
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Nagy I, Schoofs G, Vanderleyden J, De Mot R. Transposition of the IS21-related element IS1415 in Rhodococcus erythropolis. J Bacteriol 1997; 179:4635-8. [PMID: 9226278 PMCID: PMC179304 DOI: 10.1128/jb.179.14.4635-4638.1997] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Three copies of the IS21-related transposable element IS1415 were identified in Rhodococcus erythropolis NI86/21. Adjacent to one of the IS1415 copies, a 47-bp sequence nearly identical to the conserved 5' end of integrons was found. Accurate transposition of IS1415 carrying a chloramphenicol resistance gene (Tn5561) was demonstrated following delivery from a suicide vector to R. erythropolis SQ1.
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Affiliation(s)
- I Nagy
- F.A. Janssens Laboratory of Genetics, Catholic University of Leuven, Heverlee, Belgium
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12
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Freiberg C, Fellay R, Bairoch A, Broughton WJ, Rosenthal A, Perret X. Molecular basis of symbiosis between Rhizobium and legumes. Nature 1997; 387:394-401. [PMID: 9163424 DOI: 10.1038/387394a0] [Citation(s) in RCA: 461] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Access to mineral nitrogen often limits plant growth, and so symbiotic relationships have evolved between plants and a variety of nitrogen-fixing organisms. These associations are responsible for reducing 120 million tonnes of atmospheric nitrogen to ammonia each year. In agriculture, independence from nitrogenous fertilizers expands crop production and minimizes pollution of water tables, lakes and rivers. Here we present the complete nucleotide sequence and gene complement of the plasmid from Rhizobium sp. NGR234 that endows the bacterium with the ability to associate symbiotically with leguminous plants. In conjunction with transcriptional analyses, these data demonstrate the presence of new symbiotic loci and signalling mechanisms. The sequence and organization of genes involved in replication and conjugal transfer are similar to those of Agrobacterium, suggesting a recent lateral transfer of genetic information.
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Affiliation(s)
- C Freiberg
- Institut für Molekulare Biotechnologie, Abteilung Genomanalyse, Jena, Germany
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