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Current Progress in Nitrogen Fixing Plants and Microbiome Research. PLANTS 2020; 9:plants9010097. [PMID: 31940996 PMCID: PMC7020401 DOI: 10.3390/plants9010097] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/02/2020] [Accepted: 01/08/2020] [Indexed: 01/10/2023]
Abstract
In agroecosystems, nitrogen is one of the major nutrients limiting plant growth. To meet the increased nitrogen demand in agriculture, synthetic fertilizers have been used extensively in the latter part of the twentieth century, which have led to environmental challenges such as nitrate pollution. Biological nitrogen fixation (BNF) in plants is an essential mechanism for sustainable agricultural production and healthy ecosystem functioning. BNF by legumes and associative, endosymbiotic, and endophytic nitrogen fixation in non-legumes play major roles in reducing the use of synthetic nitrogen fertilizer in agriculture, increased plant nutrient content, and soil health reclamation. This review discusses the process of nitrogen-fixation in plants, nodule formation, the genes involved in plant-rhizobia interaction, and nitrogen-fixing legume and non-legume plants. This review also elaborates on current research efforts involved in transferring nitrogen-fixing mechanisms from legumes to non-legumes, especially to economically important crops such as rice, maize, and wheat at the molecular level and relevant other techniques involving the manipulation of soil microbiome for plant benefits in the non-legume root environment.
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Geddes BA, Paramasivan P, Joffrin A, Thompson AL, Christensen K, Jorrin B, Brett P, Conway SJ, Oldroyd GED, Poole PS. Engineering transkingdom signalling in plants to control gene expression in rhizosphere bacteria. Nat Commun 2019; 10:3430. [PMID: 31366919 PMCID: PMC6668481 DOI: 10.1038/s41467-019-10882-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 06/07/2019] [Indexed: 01/10/2023] Open
Abstract
The root microbiota is critical for agricultural yield, with growth-promoting bacteria able to solubilise phosphate, produce plant growth hormones, antagonise pathogens and fix N2. Plants control the microorganisms in their immediate environment and this is at least in part through direct selection, the immune system, and interactions with other microorganisms. Considering the importance of the root microbiota for crop yields it is attractive to artificially regulate this environment to optimise agricultural productivity. Towards this aim we express a synthetic pathway for the production of the rhizopine scyllo-inosamine in plants. We demonstrate the production of this bacterial derived signal in both Medicago truncatula and barley and show its perception by rhizosphere bacteria, containing bioluminescent and fluorescent biosensors. This study lays the groundwork for synthetic signalling networks between plants and bacteria, allowing the targeted regulation of bacterial gene expression in the rhizosphere for delivery of useful functions to plants. The root microbiota is critical for promoting crop yield. Here, the authors create a synthetic pathway for the production of the rhizopine scyllo-inosamine in Medicago truncatula and barley, and show its perception by rhizosphere bacteria for targeted regulation of bacterial gene expression.
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Affiliation(s)
- Barney A Geddes
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Ponraj Paramasivan
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
| | - Amelie Joffrin
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Amber L Thompson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Kirsten Christensen
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Beatriz Jorrin
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Paul Brett
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Stuart J Conway
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Giles E D Oldroyd
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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Andreani NA, Carraro L, Zhang L, Vos M, Cardazzo B. Transposon mutagenesis in Pseudomonas fluorescens reveals genes involved in blue pigment production and antioxidant protection. Food Microbiol 2019; 82:497-503. [PMID: 31027811 DOI: 10.1016/j.fm.2019.03.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/29/2019] [Accepted: 03/30/2019] [Indexed: 12/18/2022]
Abstract
Pseudomonas fluorescens Ps_77 is a blue-pigmenting strain able to cause food product discoloration, causing relevant economic losses especially in the dairy industry. Unlike non-pigmenting P. fluorescens, blue pigmenting strains previously were shown to carry a genomic region that includes homologs of trpABCDF genes, pointing at a possible role of the tryptophan biosynthetic pathway in production of the pigment. Here, we employ random mutagenesis to first identify the genes involved in blue-pigment production in P. fluorescens Ps_77 and second to investigate the biological function of the blue pigment. Genetic analyses based on the mapping of the random insertions allowed the identification of eight genes involved in pigment production, including the second copy of trpB (trpB_1) gene. Phenotypic characterization of Ps_77 white mutants demonstrated that the blue pigment increases oxidative-stress resistance. Indeed, while Ps_77 was growing at a normal rate in presence of 5 mM of H2O2, white mutants were completely inhibited. The antioxidative protection is not available for non-producing bacteria in co-culture with Ps_77.
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Affiliation(s)
- Nadia Andrea Andreani
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 16, Legnaro, 35020, Padova, Italy; European Centre for Environment and Human Health University of Exeter ESI Building, Penryn Campus, TR109FE, Penryn, UK
| | - Lisa Carraro
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 16, Legnaro, 35020, Padova, Italy
| | - Lihong Zhang
- European Centre for Environment and Human Health University of Exeter ESI Building, Penryn Campus, TR109FE, Penryn, UK
| | - Michiel Vos
- European Centre for Environment and Human Health University of Exeter ESI Building, Penryn Campus, TR109FE, Penryn, UK
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 16, Legnaro, 35020, Padova, Italy.
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Schneiker-Bekel S, Wibberg D, Bekel T, Blom J, Linke B, Neuweger H, Stiens M, Vorhölter FJ, Weidner S, Goesmann A, Pühler A, Schlüter A. The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome. J Biotechnol 2011; 155:20-33. [DOI: 10.1016/j.jbiotec.2010.12.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 11/25/2010] [Accepted: 12/08/2010] [Indexed: 10/18/2022]
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Schoffers E, Gurung SR, Kohler PR, Rossbach S. Chemical synthesis of scyllo-inosamine and catabolism studies in Sinorhizobium meliloti. Bioorg Med Chem 2008; 16:7838-42. [DOI: 10.1016/j.bmc.2008.06.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 06/14/2008] [Accepted: 06/20/2008] [Indexed: 11/26/2022]
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Phenix CP, Nienaber K, Tam PH, Delbaere LTJ, Palmer DRJ. Structural, Functional and Calorimetric Investigation of MosA, a Dihydrodipicolinate Synthase fromSinorhizobium melilotiL5–30, does not Support Involvement in Rhizopine Biosynthesis. Chembiochem 2008; 9:1591-602. [DOI: 10.1002/cbic.200700569] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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Ferrières L, Francez-Charlot A, Gouzy J, Rouillé S, Kahn D. FixJ-regulated genes evolved through promoter duplication in Sinorhizobium meliloti. Microbiology (Reading) 2004; 150:2335-2345. [PMID: 15256575 DOI: 10.1099/mic.0.27081-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The FixLJ two-component system ofSinorhizobium melilotiis a global regulator, turning on nitrogen-fixation genes in microaerobiosis. Up to now,nifAandfixKwere the only genes known to be directly regulated by FixJ. We used a genomic SELEX approach in order to isolate new FixJ targets in the genome. This led to the identification of 22 FixJ binding sites, including the known sites in thefixK1andfixK2promoters. FixJ binding sites are unevenly distributed among the three replicons constituting theS. melilotigenome: a majority are carried either by pSymA or by a short chromosomal region of non-chromosomal origin. Thus FixJ binding sites appear to be preferentially associated with the pSymA replicon, which carries thefixJgene. Functional analysis of FixJ targets led to the discovery of two new FixJ-regulated genes,smc03253andproB2. This FixJ-dependent regulation appears to be mediated by a duplication of the wholefixKpromoter region, including the beginning of thefixKgene. Similar duplications were previously reported for thenifHpromoter. By systematic comparison of all promoter regions we found 17 such duplications throughout the genome, indicating that promoter duplication is a common mechanism for the evolution of regulatory pathways inS. meliloti.
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Affiliation(s)
- Lionel Ferrières
- Laboratoire des Interactions Plantes-Microorganismes, UMR 2594 INRA-CNRS, Chemin de Borde-Rouge, BP 27, 31326 Castanet-Tolosan Cedex, France
| | - Anne Francez-Charlot
- Laboratoire des Interactions Plantes-Microorganismes, UMR 2594 INRA-CNRS, Chemin de Borde-Rouge, BP 27, 31326 Castanet-Tolosan Cedex, France
| | - Jérôme Gouzy
- Laboratoire des Interactions Plantes-Microorganismes, UMR 2594 INRA-CNRS, Chemin de Borde-Rouge, BP 27, 31326 Castanet-Tolosan Cedex, France
| | - Stéphane Rouillé
- Laboratoire des Interactions Plantes-Microorganismes, UMR 2594 INRA-CNRS, Chemin de Borde-Rouge, BP 27, 31326 Castanet-Tolosan Cedex, France
| | - Daniel Kahn
- Laboratoire des Interactions Plantes-Microorganismes, UMR 2594 INRA-CNRS, Chemin de Borde-Rouge, BP 27, 31326 Castanet-Tolosan Cedex, France
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8
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Lestrate P, Dricot A, Delrue RM, Lambert C, Martinelli V, De Bolle X, Letesson JJ, Tibor A. Attenuated signature-tagged mutagenesis mutants of Brucella melitensis identified during the acute phase of infection in mice. Infect Immun 2004; 71:7053-60. [PMID: 14638795 PMCID: PMC308902 DOI: 10.1128/iai.71.12.7053-7060.2003] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For this study, we screened 1,152 signature-tagged mutagenesis mutants of Brucella melitensis 16M in a mouse model of infection and found 36 of them to be attenuated in vivo. Molecular characterization of transposon insertion sites showed that for four mutants, the affected genes were only present in Rhizobiaceae. Another mutant contained a disruption in a gene homologous to mosA, which is involved in rhizopine biosynthesis in some strains of Rhizobium, suggesting that this sugar may be involved in Brucella pathogenicity. A mutant was disrupted in a gene homologous to fliF, a gene potentially coding for the MS ring, a basal component of the flagellar system. Surprisingly, a mutant was affected in the rpoA gene, coding for the essential alpha-subunit of the RNA polymerase. This disruption leaves a partially functional protein, impaired for the activation of virB transcription, as demonstrated by the absence of induction of the virB promoter in the Tn5::rpoA background. The results presented here highlight the fact that the ability of Brucella to induce pathogenesis shares similarities with the molecular mechanisms used by both Rhizobium and Agrobacterium to colonize their hosts.
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Affiliation(s)
- P Lestrate
- Unité de Recherche en Biologie Moléculaire (URBM), Laboratoire d'Immunologie et de Microbiologie, University of Namur, 5000 Namur, Belgium
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9
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Letesson JJ, Lestrate P, Delrue RM, Danese I, Bellefontaine F, Fretin D, Taminiau B, Tibor A, Dricot A, Deschamps C, Haine V, Leonard S, Laurent T, Mertens P, Vandenhaute J, De Bolle X. Fun stories about Brucella: the "furtive nasty bug". Vet Microbiol 2002; 90:317-28. [PMID: 12414152 DOI: 10.1016/s0378-1135(02)00208-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Although Brucella is responsible for one of the major worldwide zoonosis, our understanding of its pathogenesis remains in its infancy. In this paper, we summarize some of the research in progress in our laboratory that we think could contribute to a better understanding of the Brucella molecular virulence mechanisms and their regulation.
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Affiliation(s)
- J-J Letesson
- Laboratoire d'Immunologie et de Microbiologie, Unité de Recherche en Biologie Moleculaire, Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles 61, B-5000 Namur, Belgium.
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Savka MA, Dessaux Y, Oger P, Rossbach S. Engineering bacterial competitiveness and persistence in the phytosphere. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2002; 15:866-874. [PMID: 12236593 DOI: 10.1094/mpmi.2002.15.9.866] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Several tactics exist to improve the survival of an introduced microorganism of interest in the plant environment. One, derived from studies on the Agrobacterium-plant interaction and the role of opines in this interaction, proposes to promote growth of the inoculant in the plant environment via the establishment of a bias in the rhizosphere. It is supported by the occurrence of natural biases, such as those generated by opine-like molecules, by calestegins, or by mimosine. Opine-mediated biases have allowed several investigators to favor the growth of opine-degrading bacteria or communities under sterile or axenic environments or in microcosms mimicking near field conditions. Another way to favor a given microbe consists in impeding growth of competing microorganisms. Experiments performed using detergent or bacteriostatic agents as amendments under field or near field conditions yielded promising results. Research perspectives for engineering plant-microbe interactions also include specific engineering of predation and strategies designed to interfere with some of the signals perceived by the microbes, provided these signals control the expression of functions central to microbial fitness. In this respect, quorum-sensing signal molecules, such as N-acyl-homoserine lactones, may be valuable targets for the development of biocontrol agents and procedures.
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Affiliation(s)
- Michael A Savka
- Department of Biological Sciences, Rochester Institute of Technology, NY 14623, USA
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11
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Bell KS, Avrova AO, Holeva MC, Cardle L, Morris W, De Jong W, Toth IK, Waugh R, Bryan GJ, Birch PRJ. Sample sequencing of a selected region of the genome of Erwinia carotovora subsp. atroseptica reveals candidate phytopathogenicity genes and allows comparison with Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2002; 148:1367-1378. [PMID: 11988510 DOI: 10.1099/00221287-148-5-1367] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Genome sequencing is making a profound impact on microbiology. Currently, however, only one plant pathogen genome sequence is publicly available and no genome-sequencing project has been initiated for any species of the genus Erwinia, which includes several important plant pathogens. This paper describes a targeted sample sequencing approach to study the genome of Erwinia carotovora subsp. atroseptica (Eca), a major soft-rot pathogen of potato. A large insert DNA (approx. 115 kb) library of Eca was constructed using a bacterial artificial chromosome (BAC) vector. Hybridization and end-sequence data revealed two overlapping BAC clones that span an entire hrp gene cluster. Random subcloning and one-fold sequence coverage (>200 kb) across these BACs identified 25 (89%) of 28 hrp genes predicted from the orthologous hrp cluster of Erwinia amylovora. Regions flanking the hrp cluster contained orthologues of known or putative pathogenicity operons from other Erwinia species, including dspEF (E. amylovora), hecAB and pecSM (E. chrysanthemi), sequences similar to genes from the plant pathogen Xylella fastidiosa, including haemagglutinin-like genes, and sequences similar to genes involved in rhizobacterium-plant interactions. Approximately 10% of the sequences showed strongest nucleotide similarities to genes in the closely related model bacterium and animal pathogen Escherichia coli. However, the positions of some of these genes were different in the two genomes. Approximately 30% of sequences showed no significant similarity to any database entries. A physical map was made across the genomic region spanning the hrp cluster by hybridization to the BAC library and to digested BAC clones, and by PCR between sequence contigs. A multiple genome coverage BAC library and one-fold sample sequencing are an effective combination for extracting useful information from important regions of the Eca genome, providing a wealth of candidate novel pathogenicity genes for functional analyses. Other genomic regions could be similarly targeted.
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Affiliation(s)
- Kenneth S Bell
- Unit of Mycology, Bacteriology and Nematology1 and Unit of Genomics2, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Anna O Avrova
- Unit of Mycology, Bacteriology and Nematology1 and Unit of Genomics2, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Maria C Holeva
- Unit of Mycology, Bacteriology and Nematology1 and Unit of Genomics2, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Linda Cardle
- Unit of Mycology, Bacteriology and Nematology1 and Unit of Genomics2, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Wayne Morris
- Unit of Mycology, Bacteriology and Nematology1 and Unit of Genomics2, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Walter De Jong
- Unit of Mycology, Bacteriology and Nematology1 and Unit of Genomics2, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Ian K Toth
- Unit of Mycology, Bacteriology and Nematology1 and Unit of Genomics2, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Robbie Waugh
- Unit of Mycology, Bacteriology and Nematology1 and Unit of Genomics2, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Glenn J Bryan
- Unit of Mycology, Bacteriology and Nematology1 and Unit of Genomics2, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Paul R J Birch
- Unit of Mycology, Bacteriology and Nematology1 and Unit of Genomics2, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
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12
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Fry J, Wood M, Poole PS. Investigation of myo-inositol catabolism in Rhizobium leguminosarum bv. viciae and its effect on nodulation competitiveness. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2001; 14:1016-25. [PMID: 11497462 DOI: 10.1094/mpmi.2001.14.8.1016] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Three discrete loci required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae have been characterized. Two of these are catabolic loci that code for malonate semialdehyde dehydrogenase (iolA) and malonate semialdehyde dehydrogenase (iolD). IolD is part of a possible operon, iolDEB, although the functions of IolE and IolB are unknown. The third locus, int, codes for an ABC transport system that is highly specific for myo-inositol. LacZ analysis showed that mutation of iolD, which codes for one of the last steps in the catabolic pathway, prevents increased transcription of the entire pathway. It is likely that the pathway is induced by an end product of catabolism rather than myo-inositol itself. Mutants in any of the loci nodulated peas (Pisum sativum) and vetch (Vicia sativa) at the same rate as the wild type. Acetylene reduction rates and plant dry weights also were the same in the mutants and wild type, indicating no defects in nitrogen fixation. When wild-type 3841 was coinoculated onto vetch plants with either catabolic mutant iolD (RU360) or iolA (RU361), however, >95% of the nodules were solely infected with the wild type. The competitive advantage of the wild type was unaffected, even when the mutants were at 100-fold excess. The myo-inositol transport mutant (RU1487), which grows slowly on myo-inositol, was only slightly less competitive than the wild type. The nodulation advantage of the wild type was not the result of superior growth in the rhizosphere. Instead, it appears that the wild type may displace the mutants early on in the infection and nodulation process, suggesting an important role for myo-inositol catabolism.
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Affiliation(s)
- J Fry
- School of Animal and Microbial Sciences and Department of Soil Science, University of Reading, UK
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Bahar M, de Majnik J, Wexler M, Fry J, Poole PS, Murphy PJ. A model for the catabolism of rhizopine in Rhizobium leguminosarum involves a ferredoxin oxygenase complex and the inositol degradative pathway. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 1998; 11:1057-1068. [PMID: 9805393 DOI: 10.1094/mpmi.1998.11.11.1057] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Rhizopines are nodule-specific compounds that confer an intraspecies competitive nodulation advantage to strains that can catabolize them. The rhizopine (3-O-methyl-scyllo-inosamine, 3-O-MSI) catabolic moc gene cluster mocCABRDE(F) in Rhizobium leguminosarum bv. viciae strain 1a is located on the Sym plasmid. MocCABR are homologous to the mocCABR gene products from Sinorhizobium meliloti. MocD and MocE contain motifs corresponding to a TOL-like oxygenase and a [2Fe-2S] Rieske-like ferredoxin, respectively. The mocF gene encodes a ferredoxin reductase that would complete the oxygenase system, but is not essential for rhizopine catabolism. We propose a rhizopine catabolic model whereby MocB transports rhizopine into the cell and MocDE and MocF (or a similar protein elsewhere in the genome), under the regulation of MocR, act in concert to form a ferredoxin oxygenase system that demethylates 3-O-MSI to form scyllo-inosamine (SI). MocA, an NAD(H)-dependent dehydrogenase, and MocC continue the catabolic process. Compounds formed then enter the inositol catabolic pathway.
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Affiliation(s)
- M Bahar
- Department of Crop Protection, University of Adelaide, Australia
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14
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Galbraith MP, Feng SF, Borneman J, Triplett EW, de Bruijn FJ, Rossbachl S. A functional myo-inositol catabolism pathway is essential for rhizopine utilization by Sinorhizobium meliloti. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 10):2915-2924. [PMID: 9802033 DOI: 10.1099/00221287-144-10-2915] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Rhizopine (L-3-O-methyl-scyllo-inosamine) is a symbiosis-specific compound found in alfalfa nodules induced by specific Sinorhizobium meliloti strains. It has been postulated that rhizobial strains able to synthesize and catabolize rhizopine gain a competitive advantage in the rhizosphere. The pathway of rhizopine degradation is analysed here. Since rhizopine is an inositol derivative, it was tested whether inositol catabolism is involved in rhizopine utilization. A genetic locus required for the catabolism of inositol as sole carbon source was cloned from S. meliloti. This locus was delimited by transposon Tn5 mutagenesis and its DNA sequence was determined. Based on DNA similarity studies and enzyme assays, this genetic region was shown to encode an S. meliloti myo-inositol dehydrogenase. Strains that harboured a mutation in the myo-inositol dehydrogenase gene (idhA) did not display myo-inositol dehydrogenase activity, were unable to utilize myo-inositol as sole carbon/energy source, and were unable to catabolize rhizopine. Thus, myo-inositol dehydrogenase activity is essential for rhizopine utilization in S. meliloti.
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Affiliation(s)
- Mark P Galbraith
- Department of Biological Sciences, Western, Michigan UniversityKalamazoo, MI 49008USA
| | - Szi Fei Feng
- Department of Biological Sciences, Western, Michigan UniversityKalamazoo, MI 49008USA
| | - James Borneman
- Department of Agronomy and Center for the Study of Nitrogen Fixation, University of Wisconsin- MadisonMadison, WI 53706USA
| | - Eric W Triplett
- Department of Agronomy and Center for the Study of Nitrogen Fixation, University of Wisconsin- MadisonMadison, WI 53706USA
| | - Frans J de Bruijn
- MSU-DOE Plant Research Laboratory, Department of Microbiology, NSF Center for Microbial Ecology, Michigan State UniversityEast Lansing, MI 48824USA
| | - Silvia Rossbachl
- Department of Biological Sciences, Western, Michigan UniversityKalamazoo, MI 49008USA
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Blickling S, Beisel HG, Bozic D, Knäblein J, Laber B, Huber R. Structure of dihydrodipicolinate synthase of Nicotiana sylvestris reveals novel quaternary structure. J Mol Biol 1997; 274:608-21. [PMID: 9417939 DOI: 10.1006/jmbi.1997.1393] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DHDPS is the first enzyme unique to the lysine biosynthetic pathway in plants and bacteria and catalyses the formation of (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid. It is feedback-regulated in plants by L-lysine. The crystal structure of Nicotiana sylvestris DHDPS with and without inhibitory lysine bound to the enzyme has been solved to a resolution of 2.8 A. The molecule is a homotetramer composed of a dimer of dimers. Comparison with the structure of Escherichia coli DHDPS showed a novel quaternary structure by a profound rearrangement of the dimers forming the tetramer. The crystal structure of the enzyme in the presence of L-lysine revealed substantial changes. These changes together with the novel quaternary structure provide a structural basis for the strong inhibition of plant DHDPS enzymes by L-lysine.
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Affiliation(s)
- S Blickling
- Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Martinsried, Germany
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Babbitt PC, Gerlt JA. Understanding enzyme superfamilies. Chemistry As the fundamental determinant in the evolution of new catalytic activities. J Biol Chem 1997; 272:30591-4. [PMID: 9388188 DOI: 10.1074/jbc.272.49.30591] [Citation(s) in RCA: 205] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- P C Babbitt
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143-0466, USA
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17
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Piepersberg W. Molecular Biology, Biochemistry and Fermentation of Aminoglycoside Antibiotics. DRUGS AND THE PHARMACEUTICAL SCIENCES 1997. [DOI: 10.1201/b14856-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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18
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Lawrence MC, Barbosa JA, Smith BJ, Hall NE, Pilling PA, Ooi HC, Marcuccio SM. Structure and mechanism of a sub-family of enzymes related to N-acetylneuraminate lyase. J Mol Biol 1997; 266:381-99. [PMID: 9047371 DOI: 10.1006/jmbi.1996.0769] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We describe here a sub-family of enzymes related both structurally and functionally to N-acetylneuraminate lyase. Two members of this family (N-acetylneuraminate lyase and dihydrodipicolinate synthase) have known three-dimensional structures and we now proceed to show their structural and functional relationship to two further proteins, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase and D-4-deoxy-5-oxoglucarate dehydratase. These enzymes are all thought to involve intermediate Schiff-base formation with their respective substrates. In order to understand the nature of this intermediate, we have determined the three-dimensional structure of N-acetylneuraminate lyase in complex with hydroxypyruvate (a product analogue) and in complex with one of its products (pyruvate). From these structures we deduce the presence of a closely similar Schiff-base forming motif in all members of the N-acetylneuraminate lyase sub-family. A fifth protein, MosA, is also confirmed to be a member of the sub-family although the involvement of an intermediate Schiff-base in its proposed reaction is unclear.
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Affiliation(s)
- M C Lawrence
- Biomolecular Research Institute, Parkville, Victoria, Australia
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19
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Simon HM, Homer MJ, Roberts GP. Perturbation of nifT expression in Klebsiella pneumoniae has limited effect on nitrogen fixation. J Bacteriol 1996; 178:2975-7. [PMID: 8631690 PMCID: PMC178037 DOI: 10.1128/jb.178.10.2975-2977.1996] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In the nitrogenase system of Klebsiella pneumoniae, nifT is located between nifDK, the structural genes for dinitrogenase, and nifY, whose product is involved in nitrogenase maturation. It is, therefore, a reasonable hypothesis that the NifT protein might also have a role in the maturation of nitrogenase. However, the phenotypic characterization of nifT and nifT-overexpressing strains for effects on the regulation, maturation, and activity of nitrogenase identified no properties that were distinct from those of the wild type. We conclude that the K. pneumoniae NifT protein is not essential for nitrogen fixation under the conditions examined.
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Affiliation(s)
- H M Simon
- Department of Bacteriology, University of Wisconsin-Madison 53706, USA
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20
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Peschke U, Schmidt H, Zhang HZ, Piepersberg W. Molecular characterization of the lincomycin-production gene cluster of Streptomyces lincolnensis 78-11. Mol Microbiol 1995; 16:1137-56. [PMID: 8577249 DOI: 10.1111/j.1365-2958.1995.tb02338.x] [Citation(s) in RCA: 177] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The lincomycin (LM)-production gene cluster of the overproducing strain Streptomyces lincolnensis 78-11 was cloned, analysed by hybridization, as well as by DNA sequencing, and compared with the respective genome segments of other lincomycin producers. The lmb/lmr gene cluster is composed of 27 open reading frames with putative biosynthetic or regulatory functions (lmb genes) and three resistance (lmr) genes, two of which, lmrA and lmrC, flank the cluster. A very similar overall organization of the lmb/lmr cluster seems to be conserved in four other LM producers, although the clusters are embedded in non-homologous genomic surroundings. In the wild-type strain (S. lincolnensis NRRL2936), the lmb/lmr-cluster apparently is present only in single copy. However, in the industrial strain S. lincolnensis 78-11 the non-adjacent gene clusters for the production of LM and melanin (melC) both are duplicated on a large (0.45-0.5 Mb) fragment, accompanied by deletion events. This indicates that enhanced gene dosage is one of the factors for the overproduction of LM and demonstrates that large-scale genome rearrangements can be a result of classical strain improvement by mutagenesis. Only a minority of the putative Lmb proteins belong to known protein families. These include members of the gamma-glutamyl transferases (LmbA), amino acid acylases (LmbC), aromatic amino acid aminotransferases (LmbF), imidazoleglycerolphosphate dehydratases (LmbK), dTDP-glucose synthases (LmbO), dTDP-glucose 4,6-dehydratases (LmbM) and (NDP-) ketohexose (or ketocyclitol) aminotransferases (LmbS). In contrast to earlier proposals on the biosynthetic pathway of the C-8 sugar moiety (methylthiolincosaminide), this branch of the LM pathway actually seems to be based on nucleotide-activated sugars as precursors.
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Affiliation(s)
- U Peschke
- Bergische Universität GH Wuppertal, Germany
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Affiliation(s)
- W Piepersberg
- Fachbereich Mikrobiologie, Bergische Universität-GH Wuppertal, Germany
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Rossbach S, Kulpa DA, Rossbach U, de Bruijn FJ. Molecular and genetic characterization of the rhizopine catabolism (mocABRC) genes of Rhizobium meliloti L5-30. MOLECULAR & GENERAL GENETICS : MGG 1994; 245:11-24. [PMID: 7845353 DOI: 10.1007/bf00279746] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Rhizopine (L-3-O-methyl-scyllo-inosamine, 3-O-MSI) is a symbiosis-specific compound, which is synthesized in nitrogen-fixing nodules of Medicago sativa induced by Rhizobium meliloti strain L5-30. 3-O-MSI is thought to function as an unusual growth substrate for R. meliloti L5-30, which carries a locus (mos) responsible for its synthesis closely linked to a locus (moc) responsible for its degradation. Here, the essential moc genes were delimited by Tn5 mutagenesis and shown to be organized into two regions, separated by 3 kb of DNA. The DNA sequence of a 9-kb fragment spanning the two moc regions was determined, and four genes were identified that play an essential role in rhizopine catabolism (mocABC and mocR). The analysis of the DNA sequence and the amino acid sequence of the deduced protein products revealed that MocA resembles NADH-dependent dehydrogenases. MocB exhibits characteristic features of periplasmic-binding proteins that are components of high-affinity transport systems. MocC does not share significant homology with any protein in the database. MocR shows homology with the GntR class of bacterial regulator proteins. These results suggest that the mocABC genes are involved in the uptake and subsequent degradation of rhizopine, whereas mocR is likely to play a regulatory role.
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Affiliation(s)
- S Rossbach
- NSF Center for Microbial Ecology, Michigan State University, East Lansing 48824
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23
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Abstract
This review presents a comparison between the complex genetic regulatory networks that control nitrogen fixation in three representative rhizobial species, Rhizobium meliloti, Bradyrhizobium japonicum, and Azorhizobium caulinodans. Transcription of nitrogen fixation genes (nif and fix genes) in these bacteria is induced primarily by low-oxygen conditions. Low-oxygen sensing and transmission of this signal to the level of nif and fix gene expression involve at least five regulatory proteins, FixL, FixJ, FixK, NifA, and RpoN (sigma 54). The characteristic features of these proteins and their functions within species-specific regulatory pathways are described. Oxygen interferes with the activities of two transcriptional activators, FixJ and NifA. FixJ activity is modulated via phosphorylation-dephosphorylation by the cognate sensor hemoprotein FixL. In addition to the oxygen responsiveness of the NifA protein, synthesis of NifA is oxygen regulated at the level of transcription. This type of control includes FixLJ in R. meliloti and FixLJ-FixK in A. caulinodans or is brought about by autoregulation in B. japonicum. NifA, in concert with sigma 54 RNA polymerase, activates transcription from -24/-12-type promoters associated with nif and fix genes and additional genes that are not directly involved in nitrogen fixation. The FixK proteins constitute a subgroup of the Crp-Fnr family of bacterial regulators. Although the involvement of FixLJ and FixK in nifA regulation is remarkably different in the three rhizobial species discussed here, they constitute a regulatory cascade that uniformly controls the expression of genes (fixNOQP) encoding a distinct cytochrome oxidase complex probably required for bacterial respiration under low-oxygen conditions. In B. japonicum, the FixLJ-FixK cascade also controls genes for nitrate respiration and for one of two sigma 54 proteins.
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Affiliation(s)
- H M Fischer
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland
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Izard T, Lawrence MC, Malby RL, Lilley GG, Colman PM. The three-dimensional structure of N-acetylneuraminate lyase from Escherichia coli. Structure 1994; 2:361-9. [PMID: 8081752 DOI: 10.1016/s0969-2126(00)00038-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND N-acetylneuraminate lyase catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetyl-D-mannosamine. The enzyme plays an important role in the regulation of sialic acid metabolism in bacteria. The reverse reaction can be exploited for the synthesis of sialic acid and some of its derivatives. RESULTS The structure of the enzyme from Escherichia coli has been determined to 2.2 A resolution by X-ray crystallography. The enzyme is shown to be a tetramer, in which each subunit consists of an alpha/beta-barrel domain followed by a carboxy-terminal extension of three alpha-helices. CONCLUSIONS The active site of the enzyme is tentatively identified as a pocket at the carboxy-terminal end of the eight-stranded beta-barrel. Lys165 lies within this pocket and is probably the reactive residue which forms a Schiff base intermediate with the substrate. The sequence of N-acetylneuraminate lyase has similarities to those of dihydrodipicolinate synthase and MosA (an enzyme implicated in rhizopine synthesis) suggesting that these last two enzymes share a similar structure to N-acetylneuraminate lyase.
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Affiliation(s)
- T Izard
- Biomolecular Research Institute, Parkville, Australia
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Abstract
Rhizobia are gram-negative bacteria with two distinct habitats: the soil rhizosphere in which they have a saprophytic and, usually, aerobic life and a plant ecological niche, the legume nodule, which constitutes a microoxic environment compatible with the operation of the nitrogen reducing enzyme nitrogenase. The purpose of this review is to summarize the present knowledge of the changes induced in these bacteria when shifting to a microoxic environment. Oxygen concentration regulates the expression of two major metabolic pathways: energy conservation by respiratory chains and nitrogen fixation. After reviewing the genetic data on these metabolic pathways and their response to oxygen we will put special emphasis on the regulatory molecules which are involved in the control of gene expression. We will show that, although homologous regulatory molecules allow response to oxygen in different species, they are assembled in various combinations resulting in a variable regulatory coupling between genes for microaerobic respiration and nitrogen fixation genes. The significance of coordinated regulation of genes not essential for nitrogen fixation with nitrogen fixation genes will also be discussed.
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Affiliation(s)
- J Batut
- Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, CNRS INRA, Castanet-Tolosan, France
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Abstract
Actinomycetes represent the microbial group richest in production of variable secondary metabolites. These mostly bioactive molecules are the end products of complex multistep biosynthetic pathways. Recent progress in the molecular genetics and biochemistry of the biosynthetic capacities of actinomycetes enables first attempts to redesign these pathways in a directed fashion. However, in contrast to several examples of designed biochemical improvement of primary metabolic processes in microorganisms, none of the products or strains derived from pathway engineering in actinomycetes discussed herein have reached pilot or production scale. The main reasons for this slow progress are the complicated pathways themselves, their complex regulation during the actinomycete cell cycle, and their uniqueness, as most pathways and products are specific for a strain rather than for a given species or larger taxonomic group. However, the modular use of a minimum of very similar enzymes and their conversion of similar intermediates to form the building blocks for the production of a maximum of divergent end products gives hope for the future application of these genetic models for the redesign of complex pathways for modified or new natural products. Several strategies that can be followed to reach this aim are discussed, mainly for the variable 6-deoxyhexose metabolism as an ubiquitously applicable example.
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Saint CP, Wexler M, Murphy PJ, Tempé J, Tate ME, Murphy PJ. Characterization of genes for synthesis and catabolism of a new rhizopine induced in nodules by Rhizobium meliloti Rm220-3: extension of the rhizopine concept. J Bacteriol 1993; 175:5205-15. [PMID: 8349560 PMCID: PMC204988 DOI: 10.1128/jb.175.16.5205-5215.1993] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Rhizopines are selective growth substrates synthesized in nodules only by strains of rhizobia capable of their catabolism. We report the isolation and study of genes for the synthesis and catabolism of a new rhizopine, scyllo-inosamine (sIa), from alfalfa nodules induced by Rhizobium meliloti Rm220-3. This compound is similar in structure to the previously described rhizopine 3-O-methyl-scyllo-inosamine from R. meliloti L5-30 (P.J. Murphy, N. Heycke, Z. Banfalvi, M.E. Tate, F.J. de Bruijn, A. Kondorosi, J. Tempé, and J. Schell, Proc. Natl. Acad. Sci. USA 84:493-497, 1987). The synthesis (mos) and catabolism (moc) genes for the Rm220-3 rhizopine are closely linked and located on the nod-nif Sym plasmid. The mos genes are directly controlled by the NifA/NtrA regulatory system. A comparison of the sequence of the 5' regions of the two mos loci shows very extensive conservation of sequence as well as strong homology to the nifH coding region. Restriction mapping and hybridization to DNA from the four open reading frames (ORFs) of the L5-30 mos locus indicate the absence of mosA and presence of the other three ORFs (ORF1 and mosB and -C) in Rm220-3. We suggest that the L5-30 mosA gene product is involved in the conversion of scyllo-inosamine to 3-O-methyl-scyllo-inosamine. Restriction fragment length polymorphism analysis of the moc regions of both strains shows that they are very similar. Regulation studies indicate that the moc region is not controlled by the common regulatory gene nifA, ntrA, and ntrC. We discuss the striking similarities in gene structure, location, and regulation between these two rhizopine loci in relation to the rhizopine concept.
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Affiliation(s)
- C P Saint
- Department of Crop Protection, Waite Institute, University of Adelaide, Glen Osmond, Australia
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