501
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Swift S, Downie JA, Whitehead NA, Barnard AM, Salmond GP, Williams P. Quorum sensing as a population-density-dependent determinant of bacterial physiology. Adv Microb Physiol 2002; 45:199-270. [PMID: 11450110 DOI: 10.1016/s0065-2911(01)45005-3] [Citation(s) in RCA: 211] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The discovery that bacterial cells can communicate with each other has led to the realization that bacteria are capable of exhibiting much more complex patterns of co-operative behaviour than would be expected for simple unicellular microorganisms. Now generically termed 'quorum sensing', bacterial cell-to-cell communication enables a bacterial population to mount a unified response that is advantageous to its survival by improving access to complex nutrients or environmental niches, collective defence against other competitive microorganisms or eukaryotic host defence mechanisms and optimization of population survival by differentiation into morphological forms better adapted to combating environmental threats. The principle of quorum sensing encompasses the production and release of signal molecules by bacterial cells within a population. Such molecules are released into the environment and, as cell numbers increase, so does the extracellular level of signal molecule, until the bacteria sense that a threshold has been reached and gene activation, or in some cases depression or repression, occurs via the activity of sensor-regulator systems. In this review, we will describe the biochemistry and molecular biology of a number of well-characterized N-acylhomoserine lactone quorum sensing systems to illustrate how bacteria employ cell-to-cell signalling to adjust their physiology in accordance with the prevailing high-population-density environment.
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Affiliation(s)
- S Swift
- Institute of Infections and Immunity, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2RD UK
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502
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Johnston AW, Yeoman KH, Wexler M. Metals and the rhizobial-legume symbiosis--uptake, utilization and signalling. Adv Microb Physiol 2002; 45:113-56. [PMID: 11450108 DOI: 10.1016/s0065-2911(01)45003-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this review, we consider how the nitrogen-fixing root nodule bacteria, the 'rhizobia', acquire various metals, paying particular attention to the uptake of iron. We also review the literature pertaining to the roles of molybdenum and nickel in the symbiosis with legumes. We highlight some gaps in our knowledge, for example the lack of information on how rhizobia acquire molybdenum. We examine the means whereby different metals affect rhizobial physiology and the role of metals as signals for gene regulation. We describe the ways in which genetics has shown (or not) if, and how, particular metal uptake and/or metal-mediated signalling pathways are required for the symbiotic interaction with legumes.
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Affiliation(s)
- A W Johnston
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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503
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Vierheilig H, Piché Y. Signalling in arbuscular mycorrhiza: facts and hypotheses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2002; 505:23-39. [PMID: 12083464 DOI: 10.1007/978-1-4757-5235-9_3] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Horst Vierheilig
- Centre de Recherche en Biologic Forestère, Pavillon C.- E.- Marchand, Université Laval, Québec, Canada
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504
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FALK P. Exploring the Molecular Basis of Host-Microbial Interactions in the GI Tract. Biosci Microflora 2002. [DOI: 10.12938/bifidus1996.21.83] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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505
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506
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Staehelin C, Charon C, Boller T, Crespi M, Kondorosi A. Medicago truncatula plants overexpressing the early nodulin gene enod40 exhibit accelerated mycorrhizal colonization and enhanced formation of arbuscules. Proc Natl Acad Sci U S A 2001; 98:15366-71. [PMID: 11752473 PMCID: PMC65035 DOI: 10.1073/pnas.251491698] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2000] [Accepted: 09/18/2001] [Indexed: 11/18/2022] Open
Abstract
The mutualistic symbiosis between flowering plants and arbuscular mycorrhizal fungi is extremely abundant in terrestrial ecosystems. In this symbiosis, obligately biotrophic fungi colonize the root of the host plants, which can benefit from these fungi by enhanced access to mineral nutrients in the soil, especially phosphorus. One of the main goals of research on this symbiosis is to find plant genes that control fungal development in the host plant. In this work, we show that mycorrhizal colonization is regulated by enod40, an early nodulin gene known to be involved in the nodule symbiosis of legumes with nitrogen-fixing bacteria. Medicago truncatula plants overexpressing enod40 exhibited stimulated mycorrhizal colonization in comparison with control plants. Overexpression of enod40 promoted fungal growth in the root cortex and increased the frequency of arbuscule formation. Transgenic lines with suppressed levels of enod40 transcripts, likely via a cosuppression phenomenon induced by the transgene, exhibited reduced mycorrhizal colonization. Hence, enod40 might be a plant regulatory gene involved in the control of the mycorrhizal symbiosis.
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Affiliation(s)
- C Staehelin
- Institut des Sciences du Végétal, UPR2355 Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette, France.
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507
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Chazalet V, Uehara K, Geremia RA, Breton C. Identification of essential amino acids in the Azorhizobium caulinodans fucosyltransferase NodZ. J Bacteriol 2001; 183:7067-75. [PMID: 11717264 PMCID: PMC95554 DOI: 10.1128/jb.183.24.7067-7075.2001] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nodZ gene, which is present in various rhizobial species, is involved in the addition of a fucose residue in an alpha 1-6 linkage to the reducing N-acetylglucosamine residue of lipo-chitin oligosaccharide signal molecules, the so-called Nod factors. Fucosylation of Nod factors is known to affect nodulation efficiency and host specificity. Despite a lack of overall sequence identity, NodZ proteins share conserved peptide motifs with mammalian and plant fucosyltransferases that participate in the biosynthesis of complex glycans and polysaccharides. These peptide motifs are thought to play important roles in catalysis. NodZ was expressed as an active and soluble form in Escherichia coli and was subjected to site-directed mutagenesis to investigate the role of the most conserved residues. Enzyme assays demonstrate that the replacement of the invariant Arg-182 by either alanine, lysine, or aspartate results in products with no detectable activity. A similar result is obtained with the replacement of the conserved acidic position (Asp-275) into its corresponding amide form. The residues His-183 and Asn-185 appear to fulfill functions that are more specific to the NodZ subfamily. Secondary structure predictions and threading analyses suggest the presence of a "Rossmann-type" nucleotide binding domain in the half C-terminal part of the catalytic domain of fucosyltransferases. Site-directed mutagenesis combined with theoretical approaches have shed light on the possible nucleotide donor recognition mode for NodZ and related fucosyltransferases.
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Affiliation(s)
- V Chazalet
- Centre de Recherches sur les Macromolécules Végétales and Joseph Fourier University, CNRS, Grenoble, France
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508
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Hirsch AM, Lum MR, Downie JA. What makes the rhizobia-legume symbiosis so special? PLANT PHYSIOLOGY 2001. [PMID: 11743092 DOI: 10.1104/pp.010866] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Affiliation(s)
- A M Hirsch
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095, USA.
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509
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Elbeltagy A, Nishioka K, Sato T, Suzuki H, Ye B, Hamada T, Isawa T, Mitsui H, Minamisawa K. Endophytic colonization and in planta nitrogen fixation by a Herbaspirillum sp. isolated from wild rice species. Appl Environ Microbiol 2001; 67:5285-93. [PMID: 11679357 PMCID: PMC93302 DOI: 10.1128/aem.67.11.5285-5293.2001] [Citation(s) in RCA: 200] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrogen-fixing bacteria were isolated from the stems of wild and cultivated rice on a modified Rennie medium. Based on 16S ribosomal DNA (rDNA) sequences, the diazotrophic isolates were phylogenetically close to four genera: Herbaspirillum, Ideonella, Enterobacter, and Azospirillum. Phenotypic properties and signature sequences of 16S rDNA indicated that three isolates (B65, B501, and B512) belong to the Herbaspirillum genus. To examine whether Herbaspirillum sp. strain B501 isolated from wild rice, Oryza officinalis, endophytically colonizes rice plants, the gfp gene encoding green fluorescent protein (GFP) was introduced into the bacteria. Observations by fluorescence stereomicroscopy showed that the GFP-tagged bacteria colonized shoots and seeds of aseptically grown seedlings of the original wild rice after inoculation of the seeds. Conversely, for cultivated rice Oryza sativa, no GFP fluorescence was observed for shoots and only weak signals were observed for seeds. Observations by fluorescence and electron microscopy revealed that Herbaspirillum sp. strain B501 colonized mainly intercellular spaces in the leaves of wild rice. Colony counts of surface-sterilized rice seedlings inoculated with the GFP-tagged bacteria indicated significantly more bacterial populations inside the original wild rice than in cultivated rice varieties. Moreover, after bacterial inoculation, in planta nitrogen fixation in young seedlings of wild rice, O. officinalis, was detected by the acetylene reduction and (15)N(2) gas incorporation assays. Therefore, we conclude that Herbaspirillum sp. strain B501 is a diazotrophic endophyte compatible with wild rice, particularly O. officinalis.
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Affiliation(s)
- A Elbeltagy
- Institute of Genetic Ecology, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
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510
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Parker MA, Peters NK. Rhizobitoxine production and symbiotic compatibility of Bradyrhizobium from Asian and North American lineages of amphicarpaea. Can J Microbiol 2001; 47:889-94. [PMID: 11718541 DOI: 10.1139/w01-085] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Reciprocal inoculations with Bradyrhizobium sp. isolates from the North American legume Amphicarpaea bracteata (L.) Fern. (Phaseoleae-Glycininae) and from a Japanese population of its close relative Amphicarpaea edgeworthii (Benth.) var. japonica were performed to analyze relative symbiotic compatibility. Amphicarpaea edgeworthii plants formed few or no nodules with any North American bradyrhizobial strains isolated from A. bracteata, but all A. bracteata lineages formed effective nitrogen-fixing nodules with Japanese Bradyrhizobium isolates from A. edgeworthii. However, one group of A. bracteata plants (lineage Ia) when inoculated with Japanese bradyrhizobia developed a striking leaf chlorosis similar to that known to be caused by rhizobitoxine. The beta-cystathionase inhibition assay demonstrated that significant amounts of rhizobitoxine were present in nodules formed by these Japanese bradyrhizobia. No North American bradyrhizobial isolate from A. bracteata induced chlorosis on any plants, and the beta-cystathionase assay failed to detect rhizobitoxine in nodules formed by these isolates. The role of rhizobitoxine in A. edgeworthii nodulation development was tested by inoculating plants with a Bradyrhizobium elkanii rhizobitoxine-producing strain, USDA 61, and two mutant derivatives, RX17E and RX18E, which are unable to synthesize rhizobitoxine. Amphicarpaea edgeworthii inoculated with wild-type USDA 61 developed >150 nodules per plant, while plants inoculated with RX17E and RX18E developed fewer than 10 nodules per plant. Thus, efficient nodule development in A. edgeworthii appears to be highly dependent on rhizobitoxine production by Bradyrhizobium strains.
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Affiliation(s)
- M A Parker
- Department of Biological Sciences, State University of New York, Binghamton 13902, USA.
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511
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van der Holst PP, Schlaman HR, Spaink HP. Proteins involved in the production and perception of oligosaccharides in relation to plant and animal development. Curr Opin Struct Biol 2001; 11:608-16. [PMID: 11785763 DOI: 10.1016/s0959-440x(00)00255-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Chitin oligosaccharides and their derivatives are involved in developmental and defence-related signalling pathways. Major advances include the structural identification of lectins involved in development that bind chitin oligosaccharides and the links between chitin oligosaccharide and hyaluronan synthesis. Also, recent advances in the understanding of the biological role of oligosaccharides are summarised in a model for multistep glycan recognition.
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Affiliation(s)
- P P van der Holst
- Leiden University, Institute of Molecular Plant Sciences, The Netherlands
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512
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Marie C, Broughton WJ, Deakin WJ. Rhizobium type III secretion systems: legume charmers or alarmers? CURRENT OPINION IN PLANT BIOLOGY 2001; 4:336-342. [PMID: 11418344 DOI: 10.1016/s1369-5266(00)00182-5] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Mutagenesis and sequence analyses of rhizobial genomes have revealed the presence of genes encoding type III secretion systems. Considered as a machine used by plant and animal pathogens to deliver virulence factors into their hosts, this secretion apparatus has recently been proven to play a role in symbiotic bacteria-leguminous plant interactions.
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Affiliation(s)
- C Marie
- Laboratoire de Biologie Moléculaire des Plantes Supérieures, Université de Genève, 1 ch de l'Impératrice, 1292, Chambésy-Genève, Switzerland.
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513
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Whitehead NA, Barnard AM, Slater H, Simpson NJ, Salmond GP. Quorum-sensing in Gram-negative bacteria. FEMS Microbiol Rev 2001; 25:365-404. [PMID: 11524130 DOI: 10.1111/j.1574-6976.2001.tb00583.x] [Citation(s) in RCA: 918] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
It has become increasingly and widely recognised that bacteria do not exist as solitary cells, but are colonial organisms that exploit elaborate systems of intercellular communication to facilitate their adaptation to changing environmental conditions. The languages by which bacteria communicate take the form of chemical signals, excreted from the cells, which can elicit profound physiological changes. Many types of signalling molecules, which regulate diverse phenotypes across distant genera, have been described. The most common signalling molecules found in Gram-negative bacteria are N-acyl derivatives of homoserine lactone (acyl HSLs). Modulation of the physiological processes controlled by acyl HSLs (and, indeed, many of the non-acyl HSL-mediated systems) occurs in a cell density- and growth phase-dependent manner. Therefore, the term 'quorum-sensing' has been coined to describe this ability of bacteria to monitor cell density before expressing a phenotype. In this paper, we review the current state of research concerning acyl HSL-mediated quorum-sensing. We also describe two non-acyl HSL-based systems utilised by the phytopathogens Ralstonia solanacearum and Xanthomonas campestris.
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Affiliation(s)
- N A Whitehead
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Building O, Downing Site, CB2 1QW, Cambridge, UK
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514
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Bloemberg GV, Lugtenberg BJ. Molecular basis of plant growth promotion and biocontrol by rhizobacteria. CURRENT OPINION IN PLANT BIOLOGY 2001; 4:343-50. [PMID: 11418345 DOI: 10.1016/s1369-5266(00)00183-7] [Citation(s) in RCA: 355] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Plant-growth-promoting rhizobacteria (PGPRs) are used as inoculants for biofertilization, phytostimulation and biocontrol. The interactions of PGPRs with their biotic environment, for example with plants and microorganisms, are often complex. Substantial advances in elucidating the genetic basis of the beneficial effects of PGPRs on plants have been made, some from whole-genome sequencing projects. This progress will lead to a more efficient use of these strains and possibly to their improvement by genetic modification.
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Affiliation(s)
- G V Bloemberg
- Leiden University, Institute of Molecular Plant Sciences, Wassenaarseweg 64, 2333 AL, Leiden, The Netherlands.
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515
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Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, Federspiel NA, Fisher RF, Gloux S, Godrie T, Goffeau A, Golding B, Gouzy J, Gurjal M, Hernandez-Lucas I, Hong A, Huizar L, Hyman RW, Jones T, Kahn D, Kahn ML, Kalman S, Keating DH, Kiss E, Komp C, Lelaure V, Masuy D, Palm C, Peck MC, Pohl TM, Portetelle D, Purnelle B, Ramsperger U, Surzycki R, Thebault P, Vandenbol M, Vorholter FJ, Weidner S, Wells DH, Wong K, Yeh KC, Batut J. The composite genome of the legume symbiont Sinorhizobium meliloti. Science 2001; 293:668-72. [PMID: 11474104 DOI: 10.1126/science.1060966] [Citation(s) in RCA: 835] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The scarcity of usable nitrogen frequently limits plant growth. A tight metabolic association with rhizobial bacteria allows legumes to obtain nitrogen compounds by bacterial reduction of dinitrogen (N2) to ammonium (NH4+). We present here the annotated DNA sequence of the alpha-proteobacterium Sinorhizobium meliloti, the symbiont of alfalfa. The tripartite 6.7-megabase (Mb) genome comprises a 3.65-Mb chromosome, and 1.35-Mb pSymA and 1.68-Mb pSymB megaplasmids. Genome sequence analysis indicates that all three elements contribute, in varying degrees, to symbiosis and reveals how this genome may have emerged during evolution. The genome sequence will be useful in understanding the dynamics of interkingdom associations and of life in soil environments.
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Affiliation(s)
- F Galibert
- UMR6061-CNRS, Laboratoire de Génétique et Développement, Faculté de Médecine, 2 avenue du Pr. Léon Bernard, F-35043 Rennes cedex, France
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516
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Poinsot V, Bélanger E, Laberge S, Yang GP, Antoun H, Cloutier J, Treilhou M, Dénarié J, Promé JC, Debellé F. Unusual methyl-branched alpha,beta-unsaturated acyl chain substitutions in the Nod Factors of an arctic rhizobium, Mesorhizobium sp. strain N33 (Oxytropis arctobia). J Bacteriol 2001; 183:3721-8. [PMID: 11371536 PMCID: PMC95249 DOI: 10.1128/jb.183.12.3721-3728.2001] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mesorhizobium sp. strain N33 (Oxytropis arctobia), a rhizobial strain isolated in arctic Canada, is able to fix nitrogen at very low temperatures in association with a few arctic legume species belonging to the genera Astragalus, Onobrychis, and Oxytropis. Using mass spectrometry and nuclear magnetic resonance spectroscopy, we have determined the structure of N33 Nod factors, which are major determinants of nodulation. They are pentameric lipochito-oligosaccharides 6-O sulfated at the reducing end and exhibit other original substitutions: 6-O acetylation of the glucosamine residue next to the nonreducing terminal glucosamine and N acylation of the nonreducing terminal glucosamine by methyl-branched acyl chains of the iso series, some of which are alpha,beta unsaturated. These unusual substitutions may contribute to the peculiar host range of N33. Analysis of N33 whole-cell fatty acids indicated that synthesis of the methyl-branched fatty acids depended on the induction of bacteria by plant flavonoids, suggesting a specific role for these fatty acids in the signaling process between the plant and the bacteria. Synthesis of the methyl-branched alpha,beta-unsaturated fatty acids required a functional nodE gene.
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Affiliation(s)
- V Poinsot
- Laboratoire des Interactions Moléculaires-Réactivité Chimique et Photochimique, UPS-CNRS, 31062 Toulouse Cedex, France
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517
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Rogel MA, Hernández-Lucas I, Kuykendall LD, Balkwill DL, Martinez-Romero E. Nitrogen-fixing nodules with Ensifer adhaerens harboring Rhizobium tropici symbiotic plasmids. Appl Environ Microbiol 2001; 67:3264-8. [PMID: 11425750 PMCID: PMC93009 DOI: 10.1128/aem.67.7.3264-3268.2001] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ensifer adhaerens is a soil bacterium that attaches to other bacteria and may cause lysis of these other bacteria. Based on the sequence of its small-subunit rRNA gene, E. adhaerens is related to Sinorhizobium spp. E. adhaerens ATCC 33499 did not nodulate Phaseolus vulgaris (bean) or Leucaena leucocephala, but with symbiotic plasmids from Rhizobium tropici CFN299 it formed nitrogen-fixing nodules on both hosts. The nodule isolates were identified as E. adhaerens isolates by growth on selective media.
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Affiliation(s)
- M A Rogel
- Centro de Investigación sobre Fijación de Nitrógeno, UNAM. Ap. P. 565-A, Cuernavaca, México
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518
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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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519
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Moulin L, Munive A, Dreyfus B, Boivin-Masson C. Nodulation of legumes by members of the beta-subclass of Proteobacteria. Nature 2001; 411:948-50. [PMID: 11418858 DOI: 10.1038/35082070] [Citation(s) in RCA: 345] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Members of the Leguminosae form the largest plant family on Earth, with around 18,000 species. The success of legumes can largely be attributed to their ability to form a nitrogen-fixing symbiosis with specific bacteria known as rhizobia, manifested by the development of nodules on the plant roots in which the bacteria fix atmospheric nitrogen, a major contributor to the global nitrogen cycle. Rhizobia described so far belong exclusively to the alpha-subclass of Proteobacteria, where they are distributed in four distinct phylogenetic branches. Although nitrogen-fixing bacteria exist in other proteobacterial subclasses, for example Herbaspirillum and Azoarcus from the phylogenetically distant beta-subclass, none has been found to harbour the nod genes essential for establishing rhizobial symbiosis. Here we report the identification of proteobacteria from the beta-subclass that nodulate legumes. This finding shows that the ability to establish a symbiosis with legumes is more widespread in bacteria than anticipated to date.
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Affiliation(s)
- L Moulin
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD-INRA-CIRAD-ENSAM Baillarguet, Montpellier, France
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520
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Abstract
One potential outcome of the adaptive coevolution of humans and bacteria is the development of commensal relationships, where neither partner is harmed, or symbiotic relationships, where unique metabolic traits or other benefits are provided. Our gastrointestinal tract is colonized by a vast community of symbionts and commensals that have important effects on immune function, nutrient processing, and a broad range of other host activities. The current genomic revolution offers an unprecedented opportunity to identify the molecular foundations of these relationships so that we can understand how they contribute to our normal physiology and how they can be exploited to develop new therapeutic strategies.
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Affiliation(s)
- L V Hooper
- Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St. Louis, MO 63110, USA
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521
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Snoeck C, Luyten E, Poinsot V, Savagnac A, Vanderleyden J, Promé JC. Rhizobium sp. BR816 produces a complex mixture of known and novel lipochitooligosaccharide molecules. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2001; 14:678-684. [PMID: 11332733 DOI: 10.1094/mpmi.2001.14.5.678] [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
Rhizobial lipochitooligosaccharide (LCO) signal molecules induce various plant responses, leading to nodule development. We report here the LCO structures of the broadhost range strain Rhizobium sp. BR816. The LCOs produced are all pentamers, carrying common C18:1 or C18:0 fatty acyl chains, N-methylated and C-6 carbamoylated on the nonreducing terminal N-acetylglucosamine and sulfated on the reducing/terminal residue. A second acetyl group can be present on the penultimate N-acetylglucosamine from the nonreducing terminus. Two novel characteristics were observed: the reducing/terminal residue can be a glucosaminitol (open structure) and the degree of acetylation of this glucosaminitol or of the reducing residue can vary.
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Affiliation(s)
- C Snoeck
- Centre of Microbial and Plant Genetics, Heverlee, Belgium
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522
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Laguerre G, Nour SM, Macheret V, Sanjuan J, Drouin P, Amarger N. Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts. MICROBIOLOGY (READING, ENGLAND) 2001; 147:981-993. [PMID: 11283294 DOI: 10.1099/00221287-147-4-981] [Citation(s) in RCA: 388] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The nodC and nifH genes were characterized in a collection of 83 rhizobial strains which represented 23 recognized species distributed in the genera Rhizobium, Sinorhizobium, Mesorhizobium and Bradyrhizobium, as well as unclassified rhizobia from various host legumes. Conserved primers were designed from available nucleotide sequences and were able to amplify nodC and nifH fragments of about 930 bp and 780 bp, respectively, from most of the strains investigated. RFLP analysis of the PCR products resulted in a classification of these rhizobia which was in general well-correlated with their known host range and independent of their taxonomic status. The nodC and nifH fragments were sequenced for representative strains belonging to different genera and species, most of which originated from Phaselous vulgaris nodules. Phylogenetic trees were constructed and revealed close relationships among symbiotic genes of the Phaseolus symbionts, irrespective of their 16S-rDNA-based classification. The nodC and nifH phylogenies were generally similar, but cases of incongruence were detected, suggesting that genetic rearrangements have occurred in the course of evolution. The results support the view that lateral genetic transfer across rhizobial species and, in some instances, across Rhizobium and Sinorhizobium genera plays a role in diversification and in structuring the natural populations of rhizobia.
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Affiliation(s)
- Gisèle Laguerre
- Laboratoire de Microbiologie des Sols, Centre de Microbiologie du Sol et de l'Environnement, INRA, 17 rue Sully, BP 86510,F-21065 Dijon Cedex, France1
| | - Sarah M Nour
- Laboratoire de Microbiologie des Sols, Centre de Microbiologie du Sol et de l'Environnement, INRA, 17 rue Sully, BP 86510,F-21065 Dijon Cedex, France1
| | - Valérie Macheret
- Laboratoire de Microbiologie des Sols, Centre de Microbiologie du Sol et de l'Environnement, INRA, 17 rue Sully, BP 86510,F-21065 Dijon Cedex, France1
| | - Juan Sanjuan
- Departamento de Microbiologı́a del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidı́n, CSIC, Profesor Albareda 1, E-18008 Granada, Spain2
| | - Pascal Drouin
- Laboratoire de Microbiologie des Sols, Centre de Microbiologie du Sol et de l'Environnement, INRA, 17 rue Sully, BP 86510,F-21065 Dijon Cedex, France1
| | - Noëlle Amarger
- Laboratoire de Microbiologie des Sols, Centre de Microbiologie du Sol et de l'Environnement, INRA, 17 rue Sully, BP 86510,F-21065 Dijon Cedex, France1
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523
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López-Lara IM, Geiger O. The nodulation protein NodG shows the enzymatic activity of an 3-oxoacyl-acyl carrier protein reductase. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2001; 14:349-357. [PMID: 11277432 DOI: 10.1094/mpmi.2001.14.3.349] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The acyl carrier protein NodF is required for the synthesis of unusual polyunsaturated fatty acids that confer specificity to lipochitin oligosaccharide nodulation (Nod) factors of Rhizobium leguminosarum. In this study, homogeneous NodF protein was used as a ligand to identify proteins of R. leguminosarum that specifically interact with NodF and presumably are involved in the biosynthesis or transfer of the unusual fatty acids. The N-terminal amino acid sequence of a 29-kDa protein that interacts strongly with NodF revealed high similarity to NodG of Rhizobium sp. N33 and to NodG of Sinorhizobium meliloti We cloned and sequenced the gene coding for the NodG-like protein of R. leguminosarum and found it to be the product of the constitutively expressed gene fabG. FabG is the 3-oxoacyl-acyl carrier protein reductase that catalyzes the first reduction step in each cycle of fatty acid elongation. FabG of R. leguminosarum and NodG of Rhizobium sp. N33 were expressed in Escherichia coli. In both cases, the purified protein showed 3-oxoacyl-acyl carrier protein reductase activity in vitro. Therefore, NodG has the same biochemical function as FabG, and the high degree of similarity at the protein and DNA level suggest that nodG is a duplication of the housekeeping genefabG.
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Affiliation(s)
- I M López-Lara
- Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Morelos, CP.
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524
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Suarez V, Staehelin C, Arango R, Holtorf H, Hofsteenge J, Meins F. Substrate specificity and antifungal activity of recombinant tobacco class I chitinases. PLANT MOLECULAR BIOLOGY 2001; 45:609-18. [PMID: 11414619 DOI: 10.1023/a:1010619421524] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Endochitinases contribute to the defence response of plants against chitin-containing pathogens. The vacuolar class I chitinases consist of an N-terminal cysteine-rich domain (CRD) linked by a glycine-threonine-rich spacer with 4-hydroxylated prolyl residues to the catalytic domain. We examined the functional role of the CRD and spacer region in class I chitinases by comparing wild-type chitinase A (CHN A) of Nicotiana tabacum with informative recombinant forms. The chitinases were expressed in transgenic N. sylvestris plants, purified to near homogeneity, and their structures confirmed by mass spectrometry and partial sequencing. The enzymes were tested for their substrate preference towards chitin, lipo-chitooligosaccharide Nod factors of Rhizobium, and bacterial peptidoglycans (lysozyme activity) as well as for their capacity to inhibit hyphal growth of Trichoderma viride. Deletion of the CRD and spacer alone or in combination resulted in a modest <50% reduction of hydrolytic activity relative to CHN A using colloidal chitin or M. lysodeikticus walls as substrates; whereas, antifungal activity was reduced by up to 80%. Relative to CHN A, a variant with two spacers in tandem, which binds chitin, showed very low hydrolytic activity towards chitin and Nod factors, but comparable lysozyme activity and enhanced antifungal activity. Neither hydrolytic activity, substrate specificity nor antifungal activity were strictly correlated with the CRD-mediated capacity to bind chitin. This suggests that the presence of the chitin-binding domain does not have a major influence on the functions of CHN A examined. Moreover, the results with the tandem-spacer variant raise the possibility that substantial chitinolytic activity is not essential for inhibition of T. viride growth by CHN A.
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Affiliation(s)
- V Suarez
- Friedrich Miescher Institute, Novartis Research Foundation, Basel, Switzerland
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525
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Fales L, Kryszak L, Zeilstra-Ryalls J. Control of hemA expression in Rhodobacter sphaeroides 2.4.1: effect of a transposon insertion in the hbdA gene. J Bacteriol 2001; 183:1568-76. [PMID: 11160087 PMCID: PMC95041 DOI: 10.1128/jb.183.5.1568-1576.2001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The common precursor to all tetrapyrroles is 5-aminolevulinic acid (ALA), and in Rhodobacter sphaeroides its formation occurs via the Shemin pathway. ALA synthase activity is encoded by two differentially regulated genes in R. sphaeroides 2.4.1: hemA and hemT. In our investigations of hemA regulation, we applied transposon mutagenesis under aerobic conditions, followed by a selection that identified transposon insertion mutants in which hemA expression is elevated. One of these mutants has been characterized previously (J. Zeilstra-Ryalls and S. Kaplan, J. Bacteriol. 178:985-993, 1996), and here we describe our analysis of a second mutant strain. The transposon inserted into the coding sequences of hbdA, coding for S-(+)-beta-hydroxybutyryl-coenzyme A dehydrogenase and catalyzing an NAD-dependent reaction. We provide evidence that the hbdA gene product participates in polyhydroxybutyrate (PHB) metabolism and, based on our findings, we discuss possibilities as to how defective PHB metabolism might alter the level of hemA expression.
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Affiliation(s)
- L Fales
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309, USA
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526
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Abstract
Rhizobia are soil bacteria that can engage in a symbiosis with leguminous plants that produces nitrogen-fixing root nodules. This symbiosis is based on specific recognition of signal molecules, which are produced by both the bacterial and plant partners. In this review, recognition factors from the bacterial endosymbionts are discussed, with particular attention to secreted and cell surface glycans. Glycans that are discussed include the Nod factors, the extracellular polysaccharides, the lipopolysaccharides, the K-antigens, and the cyclic glucans. Recent advances in the understanding of the biosynthesis, secretion, and regulation of production of these glycans are reviewed, and their functions are compared with glycans produced by other bacteria, such as plant pathogens.
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Affiliation(s)
- H P Spaink
- Institute of Molecular Plant Sciences, Leiden University, 2333 AL Leiden, The Netherlands.
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527
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Cullimore JV, Ranjeva R, Bono JJ. Perception of lipo-chitooligosaccharidic Nod factors in legumes. TRENDS IN PLANT SCIENCE 2001; 6:24-30. [PMID: 11164374 DOI: 10.1016/s1360-1385(00)01810-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Lipo-chitooligosaccharides produced by rhizobia are a class of signalling molecules that mediate recognition and nodule organogenesis in the legume-rhizobia symbiosis. Their synthesis is specified by the nodulation genes of rhizobia and hence they are commonly known as Nod factors. They are amphiphilic molecules and induce a variety of responses in the roots of the legume hosts. Studies using plant and rhizobial mutants and purified molecules suggest that Nod factors are recognized by more than one receptor. In this article, we review evidence about the affinity, specificity and location of these putative receptors and describe recent studies with regard to their identification.
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Affiliation(s)
- J V Cullimore
- Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, UMR INRA-CNRS 215, BP 27, 31326, Castanet-Tolosan, France
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528
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Abstract
Nitrogen-fixing nodules on plants such as alfalfa, pea and vetch arise from the root inner cortex and grow via a persistent meristem. Thus, these nodules are defined as indeterminate. The formation of functional indeterminate nodules requires that symbiotic bacteria, collectively called rhizobia, gain access to the interior of roots and root nodules via infection threads. Recent work has begun to elucidate the important functions of the root cell cytoskeleton in infection thread formation. It has also recently become apparent that rhizobial Nod factors and rhizobial exopolysaccharides play key roles in the initiation and elongation of infection threads.
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Affiliation(s)
- D J Gage
- Department of Molecular and Cellular Biology, University of Connecticut, Stoors, CT 06269, USA
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529
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Ulrich A, Zaspel I. Phylogenetic diversity of rhizobial strains nodulating Robinia pseudoacacia L. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 11):2997-3005. [PMID: 11065378 DOI: 10.1099/00221287-146-11-2997] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lack of knowledge exists regarding the diversity of rhizobial strains nodulating black locust (Robinia pseudoacacia L.), which is a neophytic tree species widely distributed in Europe. Seventeen rhizobial strains isolated from nodules of black locust at a German location were examined by phenotypic characterization and 16S rDNA analysis. The isolates were classified in nine 16S rDNA genotypes using a set of seven endonucleases. Based on RFLP analysis and sequencing, the strains were shown to belong to the genera Mesorhizobium (76%) and Rhizobium (24%). Five genotypes were identical to the species Mesorhizobium amorphae, Mesorhizobium loti, Mesorhizobium huakuii, Rhizobium leguminosarum and Rhizobium tropici. A strong similarity between the 16S rDNA sequence of another two genotypes and M. amorphae (99.9%) as well as the Mesorhizobium strain R88b (99.8%) was found. The two remaining genotypes were classified in the genus Rhizobium, without a significant relationship at the species level. Comparing isolates nodulating Rob. pseudoacacia and Amorpha fruticosa, a parallel picture of phylogenetic diversity was detected with a range of phylogenetically different rhizobia and M. amorphae dominating. For this study, 18 rhizobial strains which had originally been isolated from a forest in Maryland where black locust is native were additionally analysed. Results revealed seven genotypes all belonging to the genus Mesorhizobium, with four genotypes identical to the isolates from the German sampling location. Whereas the genotype identical to M. amorphae dominated within the strains obtained from the German location, the dominance of a genotype identical to M. huakuii was found among the strains from the native location. Summarizing data from both locations, Rob. pseudoacacia was nodulated with various genomic species, most of which belonged to the genus Mesorhizobium. Concerning phenotypic features such as growth rate, pH tolerance or use of certain carbohydrates, most isolates corresponded to described species and genera. However, there were differences in salt tolerance between these isolates and the corresponding reference strains. Overall, the results demonstrated a high phenotypic and phylogenetic diversity of rhizobial strains nodulating Rob. pseudoacacia. This may be a characteristic of neophytic and other widely spread legumes and may contribute to the success of black locust as a pioneer tree species for the temperate zone.
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Affiliation(s)
- Andreas Ulrich
- ZALF - Centre for Agricultural Landscape and Land Use Research, Institute of Primary Production and Microbial Ecology, Eberswalder Str. 84, D-15374 Müncheberg, Germany1
| | - Irmtraut Zaspel
- Federal Research Centre for Forestry and Forest Products, Institute for Forest Genetics and Forest Tree Breeding, Eberswalder Chaussee 3, D-15377 Waldsieversdorf, Germany2
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530
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Affiliation(s)
- W J Broughton
- Laboratoire de Biologie Moléculaire des Plantes Supérieures, Université de Genève, 1292 Chambésy/Geneva, Switzerland.
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531
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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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