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Todd JD, Curson ARJ, Dupont CL, Nicholson P, Johnston AWB. ThedddPgene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some Ascomycete fungi. Environ Microbiol 2009. [DOI: 10.1111/j.1462-2920.2009.01919.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Todd JD, Curson ARJ, Dupont CL, Nicholson P, Johnston AWB. The dddP gene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some Ascomycete fungi. Environ Microbiol 2009; 11:1376-85. [PMID: 19220400 DOI: 10.1111/j.1462-2920.2009.01864.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The marine alphaproteobacterium Roseovarius nubinhibens ISM can produce the gas dimethyl sulfide (DMS) from dimethylsulfoniopropionate (DMSP), a widespread secondary metabolite that occurs in many phytoplankton. Roseovarius possesses a novel gene, termed dddP, which when cloned, confers on Escherichia coli the ability to produce DMS. The DddP polypeptide is in the large family of M24 metallopeptidases and is wholly different from two other enzymes, DddD and DddL, which were previously shown to generate DMS from dimethylsulfoniopropionate. Close homologues of DddP occur in other alphaproteobacteria and more surprisingly, in some Ascomycete fungi. These were the biotechnologically important Aspergillus oryzae and the plant pathogen, Fusarium graminearum. The dddP gene is abundant in the bacterial metagenomic sequences in the Global Ocean Sampling Expedition. Thus, dddP has several novel features and is widely dispersed, both taxonomically and geographically.
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Affiliation(s)
- J D Todd
- School of Biological Sciences, University of East Anglia, Norwich, UK
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Curson ARJ, Rogers R, Todd JD, Brearley CA, Johnston AWB. Molecular genetic analysis of a dimethylsulfoniopropionate lyase that liberates the climate-changing gas dimethylsulfide in several marine alpha-proteobacteria and Rhodobacter sphaeroides. Environ Microbiol 2008; 10:757-67. [PMID: 18237308 DOI: 10.1111/j.1462-2920.2007.01499.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The alpha-proteobacterium Sulfitobacter EE-36 makes the gas dimethylsulfide (DMS) from dimethylsulfoniopropionate (DMSP), an abundant antistress molecule made by many marine phytoplankton. We screened a cosmid library of Sulfitobacter for clones that conferred to other bacteria the ability to make DMS. One gene, termed dddL, was sufficient for this phenotype when cloned in pET21a and introduced into Escherichia coli. Close DddL homologues exist in the marine alpha-proteobacteria Fulvimarina, Loktanella Oceanicola and Stappia, all of which made DMS when grown on DMSP. There was also a dddL homologue in Rhodobacter sphaeroides strain 2.4.1, but not in strain ATCC 17025; significantly, the former, but not the latter, emits DMS when grown with DMSP. Escherichia coli containing the cloned, overexpressed dddL genes of R. sphaeroides 2.4.1 and Sulfitobacter could convert DMSP to acrylate plus DMS. This is the first identification of such a 'DMSP lyase'. Thus, DMS can be made either by this DddL lyase or by a DMSP acyl CoA transferase, specified by dddD, a gene that we had identified in several other marine bacteria.
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Affiliation(s)
- A R J Curson
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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Curson ARJ, Rogers R, Todd JD, Brearley CA, Johnston AWB. Molecular genetic analysis of a dimethylsulfoniopropionate lyase that liberates the climate-changing gas dimethylsulfide in several marine α-proteobacteria and Rhodobacter sphaeroides. Environ Microbiol 2008. [DOI: 10.1111/j.1462-2920.2008.01592.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Yeoman KH, Curson ARJ, Todd JD, Sawers G, Johnston AWB. Evidence that the Rhizobium regulatory protein RirA binds to cis-acting iron-responsive operators (IROs) at promoters of some Fe-regulated genes. Microbiology (Reading) 2005; 150:4065-74. [PMID: 15583159 DOI: 10.1099/mic.0.27419-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mutations in rirA of Rhizobium have been shown to deregulate expression of several genes that are normally repressed by iron. A conserved sequence, the iron-responsive operator (IRO), was identified near promoters of vbsC (involved in the synthesis of the siderophore vicibactin), rpoI (specifies an ECF sigma factor needed for vicibactin synthesis) and the two fhuA genes (encoding vicibactin receptor). Removal of these IRO sequences abolished Fe-responsive repression. Most of these genes were constitutively expressed in the heterologous host, Paracoccus denitrificans, but introduction of the cloned rirA gene repressed expression of these Rhizobium genes in this heterologous host if the corresponding IRO sequences were also intact. These observations are the first to examine the mechanisms of RirA, which has no sequence similarity to well-known iron-responsive regulators such as Fur or DtxR. They provide strong circumstantial evidence that RirA is a transcriptional regulator that binds to cis-acting regulatory sequences near the promoters of at least some of the genes whose expression it controls in response to Fe availability.
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Affiliation(s)
- K H Yeoman
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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Díaz-Mireles E, Wexler M, Sawers G, Bellini D, Todd JD, Johnston AWB. The Fur-like protein Mur of Rhizobium leguminosarum is a Mn(2+)-responsive transcriptional regulator. Microbiology (Reading) 2004; 150:1447-1456. [PMID: 15133106 DOI: 10.1099/mic.0.26961-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In wild-type Rhizobium leguminosarum, the sitABCD operon specifies a Mn(2+) transporter whose expression is severely reduced in cells grown in the presence of this metal. Mutations in the R. leguminosarum gene, mur (manganese uptake regulator), whose product resembles the Fur transcriptional regulator, cause high-level expression of sitABCD in the presence of Mn(2+). In gel-shift mobility assays, purified R. leguminosarum Mur protein bound to at least two regions near the sitABCD promoter region, although this DNA has no conventional consensus Fur-binding sequences (fur boxes). Thus, in contrast to gamma-proteobacteria, where Fur binds Fe(2+), the R. leguminosarum Fur homologue, Mur, act as a Mn(2)-responsive transcriptional regulator.
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Affiliation(s)
- E Díaz-Mireles
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - M Wexler
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - G Sawers
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - D Bellini
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - J D Todd
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - A W B Johnston
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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Wexler M, Todd JD, Kolade O, Bellini D, Hemmings AM, Sawers G, Johnston AWB. Fur is not the global regulator of iron uptake genes in Rhizobium leguminosarum. Microbiology (Reading) 2003; 149:1357-1365. [PMID: 12724397 DOI: 10.1099/mic.0.26130-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Rhizobium leguminosarum fur mutants were unaffected in Fe-dependent regulation of several operons that specify different Fe uptake systems, yet cloned R. leguminosarum fur partially corrected an Escherichia coli fur mutant and R. leguminosarum Fur protein bound to canonical fur boxes. The lack of a phenotype in fur mutants is not due to functional redundancy with Irr, another member of the Fur superfamily found in the rhizobia, since irr fur double mutants are also unaffected in Fe-responsive regulation of several operons involved in Fe uptake. Neither Irr nor Fur is needed for symbiotic N(2) fixation on peas. As in Bradyrhizobium japonicum, irr mutants accumulated protoporphyrin IX. R. leguminosarum irr is not regulated by Fur and its Irr protein lacks the motif needed for haem-dependent post-translational modification that occurs in B. japonicum Irr. The similarities and differences in the Fur superfamily in the rhizobia and other Gram-negative bacteria are discussed.
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Affiliation(s)
- M Wexler
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - J D Todd
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - O Kolade
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - D Bellini
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - A M Hemmings
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - G Sawers
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - A W B Johnston
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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Kolade OO, Bellini P, Wexler M, Johnston AWB, Grossmann JG, Hemmings AM. Structural studies of the Fur protein from Rhizobium leguminosarum. Biochem Soc Trans 2002; 30:771-4. [PMID: 12196192 DOI: 10.1042/bst0300771] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The X-ray crystal structure of the apo-form of the Fur protein from Rhizobium leguminosarum has been solved at 2.7 A resolution. Small-angle X-ray scattering was used to give information on the solution conformation of the protein. The Fur homodimer folds into two domains. The N-terminal domain is formed from the packing of two helix-turn-helix motifs while the C-terminal domain appears primarily to stabilize the dimeric state of the protein.
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Affiliation(s)
- O O Kolade
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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Carter RA, Worsley PS, Sawers G, Challis GL, Dilworth MJ, Carson KC, Lawrence JA, Wexler M, Johnston AWB, Yeoman KH. The vbs genes that direct synthesis of the siderophore vicibactin in Rhizobium leguminosarum: their expression in other genera requires ECF sigma factor RpoI. Mol Microbiol 2002; 44:1153-66. [PMID: 12028377 DOI: 10.1046/j.1365-2958.2002.02951.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A cluster of eight genes, vbsGSO, vbsADL, vbsC and vbsP, are involved in the synthesis of vicibactin, a cyclic, trihydroxamate siderophore made by the symbiotic bacterium Rhizobium leguminosarum. None of these vbs genes was required for symbiotic N2 fixation on peas or Vicia. Transcription of vbsC, vbsGSO and vbsADL (but not vbsP) was enhanced by growth in low levels of Fe. Transcription of vbsGSO and vbsADL, but not vbsP or vbsC, required the closely linked gene rpoI, which encodes an ECF sigma factor of RNA polymerase. Transfer of the cloned vbs genes, plus rpoI, to Rhodobacter, Paracoccus and Sinorhizobium conferred the ability to make vicibactin on these other genera. We present a biochemical genetic model of vicibactin synthesis, which accommodates the phenotypes of different vbs mutants and the homologies of the vbs gene products. In this model, VbsS, which is similar to many non-ribosomal peptide synthetase multienzymes, has a central role. It is proposed that VbsS activates L-N5-hydroxyornithine via covalent attachment as an acyl thioester to a peptidyl carrier protein domain. Subsequent VbsA-catalysed acylation of the hydroxyornithine, followed by VbsL-mediated epimerization and acetylation catalysed by VbsC, yields the vicibactin subunit, which is then trimerized and cyclized by the thioesterase domain of VbsS to give the completed siderophore.
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Affiliation(s)
- R A Carter
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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Carter RA, Yeoman KH, Klein A, Hosie AHF, Sawers G, Poole PS, Johnston AWB. dpp genes of Rhizobium leguminosarum specify uptake of delta-aminolevulinic acid. Mol Plant Microbe Interact 2002; 15:69-74. [PMID: 11858173 DOI: 10.1094/mpmi.2002.15.1.69] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
An operon with homology to the dppABCDF genes required to transport dipeptides in bacteria was identified in the N2-fixing symbiont, Rhizobium leguminosarum. As in other bacteria, dpp mutants were severely affected in the import of delta-aminolevulinic acid (ALA), a heme precursor. ALA uptake was antagonized by adding dipeptides, indicating that these two classes of molecule share the same transporter. Mutations in dppABCDF did not affect symbiotic N2 fixation on peas, suggesting that the ALA needed for heme synthesis is not supplied by the plant or that another uptake system functions in the bacteroids. The dppABCDF operon of R. leguminosarum resembles that in other bacteria, with a gap between dppA and dppB containing inverted repeats that may stabilize mRNA and may explain why transcription of dppA alone was higher than that of dppBCDF. The dppABCDF promoter was mapped and is most likely recognized by sigma70.
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Affiliation(s)
- R A Carter
- School of Biological Sciences, University of East Anglia, Norwich, UK
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Economou A, Davies AE, Johnston AWB, Downie JA. The Rhizobium leguminosarum biovar viciae nodO gene can enable a nodE mutant of Rhizobium leguminosarum biovar trifolii to nodulate vetch. Microbiology (Reading) 1994. [DOI: 10.1099/13500872-140-9-2341] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Aird ELH, Brightwell G, Jones MA, Johnston AWB. Identification of the exo loci required for exopolysaccharide synthesis in Agrobacterium radiobacter NCIB 11883. ACTA ACUST UNITED AC 1991. [DOI: 10.1099/00221287-137-10-2287] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Hawkins FKL, Kennedy C, Johnston AWB. A Rhizobium leguminosarum gene required for symbiotic nitrogen fixation, melanin synthesis and normal growth on certain growth media. ACTA ACUST UNITED AC 1991. [DOI: 10.1099/00221287-137-7-1721] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Firmin JL, Wilson KE, Rossen L, Johnston AWB. Flavonoid activation of nodulation genes in Rhizobium reversed by other compounds present in plants. Nature 1986. [DOI: 10.1038/324090a0] [Citation(s) in RCA: 267] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Borthakur D, Barber CE, Lamb JW, Daniels MJ, Downie JA, Johnston AWB. A mutation that blocks exopolysaccharide synthesis prevents nodulation of peas by Rhizobium leguminosarum but not of beans by R. phaseoli and is corrected by cloned DNA from Rhizobium or the phytopathogen Xanthomonas. ACTA ACUST UNITED AC 1986. [DOI: 10.1007/bf00333974] [Citation(s) in RCA: 106] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Lamb JW, Hombrecher G, Johnston AWB. Plasmid-determined nodulation and nitrogen-fixation abilities inRhizobium phaseoli. ACTA ACUST UNITED AC 1982. [DOI: 10.1007/bf00729468] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Dejong TM, Brewin NJ, Johnston AWB, Phillips DA. Improvement of Symbiotic Properties in Rhizobium leguminosarum by Plasmid Transfer. Microbiology (Reading) 1982. [DOI: 10.1099/00221287-128-8-1829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Hombrecher G, Brewin N, Johnston AWB. Linkage of genes for nitrogenase and nodulation ability on plasmids in Rhizobium leguminosarum and R. phaseoli. ACTA ACUST UNITED AC 1981. [DOI: 10.1007/bf00422779] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Brewin NJ, DeJong TM, Phillips DA, Johnston AWB. Co-transfer of determinants for hydrogenase activity and nodulation ability in Rhizobium leguminosarum. Nature 1980. [DOI: 10.1038/288077a0] [Citation(s) in RCA: 77] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Buchanan-Wollaston AV, Beringer JE, Brewin NJ, Hirsch PR, Johnston AWB. Isolation of symbiotically defective mutants in Rhizobium leguminosarum by insertion of the transposon Tn5 into a transmissible plasmid. ACTA ACUST UNITED AC 1980. [DOI: 10.1007/bf00267228] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Johnston AWB. From ligands to legumes. Nature 1979. [DOI: 10.1038/281524a0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Johnston AWB, SETCHELL SM, BERINGER JE. Interspecific Crosses between Rhizobium leguminosarum and R. meliloti: Formation of Haploid Recombinants and of R-primes. ACTA ACUST UNITED AC 1978. [DOI: 10.1099/00221287-104-2-209] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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BERINGER JE, HOGGAN SA, Johnston AWB. Linkage Mapping in Rhizobium leguminosarum by means of R Plasmid-mediated Recombination. ACTA ACUST UNITED AC 1978. [DOI: 10.1099/00221287-104-2-201] [Citation(s) in RCA: 85] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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