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Chang ACG, Chen T, Li N, Duan J. Perspectives on Endosymbiosis in Coralloid Roots: Association of Cycads and Cyanobacteria. Front Microbiol 2019; 10:1888. [PMID: 31474965 PMCID: PMC6702271 DOI: 10.3389/fmicb.2019.01888] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 07/30/2019] [Indexed: 12/30/2022] Open
Abstract
Past endosymbiotic events allowed photosynthetic organisms to flourish and evolve in terrestrial areas. The precursor of chloroplasts was an ancient photosynthetic cyanobacterium. Presently, cyanobacteria are still capable of establishing successful symbioses in a wide range of hosts. One particular host plant among the gymnosperms is cycads (Order Cycadales) in which a special type of root system, referred to as coralloid roots, develops to house symbiotic cyanobacteria. A number of studies have explained coralloid root formation and cyanobiont invasion but the questions on mechanisms of this host-microbe association remains vague. Most researches focus on diversity of symbionts in coralloid roots but equally important is to explore the underlying mechanisms of cycads-Nostoc symbiosis as well. Besides providing an overview of relevant areas presently known about this association and citing putative genes involved in cycad-cyanobacteria symbioses, this paper aims to identify the limitations that hamper attempts to get to the root of the matter and suggests future research directions that may prove useful.
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Affiliation(s)
- Aimee Caye G. Chang
- University of Chinese Academy of Sciences, Beijing, China
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Tao Chen
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China
| | - Nan Li
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China
| | - Jun Duan
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Dai Z, Guo X, Yin H, Liang Y, Cong J, Liu X. Identification of nitrogen-fixing genes and gene clusters from metagenomic library of acid mine drainage. PLoS One 2014; 9:e87976. [PMID: 24498417 PMCID: PMC3912193 DOI: 10.1371/journal.pone.0087976] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 01/02/2014] [Indexed: 11/19/2022] Open
Abstract
Biological nitrogen fixation is an essential function of acid mine drainage (AMD) microbial communities. However, most acidophiles in AMD environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in AMD microbial communities. In this study, we used metagenomic sequencing to isolate nif genes in the AMD microbial community from Dexing Copper Mine, China. Meanwhile, a metagenome microarray containing 7,776 large-insertion fosmids was constructed to screen novel nif gene clusters. Metagenomic analyses revealed that 742 sequences were identified as nif genes including structural subunit genes nifH, nifD, nifK and various additional genes. The AMD community is massively dominated by the genus Acidithiobacillus. However, the phylogenetic diversity of nitrogen-fixing microorganisms is much higher than previously thought in the AMD community. Furthermore, a 32.5-kb genomic sequence harboring nif, fix and associated genes was screened by metagenome microarray. Comparative genome analysis indicated that most nif genes in this cluster are most similar to those of Herbaspirillum seropedicae, but the organization of the nif gene cluster had significant differences from H. seropedicae. Sequence analysis and reverse transcription PCR also suggested that distinct transcription units of nif genes exist in this gene cluster. nifQ gene falls into the same transcription unit with fixABCX genes, which have not been reported in other diazotrophs before. All of these results indicated that more novel diazotrophs survive in the AMD community.
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Affiliation(s)
- Zhimin Dai
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
| | - Xue Guo
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, P. R. China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, P. R. China
| | - Jing Cong
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, P. R. China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, P. R. China
- * E-mail:
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Mattiuzzo M, Bertani I, Ferluga S, Cabrio L, Bigirimana J, Guarnaccia C, Pongor S, Maraite H, Venturi V. The plant pathogen Pseudomonas fuscovaginae contains two conserved quorum sensing systems involved in virulence and negatively regulated by RsaL and the novel regulator RsaM. Environ Microbiol 2011; 13:145-162. [PMID: 20701623 DOI: 10.1111/j.1462-2920.2010.02316.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pseudomonas fuscovaginae is a Gram-negative fluorescent pseudomonad pathogenic towards several plant species. Despite its importance as a plant pathogen, no molecular studies of virulence have thus far been reported. In this study we show that P. fuscovaginae possesses two conserved N-acyl homoserine lactone (AHL) quorum sensing (QS) systems which we designated PfsI/R and PfvI/R. The PfsI/R system is homologous to the BviI/R system of Burkholderia vietnamiensis and produces and responds to C10-HSL and C12-HSL whereas PfvI/R is homologous to the LasI/R system of Pseudomonas aeruginosa and produces several long-chain 3-oxo-HSLs and responds to 3-oxo-C10-HSL and 3-oxo-C12-HSL and at high AHL concentrations can also respond to structurally different long-chain AHLs. Both systems were found to be negatively regulated by a repressor protein which was encoded by a gene located intergenically between the AHL synthase and LuxR-family response regulator. The pfsI/R system was regulated by a novel repressor designated RsaM while the pfvI/R system was regulated by both the RsaL repressor and by RsaM. The two systems are not transcriptionally hierarchically organized but share a common AHL response and both are required for plant virulence. Pseudomonas fuscovaginae has therefore a unique complex regulatory network composed of at least two different repressors which directly regulate the AHL QS systems and pathogenicity.
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Affiliation(s)
- Maura Mattiuzzo
- International Centre for Genetic Engineering & Biotechnology, Trieste, ItalyInternational Centre for Genetic Engineering & Biotechnology, Biosafety Outstation, Ca'Tron, Treviso, ItalyUnité de Phytopathologie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Iris Bertani
- International Centre for Genetic Engineering & Biotechnology, Trieste, ItalyInternational Centre for Genetic Engineering & Biotechnology, Biosafety Outstation, Ca'Tron, Treviso, ItalyUnité de Phytopathologie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Sara Ferluga
- International Centre for Genetic Engineering & Biotechnology, Trieste, ItalyInternational Centre for Genetic Engineering & Biotechnology, Biosafety Outstation, Ca'Tron, Treviso, ItalyUnité de Phytopathologie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Laura Cabrio
- International Centre for Genetic Engineering & Biotechnology, Trieste, ItalyInternational Centre for Genetic Engineering & Biotechnology, Biosafety Outstation, Ca'Tron, Treviso, ItalyUnité de Phytopathologie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Joseph Bigirimana
- International Centre for Genetic Engineering & Biotechnology, Trieste, ItalyInternational Centre for Genetic Engineering & Biotechnology, Biosafety Outstation, Ca'Tron, Treviso, ItalyUnité de Phytopathologie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Corrado Guarnaccia
- International Centre for Genetic Engineering & Biotechnology, Trieste, ItalyInternational Centre for Genetic Engineering & Biotechnology, Biosafety Outstation, Ca'Tron, Treviso, ItalyUnité de Phytopathologie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Sandor Pongor
- International Centre for Genetic Engineering & Biotechnology, Trieste, ItalyInternational Centre for Genetic Engineering & Biotechnology, Biosafety Outstation, Ca'Tron, Treviso, ItalyUnité de Phytopathologie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Henri Maraite
- International Centre for Genetic Engineering & Biotechnology, Trieste, ItalyInternational Centre for Genetic Engineering & Biotechnology, Biosafety Outstation, Ca'Tron, Treviso, ItalyUnité de Phytopathologie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Vittorio Venturi
- International Centre for Genetic Engineering & Biotechnology, Trieste, ItalyInternational Centre for Genetic Engineering & Biotechnology, Biosafety Outstation, Ca'Tron, Treviso, ItalyUnité de Phytopathologie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
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Morris J, O'sullivan DJ, Koster M, Leong J, Weisbeek PJ, O'gara F. Characterization of Fluorescent Siderophore-Mediated Iron Uptake in Pseudomonas sp. Strain M114: Evidence for the Existence of an Additional Ferric Siderophore Receptor. Appl Environ Microbiol 2010; 58:630-5. [PMID: 16348650 PMCID: PMC195294 DOI: 10.1128/aem.58.2.630-635.1992] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Pseudomonas sp. strain M114, the outer membrane receptor for ferric pseudobactin M114 was shown to transport ferric pseudobactins B10 and A225, in addition to its own. The gene encoding this receptor, which was previously cloned on pCUP3, was localized by Tn5 mutagenesis to a region comprising >1.6 kb of M114 DNA. A mutant (strain M114R1) lacking this receptor was then created by a marker exchange technique. Characterization of this mutant by using purified pseudobactin M114 in radiolabeled ferric iron uptake studies confirmed that it was completely unable to utilize this siderophore for acquisition of iron. In addition, it lacked an outer membrane protein band of 89 kDa when subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis. As a result, growth of the mutant was severely restricted under low-iron conditions. However, this phenotype was reversed in the presence of another fluorescent siderophore (pseudobactin MT3A) from Pseudomonas sp. strain MT3A, suggesting the presence of a second receptor in strain M114. Furthermore, wild-type Pseudomonas sp. strain B24 was not able to utilize ferric pseudobactin MT3A, and this phenotype was not reversed upon expression of the M114 receptor encoded on pCUP3. However, a cosmid clone (pMS1047) that enabled strain B24 to utilize ferric pseudobactin MT3A was isolated from an M114 gene bank. Radiolabel transport assays with purified pseudobactin MT3A confirmed this event. Plasmid pMS1047 was shown to encode an outer membrane protein of 81 kDa in strain B24 under iron-limiting conditions; this protein corresponds to a similar protein in strain M114.
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Affiliation(s)
- J Morris
- Microbiology Department, University College, Cork, Ireland, and Department of Molecular Cell Biology, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Corbin D, Barran L, Ditta G. Organization and expression of Rhizobium meliloti nitrogen fixation genes. Proc Natl Acad Sci U S A 2010; 80:3005-9. [PMID: 16593313 PMCID: PMC393962 DOI: 10.1073/pnas.80.10.3005] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The boundaries of a nif gene cluster in Rhizobium meliloti were determined by Tn5 mutagenesis. These genes are clustered within a 14- to 15-kilobase (kb) region that includes the nitrogenase structural genes. Sequences within 10 kb on either side of this region are devoid of symbiotically essential gene function. RNA blot analysis identified a 5- to 6-kb transcript that corresponds to the nitrogenase structural gene operon. The 5' end of this transcript and its polarity were determined by nuclease S1 mapping. The 5' end of another nif transcript was also identified by nuclease S1 mapping. The promoter regions for these two nif transcripts control transcription in divergent directions and are separated by 1.9 kb of symbiotically unessential DNA. One Tn5 insertion within the nitrogenase operon did not create a polar mutation. The implications of this finding and the overall emerging picture of the genetic organization of this nif region are discussed.
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Affiliation(s)
- D Corbin
- Department of Biology, University of California at San Diego, La Jolla, California 92093
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Quinto C, De La Vega H, Flores M, Leemans J, Cevallos MA, Pardo MA, Azpiroz R, De Lourdes Girard M, Calva E, Palacios R. Nitrogenase reductase: A functional multigene family in Rhizobium phaseoli. Proc Natl Acad Sci U S A 2010; 82:1170-4. [PMID: 16593543 PMCID: PMC397216 DOI: 10.1073/pnas.82.4.1170] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The complete coding sequence of the nitrogenase reductase gene (nifH) is present in three different regions of a Rhizobium phaseoli symbiotic plasmid. Homology between two of the regions containing nifH coding sequences extends over 5 kilobases. These in turn share 1.3 kilobases of homology with the third region. The nucleotide sequences of the three nitrogenase reductase genes were found to be identical. Site-directed insertion mutagenesis indicated that none of the three genes is indispensable for nitrogen fixation during symbiosis with Phaseolus vulgaris. This implies that at least two of the reiterated genes can be functionally expressed.
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Affiliation(s)
- C Quinto
- Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apartado postal 565-A, Cuernavaca, Morelos, Mexico
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Toro N, Olivares J. Analysis of Rhizobium meliloti Sym Mutants Obtained by Heat Treatment. Appl Environ Microbiol 2010; 51:1148-50. [PMID: 16347063 PMCID: PMC239028 DOI: 10.1128/aem.51.5.1148-1150.1986] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Deletions in the pSym megaplasmid of Rhizobium meliloti were produced at a high frequency, and their lengths varied according to incubation temperature. Morphological differentiation into large and small colonies occurred after heat treatment. Small colonies elicited pseudonodules on alfalfa roots.
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Affiliation(s)
- N Toro
- Departamento de Microbiología, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008-Granada, Spain
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LasI/R and RhlI/R quorum sensing in a strain of Pseudomonas aeruginosa beneficial to plants. Appl Environ Microbiol 2009; 75:5131-40. [PMID: 19525275 DOI: 10.1128/aem.02914-08] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa possesses three quorum-sensing (QS) systems which are key in the expression of a large number of genes, including many virulence factors. Most studies of QS in P. aeruginosa have been performed in clinical isolates and have therefore focused on its role in pathogenicity. P. aeruginosa, however, is regarded as a ubiquitous organism capable of colonizing many different environments and also of establishing beneficial associations with plants. In this study we examined the role of the two N-acyl homoserine lactone systems known as RhlI/R and LasI/R in the environmental rice rhizosphere isolate P. aeruginosa PUPa3. Both the Rhl and Las systems are involved in the regulation of plant growth-promoting traits. The environmental P. aeruginosa PUPa3 is pathogenic in two nonmammalian infection models, and only the double las rhl mutants are attenuated for virulence. In fact it was established that the two QS systems are not hierarchically organized and that they are both important for the colonization of the rice rhizosphere. This is an in-depth genetic and molecular study of QS in an environmental P. aeruginosa strain and highlights several differences with QS regulation in the clinical isolate PAO1.
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10
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Degrassi G, Devescovi G, Kim J, Hwang I, Venturi V. Identification, characterization and regulation of two secreted polygalacturonases of the emerging rice pathogen Burkholderia glumae. FEMS Microbiol Ecol 2008; 65:251-62. [DOI: 10.1111/j.1574-6941.2008.00516.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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11
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Licciardello G, Bertani I, Steindler L, Bella P, Venturi V, Catara V. Pseudomonas corrugata contains a conserved N-acyl homoserine lactone quorum sensing system; its role in tomato pathogenicity and tobacco hypersensitivity response. FEMS Microbiol Ecol 2007; 61:222-34. [PMID: 17537174 DOI: 10.1111/j.1574-6941.2007.00338.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Pseudomonas corrugata is a phytopathogenic bacterium, causal agent of tomato pith necrosis, yet it is an ubiquitous bacterium that is part of the microbial community in the soil and in the rhizosphere of different plant species. Although it is a very heterogeneous species, all the strains tested were able to produce short chain acyl homoserine lactone (AHL) quorum sensing signal molecules. The main AHL produced was N-hexanoyl-L-homoserine lactone (C(6)-AHL). An AHL quorum sensing system, designated PcoI/PcoR, was identified and characterized. The role of the quorum sensing system in the expression of a variety of traits was evaluated. Inactivation of pcoI abolished the production of AHLs. The pcoR mutant, but not the pcoI mutant, was impaired in swarming, unable to cause a hypersensitivity response on tobacco and resulted in a reduced tomato pith necrosis phenotype. The pcoI mutant showed a reduced antimicrobial activity against various fungi and bacteria when assayed on King's B medium. These results demonstrate that the AHL quorum sensing in Ps. corrugata regulates traits that contribute to virulence, antimicrobial activity and fitness. This is the first report of genes of Ps. corrugata involved in the disease development and biological control activity.
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Affiliation(s)
- Grazia Licciardello
- Parco Scientifico e Tecnologico della Sicilia, z.i. Blocco Palma I, Catania, Italy
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Rampioni G, Polticelli F, Bertani I, Righetti K, Venturi V, Zennaro E, Leoni L. The Pseudomonas quorum-sensing regulator RsaL belongs to the tetrahelical superclass of H-T-H proteins. J Bacteriol 2006; 189:1922-30. [PMID: 17172347 PMCID: PMC1855778 DOI: 10.1128/jb.01552-06] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the opportunistic human pathogen Pseudomonas aeruginosa, quorum sensing (QS) is crucial for virulence. The RsaL protein directly represses the transcription of lasI, the synthase gene of the main QS signal molecule. On the basis of sequence homology, RsaL cannot be predicted to belong to any class of characterized DNA-binding proteins. In this study, an in silico model of the RsaL structure was inferred showing that RsaL belongs to the tetrahelical superclass of helix-turn-helix proteins. The overall structure of RsaL is very similar to the N-terminal domain of the lambda cI repressor and to the POU-specific domain of the mammalian transcription factor Oct-1 (Oct-1 POUs). Moreover, residues of Oct-1 POUs important for structural stability and/or DNA binding are conserved in the same positions in RsaL and in its homologs found in GenBank. These residues were independently replaced with Ala, and the activities of the mutated variants of RsaL were compared to that of the wild-type counterpart in vivo by complementation assays and in vitro by electrophoretic mobility shift assays. The results validated the RsaL in silico model and showed that residues Arg 20, Gln 38, Ser 42, Arg 43, and Glu 45 are important for RsaL function. Our data indicate that RsaL could be the founding member of a new protein family within the tetrahelical superclass of helix-turn-helix proteins. Finally, the minimum DNA sequence required for RsaL binding on the lasI promoter was determined, and our data support the hypothesis that RsaL binds DNA as a dimer.
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Affiliation(s)
- Giordano Rampioni
- Department of Biology, University Roma Tre, Viale Marconi, 446, 00146, Rome, Italy
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Devescovi G, Venturi V. TheBurkholderia cepaciarpoEgene is not involved in exopolysaccharide production and onion pathogenicity. Can J Microbiol 2006; 52:260-5. [PMID: 16604122 DOI: 10.1139/w05-119] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Burkholderia cepacia was originally described as the causative agent of bacterial rot of onions, and it has now emerged as an important opportunistic pathogen causing severe chronic lung infections in patients having cystic fibrosis. Burkholderia cepacia is now classified into nine very closely related species (previously designated as genomovars), all of which have been isolated from both environmental and clinical sources and are collectively known as the B. cepacia complex. The alternative extracytoplasmic function σ factor, σE, has been determined in several bacterial species as making substantial contributions to bacterial survival under stress conditions. Here, we report the identification and characterization of the rpoE gene, encoding σE, of B. cepacia. It is highly similar to σEof other bacteria, including Escherichia coli and Pseudomonas aeruginosa. Studies using an rpoE knockout mutant of B. cepacia revealed that many stress adaptations, including osmotic, oxidative, desiccation, carbon, and nitrogen stress, were independent of σE. Similarly, biofilm formation; production of exopolysaccharides, N-acyl homoserine lactones, and several exoenzymes; and onion pathogenicity were not affected by the absence of σE. In contrast, σEcontributed to the adaptation to heat stress and phosphate starvation.Key words: Burkholderia cepacia, sigma factor, rpoE, extracytoplasmic function.
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Affiliation(s)
- Giulia Devescovi
- Bateriology Group, International Centre for Genetic Engineering & Biotechnology, Italy
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Bertani I, Venturi V. Regulation of the N-acyl homoserine lactone-dependent quorum-sensing system in rhizosphere Pseudomonas putida WCS358 and cross-talk with the stationary-phase RpoS sigma factor and the global regulator GacA. Appl Environ Microbiol 2004; 70:5493-502. [PMID: 15345437 PMCID: PMC520884 DOI: 10.1128/aem.70.9.5493-5502.2004] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Quorum sensing is a cell population-density dependent regulatory system which in gram-negative bacteria often involves the production and detection of N-acyl homoserine lactones (AHLs). Some Pseudomonas putida strains have been reported to produce AHLs, and one quorum-sensing locus has been identified. However, it appears that the majority of strains do not produce AHLs. In this study we report the identification and regulation of the AHL-dependent system of rhizosphere P. putida WCS358. This system is identical to the recently identified system of P. putida strain IsoF and very similar to the las system of Pseudomonas aeruginosa. It is composed of three genes, the luxI family member ppuI, the putative repressor rsaL, and the luxR family member ppuR. A genomic ppuR::Tn5 mutant of strain WCS358 was identified by its inability to produce AHLs when it was cross-streaked in close proximity to an AHL biosensor, whereas an rsaL::Tn5 genomic mutant was identified by its ability to overproduce AHL molecules. Using transcriptional promoter fusions, we studied expression profiles of the rsaL, ppuI, and ppuR promoters in various genetic backgrounds. At the onset of the stationary phase, the autoinducer synthase ppuI gene expression is under positive regulation by PpuR-AHL and under negative regulation by RsaL, indicating that the molecules could be in competition for binding at the ppuI promoter. In genomic rsaL::Tn5 mutants ppuI expression and production of AHL levels increased dramatically; however, both processes were still under growth phase regulation, indicating that RsaL is not involved in repressing AHL production at low cell densities. The roles of the global response regulator GacA and the stationary-phase sigma factor RpoS in the regulation of the AHL system at the onset of the stationary phase were also investigated. The P. putida WCS358 gacA gene was cloned and inactivated in the genome. It was determined that the three global regulatory systems are closely linked, with quorum sensing and RpoS regulating each other and GacA positively regulating ppuI expression. Studies of the regulation of AHL quorum-sensing systems have lagged behind other studies and are important for understanding how these systems are integrated into the overall growth phase and metabolic status of the cells.
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Affiliation(s)
- Iris Bertani
- Bacteriology Group, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34012 Trieste, Italy
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Bertani I, Sevo M, Kojic M, Venturi V. Role of GacA, LasI, RhlI, Ppk, PsrA, Vfr and ClpXP in the regulation of the stationary-phase sigma factor rpoS/RpoS in Pseudomonas. Arch Microbiol 2003; 180:264-71. [PMID: 12879217 DOI: 10.1007/s00203-003-0586-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2003] [Revised: 07/02/2003] [Accepted: 07/04/2003] [Indexed: 11/25/2022]
Abstract
RpoS is the stationary phase sigma factor responsible for increased transcription of a set of genes when bacterial cells enter stationary phase and under stress conditions. In Escherichia coli, RpoS expression is modulated at the level of transcription, translation, and post-translational stability whereas in Pseudomonas, previous studies have implicated four genetic loci ( psrA, gacA, lasI and rhlI) involved in rpoS transcription. In this report, the transcription, translation and proteins profiles of rpoS/RpoS were analyzed in response to growth phase of knockout genomic mutants in the P. aeruginosa transcriptional regulatory loci psrA, gacA, vfr, and in the las and rhl quorum-sensing systems. Gene expression and protein profiles were also analyzed in the ppk genomic mutant. This gene is responsible for the biosynthesis of polyphosphate, an alarmone involved in the regulation of RpoS accumulation in E. coli. Finally, the role of the ClpXP protease in RpoS regulation was also studied; in E. coli, this protease has been shown to rapidly degrade RpoS during exponential growth. These studies confirm the significant role of PsrA in rpoS transcription during the late-exponential and stationary growth phases, the probable role of Vfr in transcriptional repression during exponential phase, and the function of the ClpXP protease in RpoS degradation during exponential phase. GacA/GacS, the quorum-sensing systems, and the polyphosphate alarmone molecule were not significant in rpoS/RpoS regulation. These results demonstrate important similarities and differences with the regulation of this sigma factor in E. coli and in Pseudomonas.
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Affiliation(s)
- Iris Bertani
- Bacteriology Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, Padriciano 99, 34012, Trieste, Italy
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16
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Aguilar C, Bertani I, Venturi V. Quorum-sensing system and stationary-phase sigma factor (rpoS) of the onion pathogen Burkholderia cepacia genomovar I type strain, ATCC 25416. Appl Environ Microbiol 2003; 69:1739-47. [PMID: 12620866 PMCID: PMC150111 DOI: 10.1128/aem.69.3.1739-1747.2003] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial strains belonging to Burkholderia cepacia can be human opportunistic pathogens, plant pathogens, and plant growth promoting and have remarkable catabolic activity. B. cepacia consists of several genomovars comprising what is now known as the B. cepacia complex. Here we report the quorum-sensing system of a genomovar I onion rot type strain ATCC 25416. Quorum sensing is a cell-density-dependent regulatory response which involves the production of N-acyl homoserine lactone (HSL) signal molecules. The cep locus has been inactivated in the chromosome, and it has been shown that CepI is responsible for the biosynthesis of an N-hexanoyl HSL (C(6)-HSL) and an N-octanoyl HSL (C(8)-HSL) and that the cep locus regulates protease production as well as onion pathogenicity via the expression of a secreted polygalacturonase. A cep-lacZ-based sensor plasmid has been constructed and used to demonstrate that CepR responded to C(6)-HSL with only 15% of the molar efficiency of C(8)-HSL, that a cepR knockout mutant synthesized 70% less HSLs, and that CepR responded best towards long-chain HSLs. In addition, we also report the cloning and characterization of the stationary-phase sigma factor gene rpoS of B. cepacia ATCC 25416. It was established that quorum sensing in B. cepacia has a negative effect on rpoS expression as determined by using an rpoS-lacZ transcriptional fusion; on the other hand, rpoS-null mutants displayed no difference in the accumulation of HSL signal molecules.
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Affiliation(s)
- Claudio Aguilar
- Bacteriology Group, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34012 Trieste, Italy
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Devescovi G, Aguilar C, Majolini MB, Marugg J, Weisbeek P, Venturi V. A siderophore peptide synthetase gene from plant-growth-promoting Pseudomonas putida WCS358. Syst Appl Microbiol 2001; 24:321-30. [PMID: 11822666 DOI: 10.1078/0723-2020-00063] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Under iron limiting conditions, Pseudomonas putida WCS358 produces and secretes a fluorescent siderophore called pseudobactin 358 which consists of a nonapeptide linked to a fluorescent dihydroxy quinoline moiety. Previous studies have identified a major gene cluster involved in pseudobactin 358 biosynthesis and several regulators responsible for the activation of biosynthetic genes under iron starving conditions. In this study, we identified the promoter transcribing the pseudobactin 358 synthetase gene. Promoter deletion experiments have demonstrated that the DNA region downstream of the initiation of transcription site is necessary for proper promoter functioning. This promoter controls the expression of a gene designated ppsD which encodes a 2,247-residue protein, PpsD, which has a predicted molecular weight of 247,610 Da and contains two highly homologous domains of approximately 1000 amino acids each. ppsD::Tn5 mutants of strain WCS358 are unable to synthesise pseudobactin 358 and can be complemented when ppsD is provided in trans. It is concluded that ppsD is a peptide synthetase involved in the biosynthesis of the peptide moiety of pseudobactin 358. PpsD displays a very high degree of similarity (52% aa identity) with PvdD from P. aeruginosa, a non-ribosomal peptide synthetase involved in the biosynthesis of pyoverdine, the fluorescent siderophore produced by P. aeruginosa. It also displayed homology with other peptide synthetases from other micro-organisms involved in the biosynthesis of siderophores and peptide antibiotics.
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Affiliation(s)
- G Devescovi
- Bacteriology Group, International Centre for Genetic Engineering & Biotechnology, Trieste, Italy
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Kojic M, Venturi V. Regulation of rpoS gene expression in Pseudomonas: involvement of a TetR family regulator. J Bacteriol 2001; 183:3712-20. [PMID: 11371535 PMCID: PMC95248 DOI: 10.1128/jb.183.12.3712-3720.2001] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rpoS gene encodes the sigma factor which was identified in several gram-negative bacteria as a central regulator during stationary phase. rpoS gene regulation is known to respond to cell density, showing higher expression in stationary phase. For Pseudomonas aeruginosa, it has been demonstrated that the cell-density-dependent regulation response known as quorum sensing interacts with this regulatory response. Using the rpoS promoter of P. putida, we identified a genomic Tn5 insertion mutant of P. putida which showed a 90% decrease in rpoS promoter activity, resulting in less RpoS being present in a cell at stationary phase. Molecular analysis revealed that this mutant carried a Tn5 insertion in a gene, designated psrA (Pseudomonas sigma regulator), which codes for a protein (PsrA) of 26.3 kDa. PsrA contains a helix-turn-helix motif typical of DNA binding proteins and belongs to the TetR family of bacterial regulators. The homolog of the psrA gene was identified in P. aeruginosa; the protein showed 90% identity to PsrA of P. putida. A psrA::Tn5 insertion mutant of P. aeruginosa was constructed. In both Pseudomonas species, psrA was genetically linked to the SOS lexA repressor gene. Similar to what was observed for P. putida, a psrA null mutant of P. aeruginosa also showed a 90% reduction in rpoS promoter activity; both mutants could be complemented for rpoS promoter activity when the psrA gene was provided in trans. psrA mutants of both Pseudomonas species lost the ability to induce rpoS expression at stationary phase, but they retained the ability to produce quorum-sensing autoinducer molecules. PsrA was demonstrated to negatively regulate psrA gene expression in Pseudomonas and in Escherichia coli as well as to be capable of activating the rpoS promoter in E. coli. Our data suggest that PsrA is an important regulatory protein of Pseudomonas spp. involved in the regulatory cascade controlling rpoS gene regulation in response to cell density.
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Affiliation(s)
- M Kojic
- Bacteriology Group, International Centre for Genetic Engineering and Biotechnology, 34012 Trieste, Italy
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Bertani I, Kojic M, Venturi V. Regulation of the p-hydroxybenzoic acid hydroxylase gene (pobA) in plant-growth-promoting Pseudomonas putida WCS358. MICROBIOLOGY (READING, ENGLAND) 2001; 147:1611-1620. [PMID: 11390692 DOI: 10.1099/00221287-147-6-1611] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The regulation of the p-hydroxybenzoate hydroxylase gene (pobA) of Pseudomonas putida WCS358 involved in the catabolism of p-hydroxybenzoic acid (PHB) to the central intermediate protocatechuate was studied. Protocatechuic acid (PCA) is then degraded via the beta-ketoadipate pathway to form tricarboxylic acid intermediates. In several Gram-negative bacteria pobA has been found genetically linked to a regulator called pobR which activates pobA expression in response to PHB. In this study the identification and characterization of the pobC-pobA locus of P. putida WCS358 is presented. The p-hydroxybenzoate hydroxylase (PobA) is highly identical to other identified PobA proteins, whereas the regulatory protein PobC did not display very high identity to other PobR proteins studied and belonged to the AraC family of regulatory proteins, hence it has been designated POBC: Using the pobA promoter transcriptionally fused to a promoterless lacZ gene it was observed that induction via PobC occurred very efficiently when PHB was present and to a lesser but still significant level also in the presence of PCA. This PobC-PCA response was genetically demonstrated by making use of pobC::Tn5 and pcaH::Tn5 mutants of strain WCS358 constructed in this study. In pobC mutants both the p-hydroxybenzoic and PCA response were not observed, whereas in the pcaH mutant, which lacks a functional protocatechuate 3,4-dioxygenase, the protocatechuic-acid-dependent pobA activation was still observed. Finally, the activation of pobA by PHB varied according to the concentration and it was observed that in the pcaR::Tn5 regulatory mutant of strain WCS358 the pobA promoter activity was reduced. PcaR is a regulator involved in the regulation of several loci of the beta-ketoadipate pathway, one of which is pcaK. It was postulated that the reduction of pobA activation in pcaR::Tn5 mutants was because there was no expression of the pcaK gene encoding the PHB transport protein resulting in lower levels of PHB present inside the cell.
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Affiliation(s)
- Iris Bertani
- Bacteriology Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, Padriciano 99, 34012 Trieste, Italy1
| | - Milan Kojic
- Bacteriology Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, Padriciano 99, 34012 Trieste, Italy1
| | - Vittorio Venturi
- Bacteriology Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, Padriciano 99, 34012 Trieste, Italy1
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Báscones E, Imperial J, Ruiz-Argüeso T, Palacios JM. Generation of new hydrogen-recycling Rhizobiaceae strains by introduction of a novel hup minitransposon. Appl Environ Microbiol 2000; 66:4292-9. [PMID: 11010872 PMCID: PMC92298 DOI: 10.1128/aem.66.10.4292-4299.2000] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hydrogen evolution by nitrogenase is a source of inefficiency for the nitrogen fixation process by the Rhizobium-legume symbiosis. To develop a strategy to generate rhizobial strains with H(2)-recycling ability, we have constructed a Tn5 derivative minitransposon (TnHB100) that contains the ca. 18-kb H(2) uptake (hup) gene cluster from Rhizobium leguminosarum bv. viciae UPM791. Bacteroids from TnHB100-containing strains of R. leguminosarum bv. viciae PRE, Bradyrhizobium japonicum, R. etli, and Mesorhizobium loti expressed high levels of hydrogenase activity that resulted in full recycling of the hydrogen evolved by nitrogenase in nodules. Efficient processing of the hydrogenase large subunit (HupL) in these strains was shown by immunoblot analysis of bacteroid extracts. In contrast, Sinorhizobium meliloti, M. ciceri, and R. leguminosarum bv. viciae UML2 strains showed poor expression of the hup system that resulted in H(2)-evolving nodules. For the latter group of strains, no immunoreactive material was detected in bacteroid extracts using anti-HupL antiserum, suggesting a low level of transcription of hup genes or HupL instability. A general procedure for the characterization of the minitransposon insertion site and removal of antibiotic resistance gene included in TnHB100 has been developed and used to generate engineered strains suitable for field release.
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Affiliation(s)
- E Báscones
- Laboratorio de Microbiología, Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
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21
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Natera SH, Guerreiro N, Djordjevic MA. Proteome analysis of differentially displayed proteins as a tool for the investigation of symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2000; 13:995-1009. [PMID: 10975656 DOI: 10.1094/mpmi.2000.13.9.995] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Two-dimensional gel electrophoresis was used to identify differentially displayed proteins expressed during the symbiotic interaction between the bacterium Sinorhizobium meliloti strain 1021 and the legume Melilotus alba (white sweetclover). Our aim was to characterize novel symbiosis proteins and to determine how the two symbiotic partners alter their respective metabolisms as part of the interaction, by identifying gene products that are differentially present between the symbiotic and non-symbiotic states. Proteome maps from control M. alba roots, wild-type nodules, cultured S. meliloti, and S. meliloti bacteroids were generated and compared. Over 250 proteins were induced or up-regulated in the nodule, compared with the root, and over 350 proteins were down-regulated in the bacteroid form of the rhizobia, compared with cultured cells. N-terminal amino acid sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry peptide mass fingerprint analysis, in conjunction with data base searching, were used to assign putative identity to nearly 100 nodule, bacterial, and bacteroid proteins. These included the previously identified nodule proteins leghemoglobin and NifH as well as proteins involved in carbon and nitrogen metabolism in S. meliloti. Bacteroid cells showed down-regulation of several proteins involved in nitrogen acquisition, including glutamine synthetase, urease, a urea-amide binding protein, and a PII isoform, indicating that the bacteroids were nitrogen proficient. The down-regulation of several enzymes involved in polyhydroxybutyrate synthesis and a cell division protein was also observed. This work shows that proteome analysis will be a useful strategy to link sequence information and functional genomics.
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Affiliation(s)
- S H Natera
- Plant-Microbe Interaction Group, Research School of Biological Sciences, Australian National University, Canberra City
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22
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Brito B, Monza J, Imperial J, Ruiz-Argüeso T, Palacios JM. Nickel availability and hupSL activation by heterologous regulators limit symbiotic expression of the Rhizobium leguminosarum bv. viciae hydrogenase system in Hup(-) rhizobia. Appl Environ Microbiol 2000; 66:937-42. [PMID: 10698755 PMCID: PMC91926 DOI: 10.1128/aem.66.3.937-942.2000] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A limited number of Rhizobium and Bradyrhizobium strains possess a hydrogen uptake (Hup) system that recycles the hydrogen released from the nitrogen fixation process in legume nodules. To extend this ability to rhizobia that nodulate agronomically important crops, we investigated factors that affect the expression of a cosmid-borne Hup system from Rhizobium leguminosarum bv. viciae UPM791 in R. leguminosarum bv. viciae, Rhizobium etli, Mesorhizobium loti, and Sinorhizobium meliloti Hup(-) strains. After cosmid pAL618 carrying the entire hup system of strain UPM791 was introduced, all recipient strains acquired the ability to oxidize H(2) in symbioses with their hosts, although the levels of hydrogenase activity were found to be strain and species dependent. The levels of hydrogenase activity were correlated with the levels of nickel-dependent processing of the hydrogenase structural polypeptides and with transcription of structural genes. Expression of the NifA-dependent hupSL promoter varied depending on the genetic background, while the hyp operon, which is controlled by the FnrN transcriptional regulator, was expressed at similar levels in all recipient strains. With the exception of the R. etli-bean symbiosis, the availability of nickel to bacteroids strongly affected hydrogenase processing and activity in the systems tested. Our results indicate that efficient transcriptional activation by heterologous regulators and processing of the hydrogenase as a function of the availability of nickel to the bacteroid are relevant factors that affect hydrogenase expression in heterologous rhizobia.
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Affiliation(s)
- B Brito
- Laboratorio de Microbiología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
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23
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Venturi V, Zennaro F, Degrassi G, Okeke BC, Bruschi CV. Genetics of ferulic acid bioconversion to protocatechuic acid in plant-growth-promoting Pseudomonas putida WCS358. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 4):965-973. [PMID: 9579070 DOI: 10.1099/00221287-144-4-965] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Transposon Tn5 genomic mutants of plant-growth-promoting Pseudomonas putida strain WCS358 have been isolated which no longer utilize ferulic and coumaric acids as sole sources of carbon and energy. Genetic studies confirmed previous biochemical data showing that ferulic acid is degraded via vanillic acid, and coumaric acid via hydroxybenzoic acid. The genes involved in these enzymic steps were cloned and characterized. Two proteins designated Fca (26.5 kDa) and Vdh (50.3 kDa) were identified as responsible for the conversion of ferulic acid to vanillic acid; the proteins are encoded by the fca and vdh genes which are organized in an operon structure in the chromosome. The Vdh protein is 69% identical at the amino acid level to the Vdh protein recently identified in Pseudomonas sp. strain HR199 and converts vanillin to vanillic acid. Homology studies revealed that the Vdh proteins exhibited significant identity to aldehyde dehydrogenases from different organisms whereas Fca belonged to the enoyl-CoA hydratase family of proteins. Two proteins, designated VanA (39.9 kDa) and VanB (34.3 kDa), encoded by two genes, vanA and vanB, are organized in an operon in the chromosome. They were found to be responsible for the demethylation of vanillic acid to protocatechuic acid. The VanA proteins showed no homology to any other known protein, while VanB belonged to the ferredoxin family of proteins. This two-component enzyme system demethylated another phenolic monomer, veratric acid, thus indicating broad specificity. Studies of the regulation of the vanAB operon demonstrated that the genes were induced by the substrate, vanillic acid; however, the strongest induction was observed when cells were grown in the presence of the product of the reaction, protocatechuic acid.
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Affiliation(s)
- Vittorio Venturi
- 1. Bacteriology Group Area Science Park, Padriciano 99, 34012 Trieste, Italy
| | - Francesca Zennaro
- 2. Microbiology Group International Centre for Genetic Engineering and Biotechnology, Area Science Park, Padriciano 99, 34012 Trieste, Italy
| | - Giuliano Degrassi
- 1. Bacteriology Group Area Science Park, Padriciano 99, 34012 Trieste, Italy
| | - Benedict C Okeke
- 1. Bacteriology Group Area Science Park, Padriciano 99, 34012 Trieste, Italy
| | - Carlo V Bruschi
- 2. Microbiology Group International Centre for Genetic Engineering and Biotechnology, Area Science Park, Padriciano 99, 34012 Trieste, Italy
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Huerta-Zepeda A, Ortuño L, Du Pont G, Durán S, Lloret A, Merchant-Larios H, Calderón J. Isolation and characterization of Rhizobium etli mutants altered in degradation of asparagine. J Bacteriol 1997; 179:2068-72. [PMID: 9068657 PMCID: PMC178935 DOI: 10.1128/jb.179.6.2068-2072.1997] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Rhizobium etli mutants unable to grow on asparagine as the nitrogen and carbon source were isolated. Two kinds of mutants were obtained: AHZ1, with very low levels of aspartase activity, and AHZ7, with low levels of asparaginase and very low levels of aspartase compared to the wild-type strain. R. etli had two asparaginases differentiated by their thermostabilities, electrophoretic mobilities, and modes of regulation. The AHZ mutants nodulated as did the wild-type strain and had nitrogenase levels similar to that of the wild-type strain.
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Affiliation(s)
- A Huerta-Zepeda
- Departamento de Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F
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Durán S, Sánchez-Linares L, Huerta-Saquero A, Du Pont G, Huerta-Zepeda A, Calderón J. Identification of two glutaminases in Rhizobium etli. Biochem Genet 1996; 34:453-65. [PMID: 9126674 DOI: 10.1007/bf00570126] [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: 02/04/2023]
Abstract
We present evidence that Rhizobium etli has two glutaminases differentiated by their thermostability and electrophoretic mobility. The thermostable glutaminase (B) is constitutive, in contrast with the thermolabile glutaminase (A), which is positively regulated by glutamine and negatively regulated by ammonium and by the carbon source. In distinction to glutaminase A, glutaminase B plays a minor role in the utilization of glutamine as a carbon source, but it may play a role in maintaining the balance of glutamine and glutamate. By complementation of the Rhizobium etli LM16 mutant that lacks glutaminase A, we have cloned the gene that codes for this enzyme.
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Affiliation(s)
- S Durán
- Departamento de Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México México D.F., México
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Venturi V, Otten M, Korse V, Brouwer B, Leong J, Weisbeek P. Alginate regulatory and biosynthetic gene homologs in Pseudomonas putida WCS358: correlation with the siderophore regulatory gene pfrA. Gene 1995; 155:83-8. [PMID: 7698672 DOI: 10.1016/0378-1119(94)00868-s] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A previous study [Venturi et al., Mol. Microbiol. 10 (1993) 63-73] demonstrated that the siderophore regulatory gene pfrA of Pseudomonas putida (Pp) WCS358 is highly similar and interchangeable with the alginate regulatory gene algQ (algR2) of P. aeruginosa (Pa). The algQ gene is physically linked to two other alginate regulators in the Pa chromosome, namely algR (algR1), a response regulator, and algP (algR3), a histone-like gene. In this study, we have identified the same genes and a similar genetic organization in the Pp chromosome. The two genes linked to pfrA, designated pprA and pprB, are similar to algR and algP, respectively. Chromosomal mutants of pprA and pprB were constructed showing that unlike pfrA, the two newly identified regulators are not involved in siderophore regulation. The pprA gene complemented a Pa algR mutant phenotype, suggesting that it could be involved in alginate gene regulation. The WCS358 strain is not producing alginate, but we demonstrated by Southern analysis that it also possesses, in addition to pprA and pprB, algD and algU (algT) gene homologs, two genes essential for alginate biosynthesis. Using an algD-xylE transcriptional fusion, we observed that the algD promoter is active in strain WCS358 and absolutely requires pfrA. The possibility that all five genes of Pp WCS358 are involved in alginate biosynthesis is discussed.
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Affiliation(s)
- V Venturi
- Department of Molecular Cell Biology, University of Utrecht, The Netherlands
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27
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Venturi V, Ottevanger C, Bracke M, Weisbeek P. Iron regulation of siderophore biosynthesis and transport in Pseudomonas putida WCS358: involvement of a transcriptional activator and of the Fur protein. Mol Microbiol 1995; 15:1081-93. [PMID: 7623664 DOI: 10.1111/j.1365-2958.1995.tb02283.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Pseudobactin 358 is the yellow-green fluorescent siderophore produced by Pseudomonas putida WCS358 in conditions of iron limitation. The genes encoding for siderophore biosynthesis are iron-regulated at the transcriptional level. Previous work has shown that a positive regulator, PfrA, is absolutely required for the activation under iron-limiting conditions of pseudobactin 358 biosynthesis. In this study we identified a set of Tn5 insertion mutants of strain WCS358 which lost the ability to activate an iron-regulated siderophore promoter. These mutants no longer produced pseudobactin 358. Molecular analysis revealed that they carried a Tn5 insertion in a gene, designated pfrl (Pseudomonas ferric regulator), which codes for a protein (Pfrl) of 19.5 kDa. Pfrl contains a putative helix-turn-helix motif typical of DNA-binding proteins and has homology to two DNA-binding transcriptional activators, Fecl from Escherichia coli and Pupl from P. putida. The proposed role of Pfrl in strain WCS358 is an activator protein regulating pseudobactin 358 biosynthesis under iron limitation. The pfrl promoter region contains a sequence which displays high identity to the Fur-box consensus. This 19 bp consensus sequence is recognized by Fur, an iron-binding repressor protein found in many different bacteria. The E. coli Fur protein can bind to the pfrl promoter region, indicating that this activator gene is likely to be iron-regulated by Fur. We also report the identification and characterization of the P. putida WCS358 fur gene. The Fur protein of strain WCS358 is structurally and functionally similar to other cloned Fur proteins from other bacterial species.
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Affiliation(s)
- V Venturi
- Department of Molecular Cell Biology, University of Utrecht, The Netherlands
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28
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Bosworth AH, Williams MK, Albrecht KA, Kwiatkowski R, Beynon J, Hankinson TR, Ronson CW, Cannon F, Wacek TJ, Triplett EW. Alfalfa yield response to inoculation with recombinant strains of Rhizobium meliloti with an extra copy of dctABD and/or modified nifA expression. Appl Environ Microbiol 1994; 60:3815-32. [PMID: 7986051 PMCID: PMC201891 DOI: 10.1128/aem.60.10.3815-3832.1994] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The construction of rhizobial strains which increase plant biomass under controlled conditions has been previously reported. However, there is no evidence that these newly constructed strains increase legume yield under agricultural conditions. This work tested the hypothesis that carefully manipulating expression of additional copies of nifA and dctABD in strains of Rhizobium meliloti would increase alfalfa yield in the field. The rationale for this hypothesis is based on the positive regulatory role that nifA plays in the expression of the nif regulon and the fact that a supply of dicarboxylic acids from the plant is required as a carbon and energy source for nitrogen fixation by the Rhizobium bacteroids in the nodule. These recombinant strains, as well as the wild-type strains from which they were derived, are ideal tools to examine the effects of modifying or increasing the expression of these genes on alfalfa biomass. The experimental design comprised seven recombinant strains, two wild-type strains, and an uninoculated control. Each treatment was replicated eight times and was conducted at four field sites in Wisconsin. Recombinant strain RMBPC-2, which has an additional copy of both nifA and dctABD, increased alfalfa biomass by 12.9% compared with the yield with the wild-type strain RMBPC and 17.9% over that in the uninoculated control plot at the site where soil nitrogen and organic matter content was lowest. These increases were statistically significant at the 5% confidence interval for each of the three harvests made during the growing season. Strain RMBPC-2 did increase alfalfa biomass at the Hancock site; however, no other significant increases or decreases in alfalfa biomass were observed with the seven other recombinant strains at that site. At three sites where this experiment was conducted, either native rhizobial populations or soil nitrogen concentrations were high. At these sites, none of the recombinant strains affected yield. We conclude that RMBPC -2 can increase alfalfa yields under field conditions of nitrogen limitation, low endogenous rhizobial competitors, and sufficient moisture.
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Affiliation(s)
- A H Bosworth
- Department of Agronomy, University of Wisconsin-Madison 53706
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29
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Venturi V, Ottevanger C, Leong J, Weisbeek PJ. Identification and characterization of a siderophore regulatory gene (pfrA) of Pseudomonas putida WCS358: homology to the alginate regulatory gene algQ of Pseudomonas aeruginosa. Mol Microbiol 1993; 10:63-73. [PMID: 7968519 DOI: 10.1111/j.1365-2958.1993.tb00904.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Genes encoding biosynthesis of pseudobactin 358 (a microbial iron transport agent) and its cognate outer membrane receptor protein, PupA, are transcribed only under iron limitation in plant growth-promoting Pseudomonas putida WCS358. Two cosmid clones were identified from a gene bank of WCS358 DNA which could independently and in an iron-dependent manner activate transcription from a WCS358 siderophore gene promoter in heterologous Pseudomonas strain A225. The functional region of one of the clones was localized by subcloning, transposon Tn3Gus mutagenesis, and DNA sequencing. Genomic transposon insertion mutants in the functional region lost the capacity to activate a siderophore gene promoter fusion transcriptionally; furthermore, these mutants no longer produced pseudobactin 358. The activating region consisted of a single gene designated pfrA (Pseudomonas ferric regulator). The pfrA gene codes for a single polypeptide, PfrA, of approximately 18 kDa, which has 58% identity to AlgQ (also known as AlgR2), a positive regulator involved in transcriptionally regulating alginate biosynthesis in Pseudomonas aeruginosa. Cross-complementation studies between the pfrA gene of P. putida and the algQ gene of P. aeruginosa revealed that pfrA can restore mucoidy (alginate production) in an algQ mutant and that algQ could poorly complement a pfrA genomic mutant. It is concluded that PfrA is involved in the positive regulation of siderophore biosynthetic genes in response to iron limitation; furthermore, pfrA and algQ appeared to be interchangeable between P. putida and P. aeruginosa.
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Affiliation(s)
- V Venturi
- Department of Molecular Cell Biology, University of Utrecht, The Netherlands
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30
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Lois A, Weinstein M, Ditta G, Helinski D. Autophosphorylation and phosphatase activities of the oxygen-sensing protein FixL of Rhizobium meliloti are coordinately regulated by oxygen. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)53619-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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31
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Lois AF, Ditta GS, Helinski DR. The oxygen sensor FixL of Rhizobium meliloti is a membrane protein containing four possible transmembrane segments. J Bacteriol 1993; 175:1103-9. [PMID: 8432704 PMCID: PMC193026 DOI: 10.1128/jb.175.4.1103-1109.1993] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Regulation of nitrogen fixation genes in Rhizobium meliloti is mediated by two proteins, FixL and FixJ, in response to oxygen availability. FixL is an oxygen-binding hemoprotein with kinase and phosphatase activities that is thought to sense oxygen levels directly and to transmit this signal to FixJ via phosphorylation-dephosphorylation reactions. FixJ controls the expression of other regulatory genes, including nifA, that regulate the transcription of genes required for symbiotic nitrogen fixation. We have been studying the structural and functional features of FixL that are required for oxygen sensing. We constructed mutant derivatives and confirmed that FixL consists of 505 amino acids instead of 464, as originally reported. Hydropathy plots of the full-length protein, together with TnphoA insertional analysis, lead us to propose that FixL is likely to be a polytopic integral membrane protein containing four membrane-spanning segments. We have also constructed an N-terminal deletion of the FixL protein whose in vivo activity indicates that the hydrophobic membrane-spanning regions are not absolutely required for oxygen sensing in vivo. We also report that FixL shares homology in its N terminus with other sensor proteins, including KinA from Bacillus subtilis and NtrB from Bradyrhizobium parasponia. The region of homology comprises a 70-amino-acid residue stretch that is also conserved in two oxygenases, P-450 and isopenicillin synthase.
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Affiliation(s)
- A F Lois
- Department of Biology, University of California, San Diego, La Jolla 92093-0634
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32
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Abstract
The nifA gene of Rhizobium meliloti, the bacterial endosymbiont of alfalfa, is a regulatory nitrogen fixation gene required for the induction of several key nif and fix genes. Transcription of nifA is strongly induced in planta and under microaerobic conditions ex planta. Induction of nifA, in turn, is positively controlled by the fixL and fixJ genes of R. meliloti, the sensor and regulator, respectively, of a two-component system responsible for oxygen sensing by this bacterium. This system is also responsible for the positive induction of fixK. Here, we report that chemical and oligonucleotide site-directed mutageneses of the nifA promoter (nifAp) were conducted to identify nucleotides essential for induction. Nineteen mutants, including 14 single-point mutants, were analyzed for microaerobic induction of nifAp in R. meliloti. Critical residues were identified in an upstream region between base pairs -54 and -39 relative to the transcription start site. Attempts at separating the upstream and downstream regions of the nifA promoter so as to maintain fixJ-dependent activity were unsuccessful. A 5' deletion of the fixK promoter (fixKp) to -67 indicates that sequences upstream of this position are not required for microaerobic induction. A sequence comparison of the -54 to -39 region of nifAp with the upstream sequences of fixKp does not reveal a block of identical nucleotides that could account for the fixJ-dependent microaerobic induction of both promoters. Many of the defective nifAp mutants in this region, however, are in residues with identity to fixKp in an alignment of the promoters according to their transcription start sites. Therefore, it is possible that there is a common sequence motif in the -54 to -39 region of the two promoters that is required for fixLJ-dependent microaerobic induction.
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Affiliation(s)
- P G Agron
- Biology Department, University of California, San Diego, La Jolla 92093-0634
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33
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Nagpal P, Khanuja SP, Stanfield SW. Suppression of the ndv mutant phenotype of Rhizobium meliloti by cloned exo genes. Mol Microbiol 1992; 6:479-88. [PMID: 1560776 DOI: 10.1111/j.1365-2958.1992.tb01492.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The ndvA and ndvB genes of Rhizobium meliloti are involved in the export and synthesis, respectively, of the small cyclic polysaccharide beta(1,2)glucan. We have previously shown that spontaneous symbiotic pseudorevertants of ndv mutants do not produce periplasmic beta(1,2)glucan. Here we show that the pseudorevertants also do not produce extracellular beta(1,2)glucan, but do show alterations in the amount of the major acidic exopolysaccharide produced. This exopolysaccharide is not detectably different from that produced by the wild type or by the ndv mutants. A cosmid which suppresses the symbiotic defect of both ndvA and ndvB mutants was isolated from a gene bank prepared from DNA of an ndvA pseudorevertant. This cosmid contains a number of exo genes, including exoH and exoF. Subcloning and Tn5 mutagenesis were used to show that the widely separated exoH and exoF genes are both involved in suppression of the ndv mutant phenotype and that the 3.5 kb DNA fragment which contains the exoH gene does not carry the mutation responsible for second site suppression.
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Affiliation(s)
- P Nagpal
- Center for Molecular Genetics, University of California, San Diego, La Jolla 92093-0634
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34
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Mozo T, Cabrera E, Ruiz-Argüeso T. Isolation of the replication DNA region from a Rhizobium plasmid and examination of its potential as a replicon for Rhizobiaceae cloning vectors. Plasmid 1990; 23:201-15. [PMID: 2217572 DOI: 10.1016/0147-619x(90)90052-e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The DNA region essential for replication and stability of a native plasmid (pTM5) from Rhizobium sp. (Hedysarum) has been identified and isolated within a 5.4-kb PstI restriction fragment. The isolation of this region was accomplished by cloning endonuclease-restricted pTM5 DNA into a ColE1-type replicon and selecting the recombinant plasmids containing the pTM5 replicator (pTM5 derivative plasmids) by their ability to replicate in Rhizobium. DNA homology studies revealed that pTM5-like replicons are present in cryptic plasmids from some Rhizobium sp. (Hedysarum) strains but not in plasmids from strains of other Rhizobium species or Agrobacterium tumefaciens. The pTM5 derivative plasmids were able to replicate in Escherichia coli and A. tumefaciens and in a wide range of Rhizobium species. On the basis of stability assays in the absence of antibiotic selective pressure, the pTM5 derivative plasmids were shown to be highly stable in both free-living and symbiotic cells of Rhizobium sp. (Hedysarum). The stability of these plasmids in other species of Rhizobium and in A. tumefaciens varied depending on the host and on the plasmid. Most pTM5 derivative plasmids tested showed significantly higher symbiotic stability than RK2 derivative plasmids pRK290 and pAL618 in Rhizobium sp. (Hedysarum), R. meliloti, and R. leguminosarum by. phaseoli. Consequently, we consider that the constructed pTM5 derivative plasmids are potentially useful as cloning vectors for Rhizobiaceae.
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Affiliation(s)
- T Mozo
- Laboratorio de Microbiología, ETS Ingenieros Agrónomos, Universidad Politécnica, Madrid, Spain
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35
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Dylan T, Nagpal P, Helinski DR, Ditta GS. Symbiotic pseudorevertants of Rhizobium meliloti ndv mutants. J Bacteriol 1990; 172:1409-17. [PMID: 2307652 PMCID: PMC208613 DOI: 10.1128/jb.172.3.1409-1417.1990] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Nodule development (ndv) mutants of Rhizobium meliloti cannot invade alfalfa to establish a nitrogen-fixing symbiosis and instead induce the formation of small, white, unoccupied nodules on alfalfa roots. Such mutants also fail to produce the unusual cyclic oligosaccharide beta-(1----2)-glucan and show defects in several aspects of vegetative growth and function. Here we show that ndv mutants are severely reduced, although not totally deficient, in the ability to attach to and initiate infection threads on alfalfa seedlings, and we demonstrate that the symbiotic deficiency can be separated from the rest of the mutant phenotype by isolating second-site pseudorevertants. Pseudorevertants selected for restoration of motility, a vegetative property, regained a substantial amount of attachment capability but only slight infection thread initiation and symbiotic ability. Such strains also regained partial tolerance to growth at low osmolarity, even though they did not recover the ability to synthesize periplasmic beta-(1----2)-glucan. Pseudorevertants selected on alfalfa for restoration of symbiosis were unrestored for beta-(1----2)-glucan production or any other vegetative property and regained little or no attachment or infection thread initiation capability. We take these data to indicate that wild-type R. meliloti normally has considerable excess capability for both attachment and infection thread initiation and that the symbiotic block in ndv mutants lies further along the developmental pathway than either of these processes, probably at the level of infection thread extension. Further, the fact that neither type of pseudorevertant recovered the ability to produce periplasmic beta-(1----2)-glucan raises the possibility that this oligosaccharide is not directly required for nodule development.
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Affiliation(s)
- T Dylan
- Department of Biology and Center for Molecular Genetics, University of California, San Diego, La Jolla 92093
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36
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Sharma SB, Signer ER. Temporal and spatial regulation of the symbiotic genes of Rhizobium meliloti in planta revealed by transposon Tn5-gusA. Genes Dev 1990; 4:344-56. [PMID: 2159937 DOI: 10.1101/gad.4.3.344] [Citation(s) in RCA: 169] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Tn5-gusA promoter/probe transposons have been constructed that fuse the Escherichia coli gusA reporter gene transcriptionally or translationally with a target promoter. These have been used to monitor expression of Rhizobium meliloti symbiotic genes within alfalfa nodules. Fusions in all 11 nod genes studied show the same pattern of expression: first on the root surface, then throughout the developing nodule, then mainly in the nodule meristem, falling off progressively through the central region, and then disappearing. In contrast, fusions in all five nif genes studied, all four fix genes, and syrM show a second, different pattern: expression beginning later, first throughout the nodule except for the meristem, strongest just behind the meristem, and falling off progressively through the central region. Novel features revealed by these studies include nod expression in the meristem, regulated in planta expression of control genes nodD1 and nodD3, disappearance of nod expression late in organogenesis, and properties of syrM.
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Affiliation(s)
- S B Sharma
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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37
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Ielpi L, Dylan T, Ditta GS, Helinski DR, Stanfield SW. The ndvB locus of Rhizobium meliloti encodes a 319-kDa protein involved in the production of beta-(1----2)-glucan. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39878-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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38
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Kittell BL, Helinski DR, Ditta GS. Aromatic aminotransferase activity and indoleacetic acid production in Rhizobium meliloti. J Bacteriol 1989; 171:5458-66. [PMID: 2551887 PMCID: PMC210384 DOI: 10.1128/jb.171.10.5458-5466.1989] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Bacterial indoleacetic acid (IAA) production, which has been proposed to play a role in the Rhizobium-legume symbiosis, is a poorly understood process. Previous data have suggested that IAA biosynthesis in Rhizobium meliloti can occur through an indolepyruvate intermediate derived from tryptophan by an aminotransferase activity. To further examine this biosynthetic pathway, the aromatic aminotransferase (AAT) activity of Rhizobium meliloti 102F34 (F34) was characterized. At least four proteins were detected on nondenaturing gels of F34 protein extracts that exhibited AAT activity. All four of these AATs were constitutively produced and utilized the aromatic amino acids tryptophan, phenylalanine, and tyrosine as amino substrates. Two AATs were also capable of using aspartate. Plasmids from an F34 gene bank were identified that coded for the synthesis of at least three of these proteins, and the respective gene sequences were localized by transposon mutagenesis. Selected transposon insertions were recombined into the F34 genome to produce strains defective in two of these proteins (AAT1 and AAT2). Characterization of the mutants revealed that neither was essential for the biosynthesis of IAA in the absence of exogenous tryptophan, but that both contributed to IAA biosynthesis when high levels of exogenous tryptophan were present. AAT1 and AAT2 were also not required for the production of a minimal level of aromatic amino acids, but both were able to scavenge nitrogen from the aromatic amino acids during nitrogen deprivation. Neither AAT1 nor AAT2 was essential for symbiosis with alfalfa.
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Affiliation(s)
- B L Kittell
- Department of Biology, University of California, San Diego, La Jolla 92093
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39
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Palomares AJ, DeLuca MA, Helinski DR. Firefly luciferase as a reporter enzyme for measuring gene expression in vegetative and symbiotic Rhizobium meliloti and other gram-negative bacteria. Gene 1989; 81:55-64. [PMID: 2680767 DOI: 10.1016/0378-1119(89)90336-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A DNA segment carrying a cDNA copy of the luciferase gene (luc) of the North American firefly Photinus pyralis, fused to the lambda PR promoter and expressed in Escherichia coli [de Wet et al., Proc. Natl. Acad. Sci. USA 82 (1985) 7870-7873], was inserted into a broad-host-range plasmid vector and established in a variety of Gram-negative bacteria. Luciferase activity, expressed from the lambda PR promoter, was detected in both intact cells and extracts prepared from cells of strains of Rhizobium meliloti, R. phaseoli, R. fredii, Pseudomonas aeruginosa, Agrobacterium tumefaciens, Acinetobacter calcoaceticus and Azotobacter vinelandii. The highest levels of activity, determined by measurements of both intact cells and extracts, were observed for P. aeruginosa and the three species of Rhizobium examined. Expression of luciferase activity also was relatively high in R. meliloti bacteroids of mature alfalfa nodules. This activity was readily detectable in intact nodules using x-ray film or in extracts prepared from purified bacteroids.
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Affiliation(s)
- A J Palomares
- Department of Biology, University of California, San Diego, La Jolla 92093
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40
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Expression from symbiotic promoters ofRhizobium meliloti inAzotobacter vinelandii andAzospirillum brasilense. J Biosci 1988. [DOI: 10.1007/bf02712156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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41
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Virts EL, Stanfield SW, Helinski DR, Ditta GS. Common regulatory elements control symbiotic and microaerobic induction of nifA in Rhizobium meliloti. Proc Natl Acad Sci U S A 1988; 85:3062-5. [PMID: 2834732 PMCID: PMC280143 DOI: 10.1073/pnas.85.9.3062] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We have previously demonstrated that the nifA promoter (nifAp) of Rhizobium meliloti is inducible under microaerobic conditions in the absence of alfalfa. Here we show that microaerobic activation of nifAp involves both cis- and trans-acting regulatory controls identical to those used symbiotically. The start site for nifA mRNA synthesis was found to be the same during symbiosis and microaerobiosis, and a deletion analysis of nifAp demonstrated that DNA between positions -62 and -45 is essential for induction. Mutants isolated as being unable to induce nifA microaerobically also were found to be defective in symbiotic nitrogen fixation with alfalfa. Such mutants form nodules that are equivalent cytologically to those induced by nifA::Tn5 mutants. Genetic and structural studies have localized the mutations to a cluster of fix genes 200 kilobases distant from the nod-nif region on the pSym megaplasmid [Renalier, M.-H., Batut, J., Ghai, J., Terzaghi, B., Gherardi, M., David, M., Garnerone, A.-M., Vasse, J., Truchet, G., Huguet, T. & Boistard, P. (1987) J. Bacteriol. 169, 2231-2238].
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Affiliation(s)
- E L Virts
- Biology Department, University of California at San Diego, La Jolla 92093
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42
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Mozo T, Cabrera E, Ruiz-Argüeso T. Diversity of Plasmid Profiles and Conservation of Symbiotic Nitrogen Fixation Genes in Newly Isolated
Rhizobium
Strains Nodulating Sulla (
Hedysarum coronarium
L.). Appl Environ Microbiol 1988; 54:1262-7. [PMID: 16347636 PMCID: PMC202637 DOI: 10.1128/aem.54.5.1262-1267.1988] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Forty-five
Rhizobium
strains nodulating sulla (
Hedysarum coronarium
L.), isolated from plants grown in different sites in Menorca Island and southern Spain, were examined for plasmid content and the location and organization of
nif
(nitrogen fixation) and
nod
(nodulation) sequences. A great diversity in both number and size of the plasmids was observed in this native population of strains, which could be distributed among 19 different groups according to their plasmid profiles. No correlation was found between plasmid profile and geographical origin of the strains. In each strain a single plasmid ranging from 187 to 349 megadaltons hybridized to
Rhizobium meliloti nifHD
and
nodD
DNA, and in three strains the spontaneous loss of this plasmid resulted in the loss of the nodulation capacity. In addition to the symbiotic plasmid, 18 different cryptic plasmids were identified. A characteristic cryptic plasmid of >1,000 megadaltons was present in all strains. Total DNA hybridization experiments, with
nifHD
and portions of
nodC
and
nodD
genes (coding for common nodulation functions) from
R. meliloti
as probes, demonstrated that both the sequence and organization of
nif
and common
nod
genes were highly conserved within rhizobia nodulating sulla. Evidence for reiteration of
nodD
sequences and for linkage of
nodC
to at least one copy of
nodD
was obtained for all the strains examined. From these results we conclude that
Rhizobium
strains nodulating sulla are a homogeneous group of symbiotic bacteria that are closely related to the classical fast-growing group of rhizobia.
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Affiliation(s)
- T Mozo
- Departamento de Microbiología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica, 28040 Madrid, Spain
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43
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Singh RK, Stevens S, Bryant DA. Molecular cloning and physical mapping of the nitrogenase structural genes from the filamentous, non-heterocystous cyanobacteriumPseudanabaenasp. PCC7409. FEMS Microbiol Lett 1987. [DOI: 10.1111/j.1574-6968.1987.tb02514.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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44
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Leyva A, Palacios JM, Mozo T, Ruiz-Argüeso T. Cloning and characterization of hydrogen uptake genes from Rhizobium leguminosarum. J Bacteriol 1987; 169:4929-34. [PMID: 2822654 PMCID: PMC213888 DOI: 10.1128/jb.169.11.4929-4934.1987] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A gene library of genomic DNA from the hydrogen uptake (Hup)-positive strain 128C53 of Rhizobium leguminosarum was constructed by using the broad-host-range mobilizable cosmid vector pLAFR1. The resulting recombinant cosmids contained insert DNA averaging 21 kilobase pairs (kb) in length. Two clones from the above gene library were identified by colony hybridization with DNA sequences from plasmid pHU1 containing hup genes of Bradyhizobium japonicum. The corresponding recombinant cosmids, pAL618 and pAL704, were isolated, and a region of about 28 kb containing the sequences homologous to B. japonicum hup-specific DNA was physically mapped. Further hybridization analysis with three fragments from pHU1 (5.9-kb HindIII, 2.9-kb EcoRI, and 5.0-kb EcoRI) showed that the overall arrangement of the R. leguminosarum hup-specific region closely parallels that of B. japonicum. The presence of functional hup genes within the isolated cosmid DNA was demonstrated by site-directed Tn5 mutagenesis of the 128C53 genome and analysis of the Hup phenotype of the Tn5 insertion strains in symbiosis with peas. Transposon Tn5 insertions at six different sites spanning 11 kb of pAL618 completely suppressed the hydrogenase activity of the pea bacteroids.
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Affiliation(s)
- A Leyva
- Departamento de Microbiología, Universidad Politécnica, Madrid, Spain
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45
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Leyva A, Palacios JM, Ruiz-Argüeso T. Conserved Plasmid Hydrogen-Uptake (
hup
)-Specific Sequences within Hup
+
Rhizobium leguminosarum
Strains. Appl Environ Microbiol 1987; 53:2539-43. [PMID: 16347471 PMCID: PMC204142 DOI: 10.1128/aem.53.10.2539-2543.1987] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thirteen
Rhizobium leguminosarum
strains previously reported as H
2
-uptake hydrogenase positive (Hup
+
) or negative (Hup
−
) were analyzed for the presence and conservation of DNA sequences homologous to cloned
Bradyrhizobium japonicum hup
-specific DNA from cosmid pHU1 (M. A. Cantrell, R. A. Haugland, and H. J. Evans, Proc. Natl. Acad. Sci. USA 80:181-185, 1983). The Hup phenotype of these strains was reexamined by determining hydrogenase activity induced in bacteroids from pea nodules. Five strains, including H
2
oxidation-ATP synthesis-coupled and -uncoupled strains, induced significant rates of H
2
-uptake hydrogenase activity and contained DNA sequences homologous to three probe DNA fragments (5.9-kilobase [kb]
Hin
dIII, 2.9-kb
Eco
RI, and 5.0-kb
Eco
RI) from pHU1. The pattern of genomic DNA
Hin
dIII and
Eco
RI fragments with significant homology to each of the three probes was identical in all five strains regardless of the H
2
-dependent ATP generation trait. The restriction fragments containing the homology totalled about 22 kb of DNA common to the five strains. In all instances the putative
hup
sequences were located on a plasmid that also contained
nif
genes. The molecular sizes of the identified
hup-sym
plasmids ranged between 184 and 212 megadaltons. No common DNA sequences homologous to
B. japonicum hup
DNA were found in genomic DNA from any of the eight remaining strains showing no significant hydrogenase activity in pea bacteroids. These results suggest that the identified DNA region contains genes essential for hydrogenase activity in
R. leguminosarum
and that its organization is highly conserved within Hup
+
strains in this symbiotic species.
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Affiliation(s)
- A Leyva
- Departamento de Microbiología, Escuela Tecnica Superior de Ingenieros Agrónomos, Universidad Politécnica, 28040-Madrid, Spain
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46
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Nitrogen fixation genes (nif K,D,H) in the filamentous nonheterocystous cyanobacteriumPlectonema boryanum do not rearrange. J Genet 1987. [DOI: 10.1007/bf02931656] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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47
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Rubin RA. Genetic analysis of the gentamicin resistance region of pPH1JI and incorporation into a wide host range cloning vehicle. Plasmid 1987; 18:84-8. [PMID: 2827208 DOI: 10.1016/0147-619x(87)90081-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A region of the IncP plasmid pPH1JI encoding resistance to gentamicin, spectinomycin, and streptomycin was characterized by subcloning, deletion, and insertion mutagenesis. Approximate locations of these resistance determinants were established. A 1.6-kb HindIII-SphI segment of this region expresses gentamicin resistance (Gmr) in Escherichia coli when inserted into various plasmid vectors; this DNA segment encodes a polypeptide of 17.5 kDa. Incorporation of this fragment into an IncP cloning vehicle produced a Gmr wide host range vector, pRAR209, which confers levels of Gmr comparable to those expressed by pPH1JI in E. coli, Agrobacterium tumefaciens, and Rhizobium meliloti.
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Affiliation(s)
- R A Rubin
- BioTechnica International, Inc., Cambridge, Massachusetts 02140
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David M, Domergue O, Pognonec P, Kahn D. Transcription patterns of Rhizobium meliloti symbiotic plasmid pSym: identification of nifA-independent fix genes. J Bacteriol 1987; 169:2239-44. [PMID: 2437100 PMCID: PMC212141 DOI: 10.1128/jb.169.5.2239-2244.1987] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We performed a systematic survey of transcription of a large region of the Rhizobium meliloti symbiotic plasmid pSym. This led to the discovery of two new sequences induced during symbiosis. The first sequence was linked to the known nitrogen fixation (nif-fix) gene cluster, and its expression depended on the nifA gene product. The second sequence was a novel fix locus (M.-H. Renalier, J. Batut, J. Ghai, B. Terzaghi, M. Gherardi, M. David, A.-M. Garnerone, J. Vasse, G. Truchet, T. Huguet, and P. Boistard, J. Bacteriol. 169:2231-2238, 1987) whose expression was independent of the nifA gene product; therefore this fix locus undergoes a novel type of symbiotic regulation.
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Cadah�a E, Leyva A, Ruiz-Arg�eso T. Indigenous plasmids and cultural characteristics of rhizobia nodulating chickpeas (Cicer arietinum L.). Arch Microbiol 1986. [DOI: 10.1007/bf00403223] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Prakash R, Atherly† AG. Plasmids of Rhizobium and Their Role in Symbiotic Nitrogen Fixation. INTERNATIONAL REVIEW OF CYTOLOGY 1986. [DOI: 10.1016/s0074-7696(08)61921-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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