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Ataeian M, Vadlamani A, Haines M, Mosier D, Dong X, Kleiner M, Strous M, Hawley AK. Proteome and strain analysis of cyanobacterium Candidatus "Phormidium alkaliphilum" reveals traits for success in biotechnology. iScience 2021; 24:103405. [PMID: 34877483 PMCID: PMC8633866 DOI: 10.1016/j.isci.2021.103405] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/27/2021] [Accepted: 11/03/2021] [Indexed: 11/18/2022] Open
Abstract
Cyanobacteria encompass a diverse group of photoautotrophic bacteria with important roles in nature and biotechnology. Here we characterized Candidatus “Phormidium alkaliphilum,” an abundant member in alkaline soda lake microbial communities globally. The complete, circular whole-genome sequence of Ca. “P. alkaliphilum” was obtained using combined Nanopore and Illumina sequencing of a Ca. “P. alkaliphilum” consortium. Strain-level diversity of Ca. “P. alkaliphilum” was shown to contribute to photobioreactor robustness under different operational conditions. Comparative genomics of closely related species showed that adaptation to high pH was not attributed to specific genes. Proteomics at high and low pH showed only minimal changes in gene expression, but higher productivity in high pH. Diverse photosystem antennae proteins, and high-affinity terminal oxidase, compared with other soda lake cyanobacteria, appear to contribute to the success of Ca. “P. alkaliphilum” in photobioreactors and biotechnology applications. Closed genome of the cyanobacteria Ca. P. alkaliphilum from high-pH photobioreactor Genetic factors lead this Phormidium to outcompete other cyanobacteria in photobioreactor Adaptation to high pH and alkalinity is not linked to specific genes Strain-level diversity contributes Ca. P. alkaliphilum success in changing conditions
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Affiliation(s)
- Maryam Ataeian
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | | | - Marianne Haines
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Damon Mosier
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Alyse K. Hawley
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
- School of Engineering, University of British Columbia Okanagan, Kelowna, BC, Canada
- Corresponding author
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Qiu S, Li Q, Xu Y, Shen S, Sun C. Learning from nature: Understanding hydrogenase enzyme using computational approach. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1422] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Siyao Qiu
- Science & Technology Innovation Institute Dongguan University of Technology Dongguan China
| | - Qinye Li
- School of Chemical Engineering Monash University Clayton Victoria Australia
| | - Yongjun Xu
- Science & Technology Innovation Institute Dongguan University of Technology Dongguan China
| | - Shaohua Shen
- International Research Center for Renewable Energy, State Key Laboratory of Multiphase Flow in Power Engineering Xi'an Jiaotong University Shaanxi China
| | - Chenghua Sun
- Department of Chemistry and Biotechnology, and Center for Translational Atomaterials Swinburne University of Technology Hawthorn Victoria Australia
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Piché-Choquette S, Constant P. Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes. Appl Environ Microbiol 2019; 85:e02418-18. [PMID: 30658976 PMCID: PMC6414374 DOI: 10.1128/aem.02418-18] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H2). H2 has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement. Even today, hydrogenase enzymes enabling the production and oxidation of H2 are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H2 has already been proposed as a universal growth and maintenance energy source, its potential contribution as a driver of biogeochemical cycles has received little attention. Here, we bridge this knowledge gap by providing an overview of the classification, distribution, and physiological role of hydrogenases. Distribution of these enzymes in various microbial functional groups and recent experimental evidence are finally integrated to support the hypothesis that H2-oxidizing microbes are keystone species driving C cycling along O2 concentration gradients found in H2-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H2-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H2 on C cycling and the C-cycling potential of H2-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H2 as a driver of biogeochemical processes.
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Havelka UD, Boyle MG, Hardy RWF. Biological Nitrogen Fixation. NITROGEN IN AGRICULTURAL SOILS 2015. [DOI: 10.2134/agronmonogr22.c10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- U. D. Havelka
- Central Research and Development Department E. I. du Pont de Nemours and Company; Wilmington Delaware
| | - M. G. Boyle
- Central Research and Development Department E. I. du Pont de Nemours and Company; Wilmington Delaware
| | - R. W. F. Hardy
- Central Research and Development Department E. I. du Pont de Nemours and Company; Wilmington Delaware
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Annan H, Golding AL, Zhao Y, Dong Z. Choice of hydrogen uptake (Hup) status in legume-rhizobia symbioses. Ecol Evol 2012; 2:2285-90. [PMID: 23139886 PMCID: PMC3488678 DOI: 10.1002/ece3.325] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 06/07/2012] [Accepted: 06/18/2012] [Indexed: 11/30/2022] Open
Abstract
The H2 is an obligate by-product of N-fixation. Recycling of H2 through uptake hydrogenase (Hup) inside the root nodules of leguminous plants is often considered an advantage for plants. However, many of the rhizobium-legume symbioses found in nature, especially those used in agriculture are shown to be Hup−, with the plants releasing H2 produced by nitrogenase activity from root nodules into the surrounding rhizosphere. Recent studies have suggested that, H2 induces plant-growth-promoting rhizobacteria, which may explain the widespread of Hup− symbioses in spite of the low energy efficiency of such associations. Wild legumes grown in Nova Scotia, Canada, were surveyed to determine if any plant-growth characteristics could give an indication of Hup choice in leguminous plants. Out of the plants sampled, two legumes, Securigera varia and Vicia cracca, showed Hup+ associations. Securigera varia exhibited robust root structure as compared with the other plants surveyed. Data from the literature and the results from this study suggested that plants with established root systems are more likely to form the energy-efficient Hup+ symbiotic relationships with rhizobia. Conversely, Hup− associations could be beneficial to leguminous plants due to H2-oxidizing plant-growth-promoting rhizobacteria that allow plants to compete successfully, early in the growing season. However, some nodules from V. cracca tested Hup+, while others were Hup−. This was similar to that observed in Glycine max and Pisum sativum, giving reason to believe that Hup choice might be affected by various internal and environmental factors.
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Affiliation(s)
- Henry Annan
- Department of Biology, Saint Mary's University 923 Robie Street, Halifax, Nova Scotia, Canada, B3H 3C3
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Bothe H, Schmitz O, Yates MG, Newton WE. Nitrogen fixation and hydrogen metabolism in cyanobacteria. Microbiol Mol Biol Rev 2010; 74:529-51. [PMID: 21119016 PMCID: PMC3008169 DOI: 10.1128/mmbr.00033-10] [Citation(s) in RCA: 181] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This review summarizes recent aspects of (di)nitrogen fixation and (di)hydrogen metabolism, with emphasis on cyanobacteria. These organisms possess several types of the enzyme complexes catalyzing N(2) fixation and/or H(2) formation or oxidation, namely, two Mo nitrogenases, a V nitrogenase, and two hydrogenases. The two cyanobacterial Ni hydrogenases are differentiated as either uptake or bidirectional hydrogenases. The different forms of both the nitrogenases and hydrogenases are encoded by different sets of genes, and their organization on the chromosome can vary from one cyanobacterium to another. Factors regulating the expression of these genes are emerging from recent studies. New ideas on the potential physiological and ecological roles of nitrogenases and hydrogenases are presented. There is a renewed interest in exploiting cyanobacteria in solar energy conversion programs to generate H(2) as a source of combustible energy. To enhance the rates of H(2) production, the emphasis perhaps needs not to be on more efficient hydrogenases and nitrogenases or on the transfer of foreign enzymes into cyanobacteria. A likely better strategy is to exploit the use of radiant solar energy by the photosynthetic electron transport system to enhance the rates of H(2) formation and so improve the chances of utilizing cyanobacteria as a source for the generation of clean energy.
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Affiliation(s)
- Hermann Bothe
- Botanical Institute, The University of Cologne, Zülpicher Str. 47b, D-50923 Cologne, Germany.
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Ciccolella CO, Raynard NA, Mei JHM, Church DC, Ludwig RA. Symbiotic legume nodules employ both rhizobial exo- and endo-hydrogenases to recycle hydrogen produced by nitrogen fixation. PLoS One 2010; 5:e12094. [PMID: 20838423 PMCID: PMC2930871 DOI: 10.1371/journal.pone.0012094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2010] [Accepted: 07/16/2010] [Indexed: 11/19/2022] Open
Abstract
Background In symbiotic legume nodules, endosymbiotic rhizobia (bacteroids) fix atmospheric N2, an ATP-dependent catalytic process yielding stoichiometric ammonium and hydrogen gas (H2). While in most legume nodules this H2 is quantitatively evolved, which loss drains metabolic energy, certain bacteroid strains employ uptake hydrogenase activity and thus evolve little or no H2. Rather, endogenous H2 is efficiently respired at the expense of O2, driving oxidative phosphorylation, recouping ATP used for H2 production, and increasing the efficiency of symbiotic nodule N2 fixation. In many ensuing investigations since its discovery as a physiological process, bacteroid uptake hydrogenase activity has been presumed a single entity. Methodology/Principal Findings Azorhizobium caulinodans, the nodule endosymbiont of Sesbania rostrata stems and roots, possesses both orthodox respiratory (exo-)hydrogenase and novel (endo-)hydrogenase activities. These two respiratory hydrogenases are structurally quite distinct and encoded by disparate, unlinked gene-sets. As shown here, in S. rostrata symbiotic nodules, haploid A. caulinodans bacteroids carrying single knockout alleles in either exo- or-endo-hydrogenase structural genes, like the wild-type parent, evolve no detectable H2 and thus are fully competent for endogenous H2 recycling. Whereas, nodules formed with A. caulinodans exo-, endo-hydrogenase double-mutants evolve endogenous H2 quantitatively and thus suffer complete loss of H2 recycling capability. More generally, from bioinformatic analyses, diazotrophic microaerophiles, including rhizobia, which respire H2 may carry both exo- and endo-hydrogenase gene-sets. Conclusions/Significance In symbiotic S. rostrata nodules, A. caulinodans bacteroids can use either respiratory hydrogenase to recycle endogenous H2 produced by N2 fixation. Thus, H2 recycling by symbiotic legume nodules may involve multiple respiratory hydrogenases.
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Affiliation(s)
- Christopher O. Ciccolella
- Sinsheimer Laboratories, Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Nathan A. Raynard
- Sinsheimer Laboratories, Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - John H-M. Mei
- Sinsheimer Laboratories, Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Derek C. Church
- Sinsheimer Laboratories, Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Robert A. Ludwig
- Sinsheimer Laboratories, Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
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Barraquio WL, Dumont A, Knowles R. Enumeration of free-living aerobic n(2)-fixing h(2)-oxidizing bacteria by using a heterotrophic semisolid medium and most-probable-number technique. Appl Environ Microbiol 2010; 54:1313-7. [PMID: 16347643 PMCID: PMC202655 DOI: 10.1128/aem.54.6.1313-1317.1988] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A heterotrophic semisolid medium was used with two sensitive assay methods, C(2)H(2) reduction and O(2)-dependent tritium uptake, to determine nitrogenase and hydrogenase activities, respectively. Organisms known to be positive for both activities showed hydrogenase activity in both the presence and absence of 1% C(2)H(2), and thus, it was possible to test a single culture for both activities. Hydrogen uptake activity was detected for the first time in N(2)-fixing strains of Pseudomonas stutzeri. The method was then applied to the most-probable-number method of counting N(2)-fixing and H(2)-oxidizing bacteria in some natural systems. The numbers of H(2)-oxidizing diazotrophs were considerably higher in soil surrounding nodules of white beans than they were in the other systems tested. This observation is consistent with reports that the rhizosphere may be an important ecological niche for H(2) transformation.
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Affiliation(s)
- W L Barraquio
- Department of Microbiology, Macdonald College of McGill University, 21111 Lakeshore Road, Ste. Anne de Bellevue, Québec, Canada H9X 1C0
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Cantrell MA, Haugland RA, Evans HJ. Construction of a Rhizobium japonicum gene bank and use in isolation of a hydrogen uptake gene. Proc Natl Acad Sci U S A 2010; 80:181-5. [PMID: 16593268 PMCID: PMC393335 DOI: 10.1073/pnas.80.1.181] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A gene bank of Rhizobium japonicum DNA was constructed by using the broad host range conjugative cosmid pLAFR1. Eighty-three percent of the clones in the bank contained cosmids with insert DNA averaging 22.6 kilobase pairs in length. A series of cosmids containing a hydrogen uptake (hup) gene was identified by transferring the gene bank into a H(2) uptake-negative (Hup(-)) R. japonicum point mutant (PJ17nal) and screening tetracycline-resistant colonies for the ability to grow chemolithotrophically and to reduce methylene blue in a recently devised colony assay. Hup(+) transconjugants arose at a frequency of approximately 6 x 10(-3). Plasmid DNAs from II of the Hup(+) transconjugants were isolated and used to transform Escherichia coli. EcoRI digests of all plasmids isolated from Hup(+) transconjugants had three DNA fragments in common. Eight of the E. coli transformants containing hup gene cosmids were conjugated with PJ17nal and another Hup(-) point mutant, PJ18nal. All PJ17nal transconjugants were Hup(+). The frequency of Hup(+) transconjugants with PJ18nal was approximately 10(-3). The results indicate that the hup gene cosmids may contain one gene and a portion of another.
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Affiliation(s)
- M A Cantrell
- Laboratory for Nitrogen Fixation Research, Oregon State University, Corvallis, Oregon 97331
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Maier RJ, Campbell NE, Hanus FJ, Simpson FB, Russell SA, Evans HJ. Expression of hydrogenase activity in free-living Rhizobium japonicum. Proc Natl Acad Sci U S A 2010; 75:3258-62. [PMID: 16592544 PMCID: PMC392754 DOI: 10.1073/pnas.75.7.3258] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A medium is described on which selected Rhizobium japonicum strains express hydrogenase (H(2) uptake) activity under free-living conditions. Low concentrations of carbon substrates, decreased oxygen tension, and the quantity of combined nitrogen in the medium were major factors influencing hydrogenase expression. Hydrogenase activity was dependent upon a preincubation period in the presence of H(2) under conditions such that the cells did not exhibit nitrogenase activity. H(2) uptake rates were easily measured amperometrically in aerobically or anaerobically prepared suspensions from free-living cultures. Six R. japonicum strains that formed nodules with the ability to utilize H(2) oxidized this gas when grown in free-living cultures. In comparison six randomly chosen strains forming nodules that lost H(2) in air either showed no or low capacity to take up H(2) under free-living conditions. The reduction of triphenyltetrazolium chloride in an agar medium was used to detect strains capable of oxidizing H(2). This method has enabled us to isolate a spontaneous R. japonicum mutant strain that has lost the ability to utilize H(2). This mutant strain forms nodules that evolve H(2) but other symbiotic characteristics appear normal. This strain will be useful in evaluating the importance of the hydrogenase system in the nitrogen-fixing process of legumes.
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Affiliation(s)
- R J Maier
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
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Schubert KR, Evans HJ. Hydrogen evolution: A major factor affecting the efficiency of nitrogen fixation in nodulated symbionts. Proc Natl Acad Sci U S A 2010; 73:1207-11. [PMID: 16592307 PMCID: PMC430231 DOI: 10.1073/pnas.73.4.1207] [Citation(s) in RCA: 198] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitrogenase-dependent hydrogen evolution from detached legume nodules and from reaction mixtures containing cell-free nitrogenase has been well established, but the overall effect of hydrogen evolution on the efficiency of nitrogen fixation in vivo has not been critically assessed. This paper describes a survey which revealed that hydrogen evolution is a general phenomenon associated with nitrogen fixation by many nodulated nitrogen-fixing symbionts. An evaluation of the magnitude of energy loss in terms of the efficiency of electron transfer to nitrogen, via nitrogenase, in excised nodules suggested that hydrogen production may severely reduce nitrogen fixation in many legumes where photosynthate supply is a factor limiting fixation. With most symbionts, including soybeans, only 40-60% of the electron flow to nitrogenase was transferred to nitrogen. The remainder was lost through hydrogen evolution. In situ measurements of hydrogen evolution and acetylene reduction by nodulated soybeans confirmed the results obtained with excised nodules. In an atmosphere of air, a major portion of the total electron flux available for the reduction of atmospheric nitrogen by either excised nodules or intact nodulated plants was utilized in the production of hydrogen gas. Some non-leguminous symbionts, such as Alnus rubra, and a few legumes (i.e., Vigna sinensis) apparently have evolved mechanisms of minimizing net hydrogen production, thus increasing their efficiency of electron transfer to nitrogen. Our results indicate that the extent of hydrogen evolution during nitrogen reduction is a major factor affecting the efficiency of nitrogen fixation by many agronomically important legumes.
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Affiliation(s)
- K R Schubert
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oreg. 97331
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Navarro RB, Vargas AA, Schröder EC, van Berkum P. Uptake Hydrogenase (Hup) in Common Bean (Phaseolus vulgaris) Symbioses. Appl Environ Microbiol 2010; 59:4161-5. [PMID: 16349115 PMCID: PMC195880 DOI: 10.1128/aem.59.12.4161-4165.1993] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Strains of Rhizobium forming nitrogen-fixing symbioses with common bean were systematically examined for the presence of the uptake hydrogenase (hup) structural genes and expression of uptake hydrogenase (Hup) activity. DNA with homology to the hup structural genes of Bradyrhizobium japonicum was present in 100 of 248 strains examined. EcoRI fragments with molecular sizes of approximately 20.0 and 2.2 kb hybridized with an internal SacI fragment, which contains part of both bradyrhizobial hup structural genes. The DNA with homology to the hup genes was located on pSym of one of the bean rhizobia. Hup activity was observed in bean symbioses with 13 of 30 strains containing DNA homologous with the hup structural genes. However, the Hup activity was not sufficient to eliminate hydrogen evolution from the nodules. Varying the host plant with two of the Hup strains indicated that expression of Hup activity was host regulated, as has been reported with soybean, pea, and cowpea strains.
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Affiliation(s)
- R B Navarro
- Centro de Energia Nuclear na Agricultura, Universidade de Sao Paulo, Campus Piracicaba, 13400 Piracicaba, Sao Paulo, Brazil; Biological Nitrogen Fixation Laboratory, Department of Agronomy and Soils, University of Puerto Rico, Mayagüez, Puerto Rico 00681 ; and Soybean and Alfalfa Research Laboratory, Agricultural Research Service, U.S. Department of Agriculture, HH-19, Building 011, BARC-West, Beltsville, Maryland 20705
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Hom SS, Novak PD, Maier RJ. Transposon Tn5-Generated Bradyrhizobium japonicum Mutants Unable To Grow Chemoautotrophically with H(2). Appl Environ Microbiol 2010; 54:358-63. [PMID: 16347549 PMCID: PMC202457 DOI: 10.1128/aem.54.2.358-363.1988] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Twelve Tn5-induced mutants of Bradyrhizobium japonicum unable to grow chemoautotrophically with CO(2) and H(2) (Aut) were isolated. Five Aut mutants lacked hydrogen uptake activity (Hup). The other seven Aut mutants possessed wild-type levels of hydrogen uptake activity (Hup), both in free-living culture and symbiotically. Three of the Hup mutants lacked hydrogenase activity both in free-living culture and as nodule bacteroids. The other two mutants were Hup only in free-living culture. The latter two mutants appeared to be hypersensitive to repression by oxygen, since Hup activity could be derepressed under 0.4% O(2). All five Hup mutants expressed both ex planta and symbiotic nitrogenase activities. Two of the seven Aut Hup mutants expressed no free-living nitrogenase activity, but they did express it symbiotically. These two strains, plus one other Aut Hup mutant, had CO(2) fixation activities 20 to 32% of the wild-type level. The cosmid pSH22, which was shown previously to contain hydrogenase-related genes of B. japonicum, was conjugated into each Aut mutant. The Aut Hup mutants that were Hup both in free-living culture and symbiotically were complemented by the cosmid. None of the other mutants was complemented by pSH22. Individual subcloned fragments of pSH22 were used to complement two of the Hup mutants.
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Affiliation(s)
- S S Hom
- Department of Biology and McCollum-Pratt Institute, The Johns Hopkins University, Baltimore, Maryland 21218
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Lambert GR, Harker AR, Cantrell MA, Hanus FJ, Russell SA, Haugland RA, Evans HJ. Symbiotic Expression of Cosmid-Borne Bradyrhizobium japonicum Hydrogenase Genes. Appl Environ Microbiol 2010; 53:422-8. [PMID: 16347291 PMCID: PMC203676 DOI: 10.1128/aem.53.2.422-428.1987] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The expression of cosmid-borne Bradyrhizobium japonicum hydrogenase genes in alfalfa, clover, and soybean nodules harboring Rhizobium transconjugants was studied. Cosmid pHU52 conferred hydrogen uptake (Hup) activity in both free-living bacteria and in nodules on the different plant hosts, although in nodules the instability of the cosmid resulted in low levels of Hup activity. In contrast, cosmid pHU1, which does not confer Hup activity on free-living bacteria, gave a Hup phenotype in nodules on alfalfa and soybean. Nodules formed by B. japonicum USDA 123Spc(pHU1) recycled about 90% of nitrogenase-mediated hydrogen evolution. Both subunits of hydrogenase (30- and 60-kilodalton polypeptides) were detected in enzyme-linked immunosorbent assays of bacteroid preparations from nodules harboring B. japonicum strains with pHU1 or pHU52. Neither pHU53 nor pLAFR1 conferred detectable Hup activity in either nodules or free-living bacteria. Based on the physical maps of pHU1 and pHU52, it is suggested that a 5.5-kilobase EcoRI fragment unique to pHU52 contains a gene or part of a gene required for Hup activity in free-living bacteria but not in nodules. This conclusion is supported by the observation that two Tn5 insertions in the chromosome of B. japonicum USDA 122DES obtained by marker exchange with Tn5-mutagenized pHU1 abolished Hup activity in free-living bacteria but not in nodules.
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Affiliation(s)
- G R Lambert
- Laboratory for Nitrogen Fixation Research, Oregon State University, Corvallis, Oregon 97331
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15
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Cunningham SD, Kapulnik Y, Brewin NJ, Phillips DA. Uptake Hydrogenase Activity Determined by Plasmid pRL6JI in Rhizobium leguminosarum Does Not Increase Symbiotic Nitrogen Fixation. Appl Environ Microbiol 2010; 50:791-4. [PMID: 16346912 PMCID: PMC291749 DOI: 10.1128/aem.50.4.791-794.1985] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Six mutants of Rhizobium leguminosarum 3855 lacking uptake hydrogenase activity (Hup phenotype) as a result of Tn5-mob mutagenesis of the hup-containing plasmid pRL6JI were tested for symbiotic performance on Pisum sativum L. and Vicia benghalensis L. Three pea cultivars and one vetch line, which induce four different levels of Hup activity in strain 3855, were grown to flowering under microbiologically controlled conditions in the absence of combined N. Direct Kjeldahl N measurements showed that in every case at least one Hup mutant fixed as much N(2) as the isogenic Hup strain. Measures of C(2)H(2) reduction, H(2) evolution, H(2) incorporation, and plant dry weight were consistent with the interpretation that the oxidation of H(2) produced by the nitrogenase enzyme complex was not necessarily associated with increased N(2) fixation in these symbiotic associations. Tests with a smaller subset of the Hup strains under four different root environments ranging from pH 5.0 to 8.2 likewise showed no significant advantage for the isogenic Hup strain. It was concluded that the improvements in symbiotic N(2) fixation produced by pRL6JI are associated with some trait other than the Hup phenotype.
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Affiliation(s)
- S D Cunningham
- Department of Agronomy, University of California, Davis, California 95616
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Haugland RA, Hanus FJ, Cantrell MA, Evans HJ. Rapid Colony Screening Method for Identifying Hydrogenase Activity in Rhizobium japonicum. Appl Environ Microbiol 2010; 45:892-7. [PMID: 16346252 PMCID: PMC242389 DOI: 10.1128/aem.45.3.892-897.1983] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A method has been developed for the rapid screening of Rhizobium japonicum colonies for hydrogenase activity based on their ability to reduce methylene blue in the presence of respiratory inhibitors and hydrogen. Hydrogen uptake-positive (Hup) colonies derepressed for hydrogenase activity were visualized by their localized decolorization of filter paper disks impregnated with the dye. Appropriate responses were seen with a number of Hup and Hup wild-type strains of R. japonicum as well as Hup mutants. Its specificity was further confirmed in selected strains on the basis of comparisons with chemolithotrophic growth and the presence of other genetic markers. Utilization of the method in identifying Hup colonies among 16,000 merodiploid derivatives of the Hup mutant strain PJ17nal containing cloned DNA fragments of the Hup strain 122 DES has demonstrated its applicability as a screening procedure in the genetic analysis of the R. japonicum hydrogen uptake system.
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Affiliation(s)
- R A Haugland
- Laboratory for Nitrogen Fixation Research, Oregon State University, Corvallis, Oregon 97331
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17
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A novel endo-hydrogenase activity recycles hydrogen produced by nitrogen fixation. PLoS One 2009; 4:e4695. [PMID: 19277114 PMCID: PMC2650096 DOI: 10.1371/journal.pone.0004695] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2008] [Accepted: 01/16/2009] [Indexed: 12/17/2022] Open
Abstract
Background Nitrogen (N2) fixation also yields hydrogen (H2) at 1∶1 stoichiometric amounts. In aerobic diazotrophic (able to grow on N2 as sole N-source) bacteria, orthodox respiratory hupSL-encoded hydrogenase activity, associated with the cell membrane but facing the periplasm (exo-hydrogenase), has nevertheless been presumed responsible for recycling such endogenous hydrogen. Methods and Findings As shown here, for Azorhizobium caulinodans diazotrophic cultures open to the atmosphere, exo-hydrogenase activity is of no consequence to hydrogen recycling. In a bioinformatic analysis, a novel seven-gene A. caulinodans hyq cluster encoding an integral-membrane, group-4, Ni,Fe-hydrogenase with homology to respiratory complex I (NADH : quinone dehydrogenase) was identified. By analogy, Hyq hydrogenase is also integral to the cell membrane, but its active site faces the cytoplasm (endo-hydrogenase). An A. caulinodans in-frame hyq operon deletion mutant, constructed by “crossover PCR”, showed markedly decreased growth rates in diazotrophic cultures; normal growth was restored with added ammonium—as expected of an H2-recycling mutant phenotype. Using A. caulinodans hyq merodiploid strains expressing β-glucuronidase as promoter-reporter, the hyq operon proved strongly and specifically induced in diazotrophic culture; as well, hyq operon induction required the NIFA transcriptional activator. Therefore, the hyq operon is constituent of the nif regulon. Conclusions Representative of aerobic N2-fixing and H2-recycling α-proteobacteria, A. caulinodans possesses two respiratory Ni,Fe-hydrogenases: HupSL exo-hydrogenase activity drives exogenous H2 respiration, and Hyq endo-hydrogenase activity recycles endogenous H2, specifically that produced by N2 fixation. To benefit human civilization, H2 has generated considerable interest as potential renewable energy source as its makings are ubiquitous and its combustion yields no greenhouse gases. As such, the reversible, group-4 Ni,Fe-hydrogenases, such as the A. caulinodans Hyq endo-hydrogenase, offer promise as biocatalytic agents for H2 production and/or consumption.
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18
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19
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Vignais PM, Billoud B. Occurrence, Classification, and Biological Function of Hydrogenases: An Overview. Chem Rev 2007; 107:4206-72. [PMID: 17927159 DOI: 10.1021/cr050196r] [Citation(s) in RCA: 1039] [Impact Index Per Article: 61.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Paulette M. Vignais
- CEA Grenoble, Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, UMR CEA/CNRS/UJF 5092, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), 17 rue des Martyrs, 38054 Grenoble cedex 9, France, and Atelier de BioInformatique Université Pierre et Marie Curie (Paris 6), 12 rue Cuvier, 75005 Paris, France
| | - Bernard Billoud
- CEA Grenoble, Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, UMR CEA/CNRS/UJF 5092, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), 17 rue des Martyrs, 38054 Grenoble cedex 9, France, and Atelier de BioInformatique Université Pierre et Marie Curie (Paris 6), 12 rue Cuvier, 75005 Paris, France
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20
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Baginsky C, Brito B, Imperial J, Ruiz-Argüeso T, Palacios JM. Symbiotic hydrogenase activity in Bradyrhizobium sp. (Vigna) increases nitrogen content in Vigna unguiculata plants. Appl Environ Microbiol 2005; 71:7536-8. [PMID: 16269797 PMCID: PMC1287714 DOI: 10.1128/aem.71.11.7536-7538.2005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bradyrhizobium sp. (Lupinus) and Bradyrhizobium sp. (Vigna) mutants in which hydrogenase (hup) activity was affected were constructed and analyzed. Vigna unguiculata plants inoculated with the Bradyrhizobium sp. (Vigna) hup mutant showed reduced nitrogenase activity and also a significant decrease in nitrogen content, suggesting a relevant contribution of hydrogenase activity to plant yield.
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Affiliation(s)
- Cecilia Baginsky
- Laboratory of Microbiology, Department of Biotechnology, E.T.S. Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
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21
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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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22
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Abstract
We have summarized information in four areas of the broad topic of legume-
Rhizobium
symbiosis. These include: carbon substrates provided to nodule bacteroids by the host, assimilation of fixed nitrogen by the host, O
2
metabolism in legume nodules and involvement of H
2
in nodule metabolism. Although nodules contain a variety of carbon substrates, both biochemical and genetic evidence indicate that C4 dicarboxylates are the major carbon substrates that support N
2
fixation in nodules. The biochemical pathways for utilization of products of N
2
fixation are fairly well understood but relatively little is known about the regulation of the assimilation of fixed nitrogenous compounds at the gene level. Ureides are primary nitrogenous compounds exported from nodules of the tropical legumes. Because the catabolism of these products may involve the hydrolysis of urea by nickel-dependent urease, the possible importance of nickel as a trace element in the nutrition of legumes is raised. The O
2
supply to nodule bacteroids is regulated by a barrier to free-O
2
diffusion and by leghaemoglobin. Progress has been made in understanding of the molecular genetics and biochemistry of leghaemoglobin but little is known about the mechanisms that control the physical barrier to O
2
diffusion. Legume nodules contain mechanisms for the disposition of peroxide and free radicals of oxygen. The importance of these systems as protective mechanisms for the O
2
-labile nitrogenase is discussed. Some strains of
Rhizobium
form nodules which recycle the H
2
produced as a byproduct of N
2
fixation. The genes necessary for H
2
oxidation have been cloned and transferred within and among species of
Rhizobium
. The advantages and disadvantages of H
2
recycling in legume nodules are discussed.
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23
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Linkerhägner K, Oelze J. Hydrogenase does not confer significant benefits to Azotobacter vinelandii growing diazotrophically under conditions of glucose limitation. J Bacteriol 1995; 177:6018-20. [PMID: 7592361 PMCID: PMC177436 DOI: 10.1128/jb.177.20.6018-6020.1995] [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] Open
Abstract
The presumed beneficial effect of hydrogenase on growth of diazotrophic bacteria was reinvestigated with carbon-limited chemostat cultures of the hydrogenase-deficient mutant hoxKG of Azotobacter vinelandii and its parent. The results revealed that hydrogen recycling was too low to benefit the cellular energy metabolism or activities of nitrogenase and respiration.
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Affiliation(s)
- K Linkerhägner
- Institut für Biologie II (Mikrobiologie), Universität Freiburg, Germany
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24
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25
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Hydrogenase in Bradyrhizobium japonicum: genetics, regulation and effect on plant growth. World J Microbiol Biotechnol 1993; 9:615-24. [DOI: 10.1007/bf00369567] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/26/1993] [Accepted: 05/13/1993] [Indexed: 10/26/2022]
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26
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Menon AL, Mortenson LE, Robson RL. Nucleotide sequences and genetic analysis of hydrogen oxidation (hox) genes in Azotobacter vinelandii. J Bacteriol 1992; 174:4549-57. [PMID: 1624446 PMCID: PMC206250 DOI: 10.1128/jb.174.14.4549-4557.1992] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Azotobacter vinelandii contains a heterodimeric, membrane-bound [NiFe]hydrogenase capable of catalyzing the reversible oxidation of H2. The beta and alpha subunits of the enzyme are encoded by the structural genes hoxK and hoxG, respectively, which appear to form part of an operon that contains at least one further potential gene (open reading frame 3 [ORF3]). In this study, determination of the nucleotide sequence of a region of 2,344 bp downstream of ORF3 revealed four additional closely spaced or overlapping ORFs. These ORFs, ORF4 through ORF7, potentially encode polypeptides with predicted masses of 22.8, 11.4, 16.3, and 31 kDa, respectively. Mutagenesis of the chromosome of A. vinelandii in the area sequenced was carried out by introduction of antibiotic resistance gene cassettes. Disruption of hoxK and hoxG by a kanamycin resistance gene abolished whole-cell hydrogenase activity coupled to O2 and led to loss of the hydrogenase alpha subunit. Insertional mutagenesis of ORF3 through ORF7 with a promoterless lacZ-Kmr cassette established that the region is transcriptionally active and involved in H2 oxidation. We propose to call ORF3 through ORF7 hoxZ, hoxM, hoxL, hoxO, and hoxQ, respectively. The predicted hox gene products resemble those encoded by genes from hydrogenase-related operons in other bacteria, including Escherichia coli and Alcaligenes eutrophus.
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Affiliation(s)
- A L Menon
- Department of Biochemistry, University of Georgia, Athens 30602
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27
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Abstract
The enigmatic coexistence of O2-sensitive nitrogenase and O2-evolving photosynthesis in diazotrophic cyanobacteria has fascinated researchers for over two decades. Research efforts in the past 10 years have revealed a range of O2 sensitivity of nitrogenase in different strains of cyanobacteria and a variety of adaptations for the protection of nitrogenase from damage by both atmospheric and photosynthetic sources of O2. The most complex and apparently most efficient mechanisms for the protection of nitrogenase are incorporated in the heterocysts, the N2-fixing cells of cyanobacteria. Genetic studies indicate that the controls of heterocyst development and nitrogenase synthesis are closely interrelated and that the expression of N2 fixation (nif) genes is regulated by pO2.
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Affiliation(s)
- P Fay
- Queen Mary and Westfield College, University of London, Hampstead, England
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28
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Chen JC, Mortenson LE. Two open reading frames (ORFs) identified near the hydrogenase structural genes in Azotobacter vinelandii, the first ORF may encode for a polypeptide similar to rubredoxins. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1131:122-4. [PMID: 1581355 DOI: 10.1016/0167-4781(92)90111-c] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Sequencing of 744 base pairs (bp) of a cloned section of DNA from Azotobacter vinelandii reveals two complete, closely-spaced open reading frames (ORF1 and ORF2). Both ORFs are transcribed from the same DNA strand as that of the structural genes for hydrogenase (hoxK and hoxG, Menon, A.L. et al. (1990) Gene 96, 67-74), and are located downstream from the latter genes. The distance between the end of hoxG and the beginning of ORF1 is approx. 3.0 kilobases (kb). Most of the deduced amino acid sequence of ORF1 shares high homology with rubredoxin sequences. Some of the deduced amino acid sequence of ORF2 shares homology with that of a reported partial ORF from Rhodobacter capsulatus, ORF located within a region of DNA required for dihydrogen oxidation in that organism. Implications of these findings with respect to dihydrogen metabolism are discussed.
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Affiliation(s)
- J C Chen
- Department of Biochemistry, University of Georgia, Athens 30602
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29
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Hoffmann KH, Kaemmer D, Miksch G, Lange I, Kleinert T. Leghämoglobin aus Wurzelknöllchenextrakten von Luzerne bei genotypischer Variation der Symbiose. J Basic Microbiol 1990. [DOI: 10.1002/jobm.3620301010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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30
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Changlin Fu, Tito D, Knowles R. pH dependence of uptake hydrogenases inAzospirillum brasilenseandA. amazonense. FEMS Microbiol Lett 1989. [DOI: 10.1111/j.1574-6968.1989.tb03134.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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31
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The importance of hydrogen recycling in nitrogen fixation by legumes. WORLD CROPS: COOL SEASON FOOD LEGUMES 1988. [DOI: 10.1007/978-94-009-2764-3_62] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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32
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Nautiyal CS, Hegde SV, van Berkum P. Nodulation, Nitrogen Fixation, and Hydrogen Oxidation by Pigeon Pea
Bradyrhizobium
spp. in Symbiotic Association with Pigeon Pea, Cowpea, and Soybean. Appl Environ Microbiol 1988; 54:94-97. [PMID: 16347542 PMCID: PMC202402 DOI: 10.1128/aem.54.1.94-97.1988] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The pigeon pea strains of
Bradyrhizobium
CC-1, CC-8, UASGR(S), and F4 were evaluated for nodulation, effectiveness for N
2
fixation, and H
2
oxidation with homologous and nonhomologous host plants. Strain CC-1 nodulated
Macroptilium atropurpureum, Vigna unguiculata, Glycine max
, and
G. soja
but did not nodulate
Pisum sativum, Phaseolus vulgaris, Trigonella foenum-graecum
, and
Trifolium repens
. Strain F4 nodulated
G. max
cv. Peking and PI 434937 (Malayan), but the symbioses formed were poor. Similarly,
G. max
cv. Peking, cv. Bragg, PI 434937, PR 13-28-2-8-7, and HM-1 were nodulated by strain CC-1, and symbioses were also poor.
G. max
cv. Williams and cv. Clark were not nodulated. H
2
uptake activity was expressed with pigeon pea and cowpea, but not with soybean.
G. max
cv. Bragg grown in Bangalore, India, in local soil not previously exposed to
Bradyrhizobium japonicum
formed nodules with indigenous
Bradyrhizobium
spp. Six randomly chosen isolates, each originating from a different nodule, formed effective symbioses with pigeon pea host ICPL-407, nodulated PR 13-28-2-8-7 soybean forming moderately effective symbioses, and did not nodulate Williams soybean. These results indicate the six isolates to be pigeon pea strains although they originated from soybean nodules. Host-determined nodulation of soybean by pigeon pea
Bradyrhizobium
spp. may depend upon the ancestral backgrounds of the cultivars. The poor symbioses formed by the pigeon pea strains with soybean indicate that this crop should be inoculated with
B. japonicum
for its cultivation in soils containing only pigeon pea
Bradyrhizobium
spp.
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Affiliation(s)
- C S Nautiyal
- Nitrogen Fixation and Soybean Genetics Laboratory, Agricultural Research Service, Beltsville Agricultural Research Center West, U. S. Department of Agriculture, Beltsville, Maryland 20705, and Agronomy Department, University of Maryland, College Park, Maryland 20742; and Department of Microbiology, University of Agricultural Sciences, GKVK Campus, Bangalore 560 065, India
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33
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Barate M, Reyes P, Munilla R, Fernández VM, Ballesteros A, Ruiz-Argüeso T. Effect of pH on tritium exchange and hydrogen production and uptake in free-living cells and in bacteroids of Bradyrhizobium japonicum. Arch Biochem Biophys 1987; 259:639-44. [PMID: 3322198 DOI: 10.1016/0003-9861(87)90530-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Soybean nodule bacteroids and Bradyrhizobium japonicum free-living cells induced for H2-uptake hydrogenase, actively catalyze the evolution of H2 in a reaction highly dependent on the pH. The optimal pHs for the evolution and uptake reactions were 4.0 and 7.5-8.0, respectively. No differences were found between free-living cells and bacteroids with respect to hydrogen acceptor specificity, although absolute rates of H2 uptake were higher for free-living cells. Both types of cells were able to evolve hydrogen from reduced methyl viologen at low pH. These intact cells also catalyzed the exchange reaction between tritium and water in the absence of oxygen. The pH profile of the exchange activity showed two peaks at values near the optimal pHs for the evolution and uptake reactions.
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Affiliation(s)
- M Barate
- Instituto de Catálisis, CSIC, Madrid, Spain
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34
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Chen YP, Yoch DC. Regulation of two nickel-requiring (inducible and constitutive) hydrogenases and their coupling to nitrogenase in Methylosinus trichosporium OB3b. J Bacteriol 1987; 169:4778-83. [PMID: 3115963 PMCID: PMC213854 DOI: 10.1128/jb.169.10.4778-4783.1987] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Two uptake hydrogenases were found in the obligate methanotroph Methylosinus trichosporium OB3b; one was constitutive, and a second was induced by H2. Both hydrogenases could be assayed by measuring methylene blue reduction anaerobically or by coupling their activity to nitrogenase acetylene reduction activity in vivo in an O2-dependent reaction. The H2 concentration for half-maximal activity of the inducible and constitutive hydrogenases in both assays was 0.01 and 0.5 bar (1 and 50 kPa), respectively, making it easy to distinguish these enzymes from one another both in vivo and in vitro. Hydrogen uptake was shown to be coupled to ATP synthesis in methane-starved cells. Methane, methanol, formate, succinate, and glucose all repressed the H2-mediated synthesis of the inducible hydrogenase. Furthermore, this enzyme was only expressed in N-starved cultures and was repressed by NH4+ and NO3-; synthesis of the constitutive hydrogenase was not affected by excess N in the growth medium. In nickel-free, EDTA-containing medium, the activities of these two enzymes were negligible; however, both enzyme activities appeared rapidly following the addition of nickel to the culture. Chloramphenicol, when added along with nickel, had no effect on the rapid appearance of either the constitutive or inducible activity, indicating that nickel is not required for synthesis of the hydrogenase apoproteins. These observations all suggest that these hydrogenases are nickel-containing enzymes. Finally, both hydrogenases were soluble and could be fractionated by 20% ammonium sulfate; the constitutive enzyme remained in the supernatant solution, while the inducible enzyme was precipitated under these conditions.
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Affiliation(s)
- Y P Chen
- Department of Biology, University of South Carolina, Columbia 29208
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35
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VERMA DESHPALS, STANLEY JOHN. Molecular Interactions in Endosymbiosis between Legume Plants and Nitrogen-Fixing Microbes. Ann N Y Acad Sci 1987. [DOI: 10.1111/j.1749-6632.1987.tb40615.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Škrdleta V, Lisá L, Němcová M. Comparison of peas nodulated with a hydrogen-uptake positive or negative Strain ofRhizobium leguminosarum. Folia Microbiol (Praha) 1987. [DOI: 10.1007/bf02881105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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37
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Škrdleta V, Lisá L, Němcová M. Comparison of peas nodulated with a hydrogen-uptake positive or negative strain ofRhizobium leguminosarum. Folia Microbiol (Praha) 1987. [DOI: 10.1007/bf02881104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Lespinat PA, Berlier YM, Fauque GD, Toci R, Denariaz G, LeGall J. The relationship between hydrogen metabolism, sulfate reduction and nitrogen fixation in sulfate reducers. ACTA ACUST UNITED AC 1987. [DOI: 10.1007/bf01569336] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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Kumar AP, Perraju BTVV, Singh HN. CARBON NUTRITION AND THE REGULATION OF UPTAKE HYDROGENASE ACTIVITY IN FREE-LIVING AND SYMBIOTIC ANABAENA CYCADEAE. THE NEW PHYTOLOGIST 1986; 104:115-120. [PMID: 33873814 DOI: 10.1111/j.1469-8137.1986.tb00639.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Anabaena cycadeae was grown with N2 as nitrogen source, either photoautotrophically in light or with glucose as carbon source in darkness. The rate of growth was much slower in darkness but the heterocyst frequency was much the same; nitrogenase activity (on a chlorophyll basis) was about half that of light-grown cells. Light-grown organisms contained uptake hydrogenase activity but dark-grown organisms did not. The addition of glucose to light-grown organisms was followed by the disappearance of uptake hydrogenase activity over the following 48 hours and the disappearance was independent of light. Heterocyst frequency and nitrogenase activity were much less affected by glucose addition. A. cycadeae growing symbiotically in cycad roots had much higher heterocyst frequency and nitrogenase activity than the free-living form but no detectable uptake hydrogenase activity. It is suggested that the rate of supply of carbohydrate to the heterocyst controls the development of uptake hydrogenase activity and that the absence of this activity in the symbiotic cyanobacteria indicates that the organisms in the cycad roots have an ample supply of carbohydrate.
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Affiliation(s)
- A P Kumar
- School of Life Sciences, University of Hyderabad, Hyderabad-500 134, A.P., India
| | - B T V V Perraju
- School of Life Sciences, University of Hyderabad, Hyderabad-500 134, A.P., India
| | - H N Singh
- School of Life Sciences, University of Hyderabad, Hyderabad-500 134, A.P., India
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40
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Pederson DM, Daday A, Smith GD. The use of nickel to probe the role of hydrogen metabolism in cyanobacterial nitrogen fixation. Biochimie 1986; 68:113-20. [PMID: 3089304 DOI: 10.1016/s0300-9084(86)81076-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The hydrogenase activities of the heterocystous cyanobacteria Anabaena cylindrica and Mastigocladus laminosus are nickel dependent, based on their inability to consume hydrogen with various electron acceptors or produce hydrogen with dithionite-reduced methyl viologen, after growth in nickel-depleted medium. Upon addition of nickel ions to nickel-deficient cultures of A. cylindrica, the hydrogenase activity recovered in a manner which was protein synthesis-dependent, the recovery being inhibited by chloramphenicol. We have used the nickel dependence of the hydrogenase as a probe of the possible roles of H2 consumption in enhancing nitrogen fixation, and particularly for protecting nitrogenase against oxygen inhibition. Although at the usual growth temperatures (25 degrees for A. cylindrica and 40 degrees for M. laminosus), the cells consume H2 vigorously in an oxyhydrogen reaction after growth in the presence of nickel ions, we have not found that the reaction confers any significant additional protection of nitrogenase, either at aerobic pO2 (for both organisms) or at elevated pO2 (for A. cylindrica). However, at elevated temperatures (e.g., 40 degrees for A. cylindrica and 48 degrees for M. laminosus) a definite protective effect was observed. At these temperatures both organisms rapidly lost acetylene reduction activity under aerobic conditions. When hydrogen gas (10%) was present, the cells retained approximately 50% of the nitrogenase activity observed under anaerobic conditions (argon gas phase). No such protection by hydrogen gas was observed with nickel-deficient cells. Studies with cell-free extracts of A. cylindrica showed that the predominant effect of temperature was not due to thermal inactivation of nitrogenase.
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SOYFER VALERYN. Trends in the Application of Molecular and Cell Biology to Current and Future Agronomy. Ann N Y Acad Sci 1985. [DOI: 10.1111/j.1749-6632.1985.tb30023.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Nelson LM, Grosskopf E, Tichy H, Lotz W. Characterization ofhup-specific DNA inRhizobium leguminosarumstrains of different origin. FEMS Microbiol Lett 1985. [DOI: 10.1111/j.1574-6968.1985.tb00984.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Hom SS, Graham LA, Maier RJ. Isolation of genes (nif/hup cosmids) involved in hydrogenase and nitrogenase activities in Rhizobium japonicum. J Bacteriol 1985; 161:882-7. [PMID: 3882669 PMCID: PMC214979 DOI: 10.1128/jb.161.3.882-887.1985] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Recombinant cosmids containing a Rhizobium japonicum gene involved in both hydrogenase (Hup) and nitrogenase (Nif) activities were isolated. An R. japonicum gene bank utilizing broad-host-range cosmid pLAFR1 was conjugated into Hup- Nif- R. japonicum strain SR139. Transconjugants containing the nif/hup cosmid were identified by their resistance to tetracycline (Tcr) and ability to grow chemoautotrophically (Aut+) with hydrogen. All Tcr Aut+ transconjugants possessed high levels of H2 uptake activity, as determined amperometrically. Moreover, all Hup+ transconjugants tested possessed the ability to reduce acetylene (Nif+) in soybean nodules. Cosmid DNAs from 19 Hup+ transconjugants were transferred to Escherichia coli by transformation. When the cosmids were restricted with EcoRI, 15 of the 19 cosmids had a restriction pattern with 13.2-, 4.0-, 3.0-, and 2.5-kilobase DNA fragments. Six E. coli transformants containing the nif/hup cosmids were conjugated with strain SR139. All strain SR139 transconjugants were Hup+ Nif+. Moreover, one nif/hup cosmid was transferred to 15 other R. japonicum Hup- mutants. Hup+ transconjugants of six of the Hup- mutants appeared at a frequency of 1.0, whereas the transconjugants of the other nine mutants remained Hup-. These results indicate that the nif/hup gene cosmids contain a gene involved in both nitrogenase and hydrogenase activities and at least one and perhaps other hup genes which are exclusively involved in H2 uptake activity.
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Arp DJ. Rhizobium japonicum hydrogenase: purification to homogeneity from soybean nodules, and molecular characterization. Arch Biochem Biophys 1985; 237:504-12. [PMID: 3919648 DOI: 10.1016/0003-9861(85)90303-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Rhizobium japonicum hydrogenase was purified to homogeneity from soybean root nodules by four column chromatography steps after solubilization from membranes by treatment with a nonionic detergent. The specific activity was from 40 to 65 mumol H2 oxidized min-1 mg protein-1 and was increased 450-fold relative to that in bacteroids. The yield of activity was from 7 to 12%. The molecular weight of the native enzyme was 104,000 as determined by sucrose density gradient centrifugation. Electrophoresis in the presence of sodium dodecyl sulfate revealed two subunits with molecular weights of 64,000 and 35,000, indicating an alpha beta subunit structure. The amino acid content of the protein indicated 20 cysteine residues. Analysis of the metal content indicated 0.59 +/- 0.06 mol Ni/mol hydrogenase and 6.5 +/- 1.2 mol Fe/mol hydrogenase. Antisera prepared to the hydrogenase cross-reacted with the enzyme in bacteroid extracts at all stages of the purification but did not cross-react with extracts of Alcaligenes eutrophus grown under chemolithotrophic conditions. The similarity of rhizobial hydrogenase to the particulate hydrogenases of A. eutrophus and A. latus is discussed.
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O'Brian MR, Maier RJ. Expression of cytochrome o in hydrogen uptake constitutive mutants of Rhizobium japonicum. J Bacteriol 1985; 161:507-14. [PMID: 3968033 PMCID: PMC214911 DOI: 10.1128/jb.161.2.507-514.1985] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mutant strains of Rhizobium japonicum constitutive for H2 uptake activity (Hupc) contained significantly more membrane-bound b-type cytochrome than did the wild type when grown heterotrophically. The Hupc strains contained approximately three times more dithionite- and NADH-reducible CO-reactive b-type cytochrome than did the wild type; the absorption features of the CO spectra were characteristic of cytochrome o. This component, designated cytochrome b', was not reduced by NADH in the presence of cyanide. Cytochrome o from the wild type (SR) and cytochrome b' from mutants SR476 and SR481 bound to CO with similar dissociation constants of 5.4, 7.4, and 5.6 microM, respectively. NADH-dependent reduction of cytochrome b' from SR476 and SR481 and the cytochrome o from SR followed pseudo-first-order kinetics with similar rate constants. Based on these spectral, ligand-binding, and kinetic measurements, it was concluded that cytochrome b' expressed by the Hupc mutants is equivalent to cytochrome o found in the wild type. H2, NADH, and succinate each reduced the same amount of total b-type cytochrome in membranes from SR481, and the rate of H2-dependent cytochrome o reduction was significantly less than with succinate or NADH as the reductants. It was concluded that neither cytochrome o nor any b-type cytochrome expressed by the Hupc mutants was unique to the H2 oxidation system. At low O2 concentrations, the inhibition of H2 and NADH oxidase activities by CO closely paralleled the binding of CO to cytochrome o rather than cytochromes a3 or c'. This suggested that NADH and H2 oxidation involved primarily cytochrome o as the terminal oxidase at low O2 tensions.
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Vignais PM, Colbeau A, Willison JC, Jouanneau Y. Hydrogenase, nitrogenase, and hydrogen metabolism in the photosynthetic bacteria. Adv Microb Physiol 1985; 26:155-234. [PMID: 3913292 DOI: 10.1016/s0065-2911(08)60397-5] [Citation(s) in RCA: 119] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Behki RM, Selvaraj G, Iyer VN. Derivatives of Rhizobium meliloti strains carrying a plasmid of Rhizobium leguminosarum specifying hydrogen uptake and pea-specific symbiotic functions. Arch Microbiol 1985. [DOI: 10.1007/bf00446977] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Graham LA, Stults LW, Maier RJ. Nitrogenase ? hydrogenase relationships in Rhizobium japonicum. Arch Microbiol 1984. [DOI: 10.1007/bf00454935] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Haugland RA, Cantrell MA, Beaty JS, Hanus FJ, Russell SA, Evans HJ. Characterization of Rhizobium japonicum hydrogen uptake genes. J Bacteriol 1984; 159:1006-12. [PMID: 6090382 PMCID: PMC215760 DOI: 10.1128/jb.159.3.1006-1012.1984] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Recombinant cosmids from a gene library of the DNA from Hup+ Rhizobium japonicum 122DES previously have been shown to restore hydrogenase activity when transferred by conjugation into certain Hup- mutants of R. japonicum. We generated a restriction map covering 32.2 kilobases of this cosmid DNA. At least 25.3 kilobases of the cosmid pHU1 were shown to have the same arrangement as those in the genome of strain 122DES. Analysis of Tn5 insertions into the 122DES genome indicates that hup-specific sequences occur in a region spanning about 15 kilobases of insert DNA within pHU1. Introduction of pHU1 into five out of six R. japonicum Hup- mutants resulted in a Hup+ phenotype in some transconjugants. Three of the mutations appear to be in transcriptional units completely contained within pHU1, whereas the other two must be in genes that are at least partially contained within pHU1. pBR235 derivatives containing fragments of hup DNA can be transferred into the R. japonicum Hup- mutant PJ18nal if the derivatives contain a region of homology with the R. japonicum genome. The hup mutation in strain PJ18nal appears to be dominant. The hup genes in R. japonicum strain 122DES appear to be organized in at least two, and probably three, transcriptional units.
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