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Standke HG, Kim L, Owens CP. Purification and Biochemical Characterization of the DNA Binding Domain of the Nitrogenase Transcriptional Activator NifA from Gluconacetobacter diazotrophicus. Protein J 2023; 42:802-810. [PMID: 37787923 PMCID: PMC10590331 DOI: 10.1007/s10930-023-10158-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2023] [Indexed: 10/04/2023]
Abstract
NifA is a σ54 activator that turns on bacterial nitrogen fixation under reducing conditions and when fixed cellular nitrogen levels are low. The redox sensing mechanism in NifA is poorly understood. In α- and β-proteobacteria, redox sensing involves two pairs of Cys residues within and immediately following the protein's central AAA+ domain. In this work, we examine if an additional Cys pair that is part of a C(X)5 C motif and located immediately upstream of the DNA binding domain of NifA from the α-proteobacterium Gluconacetobacter diazotrophicus (Gd) is involved in redox sensing. We hypothesize that the Cys residues' redox state may directly influence the DNA binding domain's DNA binding affinity and/or alter the protein's oligomeric sate. Two DNA binding domain constructs were generated, a longer construct (2C-DBD), consisting of the DNA binding domain with the upstream Cys pair, and a shorter construct (NC-DBD) that lacks the Cys pair. The Kd of NC-DBD for its cognate DNA sequence (nifH-UAS) is equal to 20.0 µM. The Kd of 2C-DBD for nifH-UAS when the Cys pair is oxidized is 34.5 µM. Reduction of the disulfide bond does not change the DNA binding affinity. Additional experiments indicate that the redox state of the Cys residues does not influence the secondary structure or oligomerization state of the NifA DNA binding domain. Together, these results demonstrate that the Cys pair upstream of the DNA binding domain of Gd-NifA does not regulate DNA binding or domain dimerization in a redox dependent manner.
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Affiliation(s)
- Heidi G Standke
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA, 92866, USA
| | - Lois Kim
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA, 92866, USA
| | - Cedric P Owens
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA, 92866, USA.
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Li Q, He X, Liu P, Zhang H, Wang M, Chen S. Synthesis of nitrogenase by Paenibacillus sabinae T27 in presence of high levels of ammonia during anaerobic fermentation. Appl Microbiol Biotechnol 2021; 105:2889-2899. [PMID: 33745008 DOI: 10.1007/s00253-021-11231-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/24/2021] [Accepted: 03/10/2021] [Indexed: 01/19/2023]
Abstract
Biological nitrogen fixation is usually inhibited by fixed nitrogen. Paenibacillus sabinae T27, a Gram-positive, spore-forming diazotroph, possesses high nitrogenase activity and has 3 copies of nifH (nifH, nifH2, nifH3), a copy of nifDK, and multiple nifHDK-like genes. In this study, we found that P. sabinae T27 showed nitrogenase activities not only in low (0-3 mM) concentrations of NH4+ but also in high (30-300 mM) concentrations of NH4+, no matter whether this bacterium was grown in a flask or in a fermenter on scale cultivation. qRT-PCR and western blotting analyses supported that Fe protein and MoFe protein were synthesized under both low (0-3 mM) and high (30-300 mM) concentrations of NH4+. Liquid chromatography-mass spectrometry (LC-MS) analysis revealed that MoFe protein was encoded by nifDK and Fe protein was encoded by both nifH and nifH2. The cross-reaction suggested the purified Fe and MoFe components from P. sabinae T27 grown in both nitrogen-limited and nitrogen-excess conditions were active. This is the first time to report that diazotrophs show nitrogenase activity in presence of high (30-300 mM) concentrations of NH4+. Our study will provide a clue for studying the mechanisms of nitrogen fixation in presence of the high concentration of NH4+. KEY POINTS: • P. sabinae T27 can synthesize active nitrogenase in presence of high levels of ammonia. •Fe and MoFe proteins of nitrogenase purified in absence of ammonia are the same as those purified from the high concentration of ammonia. • Fe protein is encoded by nifH and nifH2, and MoFe protein is encoded by nifDK.
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Affiliation(s)
- Qin Li
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China
| | - Xiaojuan He
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China
| | - Pengxi Liu
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China
| | - Haowei Zhang
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China
| | - Mingyang Wang
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China
| | - Sanfeng Chen
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China.
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3
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Medina MS, Bretzing KO, Aviles RA, Chong KM, Espinoza A, Garcia CNG, Katz BB, Kharwa RN, Hernandez A, Lee JL, Lee TM, Lo Verde C, Strul MW, Wong EY, Owens CP. CowN sustains nitrogenase turnover in the presence of the inhibitor carbon monoxide. J Biol Chem 2021; 296:100501. [PMID: 33667548 PMCID: PMC8047169 DOI: 10.1016/j.jbc.2021.100501] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 01/28/2021] [Accepted: 03/01/2021] [Indexed: 11/28/2022] Open
Abstract
Nitrogenase is the only enzyme capable of catalyzing nitrogen fixation, the reduction of dinitrogen gas (N2) to ammonia (NH3). Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Nitrogen-fixing bacteria rely on the protein CowN to grow in the presence of CO. However, the mechanism by which CowN operates is unknown. Here, we present the biochemical characterization of CowN and examine how CowN protects nitrogenase from CO. We determine that CowN interacts directly with nitrogenase and that CowN protection observes hyperbolic kinetics with respect to CowN concentration. At a CO concentration of 0.001 atm, CowN restores nearly full nitrogenase activity. Our results further indicate that CowN's protection mechanism involves decreasing the binding affinity of CO to nitrogenase's active site approximately tenfold without interrupting substrate turnover. Taken together, our work suggests CowN is an important auxiliary protein in nitrogen fixation that engenders CO tolerance to nitrogenase.
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Affiliation(s)
- Michael S Medina
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Kevin O Bretzing
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Richard A Aviles
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Kiersten M Chong
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Alejandro Espinoza
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Chloe Nicole G Garcia
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Benjamin B Katz
- Department of Chemistry, University of California, Irvine, Irvine, California, USA
| | - Ruchita N Kharwa
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Andrea Hernandez
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Justin L Lee
- Department of Chemistry, University of California, Irvine, Irvine, California, USA
| | - Terrence M Lee
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Christine Lo Verde
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Max W Strul
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Emily Y Wong
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Cedric P Owens
- Schmid College of Science and Technology, Chapman University, Orange, California, USA.
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Artificial, Photoinduced Activation of Nitrogenase Using Directed and Mediated Electron Transfer Processes. Catalysts 2020. [DOI: 10.3390/catal10090979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Nitrogenase, a bacteria-based enzyme, is the sole enzyme that is able to generate ammonia by atmospheric nitrogen fixation. Thus, improved understanding of its utilization and developing methods to artificially activate it may contribute to basic research, as well as to the design of future artificial systems. Here, we present methods to artificially activate nitrogenase using photoinduced reactions. Two nitrogenase variants originating from Azotobacter vinelandii were examined using photoactivated CdS nanoparticles (NPs) capped with thioglycolic acid (TGA) or 2-mercaptoethanol (ME) ligands. The effect of methyl viologen (MV) as a redox mediator of hydrogen and ammonia generation was tested and analyzed. We further determined the NPs conductive band edges and their effect on the nitrogenase photoactivation. The nano-biohybrid systems comprising CdS NPs and nitrogenase were further imaged by transmission electron microscopy, visualizing their formation for the first time. Our results show that the ME-capped CdS NPs–nitrogenase enzyme biohybrid system with added MV as a redox mediator leads to a five-fold increase in the production of ammonia compared with the non-mediated biohybrid system; nevertheless, it stills lag behind the natural process rate. On the contrary, a maximal hydrogen generation amount was achieved by the αL158C MoFe-P and the ME-capped CdS NPs.
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Zhang J, Liu GC, Dai XL, Wang J, Jin MH, Mi NN, Wang SQ. The N-terminus of MTRR plays a role in MTR reactivation cycle beyond electron transfer. Bioorg Chem 2020; 100:103836. [PMID: 32353563 DOI: 10.1016/j.bioorg.2020.103836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 03/20/2020] [Accepted: 04/06/2020] [Indexed: 11/26/2022]
Abstract
In eucaryotic cells, methionine synthase reductase (MSR/MTRR) is capable of dominating the folate-homocysteine metabolism as an irreplaceable partner in electron transfer for regeneration of methionine synthase. The N-terminus of MTRR containing a conserved domain of FMN_Red is closely concerned with the oxidation-reduction process. Maternal substitution of I22M in this domain can bring about pregnancy with high risk of spina bifida. A new variation of Arg2del was identified from a female conceiving a fetus with spina bifida cystica. Although the deletion is far from the N-terminal FMN_Red domain, the biochemical features of the variant had been seriously investigated. Curiously, the deletion of arginine(s) of MTRR could not affect the electron relay, if only the FMN_Red domain was intact, but by degrees reduced the ability to promote MTR catalysis in methionine formation. Confirmation of the interaction between the isolated MTRR N-terminal polypeptide and MTR suggested that the native MTRR N-terminus might play an extra role in MTR function. The tandem arginines at the end of MTRR N-terminus conferring high affinity to MTR were indispensable for stimulating methyltransferase activity perhaps via triggering allosteric effect that could be attenuated by removal of the arginine(s). It was concluded that MTRR could also propel MTR enzymatic reaction relying on the tandem arginines at N-terminus more than just only implicated in electron transfer in MTR reactivation cycle. Perturbance of the enzymatic cooperation due to the novel deletion could possibly invite spina bifida in clinics.
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Affiliation(s)
- Jun Zhang
- The Department of Cell Biology & Genetics, Chongqing Medical University, Chongqing 400016, China; Institute of Molecular Medicine and Oncology, Chongqing Medical University, Chongqing 400016, China.
| | - Gui-Cen Liu
- The Department of Cell Biology & Genetics, Chongqing Medical University, Chongqing 400016, China
| | - Xiao-Lu Dai
- The Department of Cell Biology & Genetics, Chongqing Medical University, Chongqing 400016, China
| | - Juan Wang
- The Department of Cell Biology & Genetics, Chongqing Medical University, Chongqing 400016, China
| | - Mu-Hua Jin
- The Department of Cell Biology & Genetics, Chongqing Medical University, Chongqing 400016, China
| | - Nan-Nan Mi
- The Department of Cell Biology & Genetics, Chongqing Medical University, Chongqing 400016, China
| | - Shu-Qin Wang
- The Department of Cell Biology & Genetics, Chongqing Medical University, Chongqing 400016, China
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