1
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Cuevas-Zuviría B, Garcia AK, Rivier AJ, Rucker HR, Carruthers BM, Kaçar B. Emergence of an Orphan Nitrogenase Protein Following Atmospheric Oxygenation. Mol Biol Evol 2024; 41:msae067. [PMID: 38526235 PMCID: PMC11018506 DOI: 10.1093/molbev/msae067] [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] [Received: 12/08/2023] [Revised: 03/06/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024] Open
Abstract
Molecular innovations within key metabolisms can have profound impacts on element cycling and ecological distribution. Yet, much of the molecular foundations of early evolved enzymes and metabolisms are unknown. Here, we bring one such mystery to relief by probing the birth and evolution of the G-subunit protein, an integral component of certain members of the nitrogenase family, the only enzymes capable of biological nitrogen fixation. The G-subunit is a Paleoproterozoic-age orphan protein that appears more than 1 billion years after the origin of nitrogenases. We show that the G-subunit arose with novel nitrogenase metal dependence and the ecological expansion of nitrogen-fixing microbes following the transition in environmental metal availabilities and atmospheric oxygenation that began ∼2.5 billion years ago. We identify molecular features that suggest early G-subunit proteins mediated cofactor or protein interactions required for novel metal dependency, priming ancient nitrogenases and their hosts to exploit these newly diversified geochemical environments. We further examined the degree of functional specialization in G-subunit evolution with extant and ancestral homologs using laboratory reconstruction experiments. Our results indicate that permanent recruitment of the orphan protein depended on the prior establishment of conserved molecular features and showcase how contingent evolutionary novelties might shape ecologically important microbial innovations.
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Affiliation(s)
| | - Amanda K Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Alex J Rivier
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Holly R Rucker
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Brooke M Carruthers
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
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2
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Willard D, Arellano JJ, Underdahl M, Lee TM, Ramaswamy AS, Fumes G, Kliman A, Wong EY, Owens CP. Mutational Analysis of the Nitrogenase Carbon Monoxide Protective Protein CowN Reveals That a Conserved C-Terminal Glutamic Acid Residue Is Necessary for Its Activity. Biochemistry 2024; 63:152-158. [PMID: 38091601 PMCID: PMC10765410 DOI: 10.1021/acs.biochem.3c00421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024]
Abstract
Nitrogenase is the only enzyme that catalyzes the reduction of nitrogen gas into ammonia. Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Many nitrogen fixing bacteria protect nitrogenase from CO inhibition using the protective protein CowN. This work demonstrates that a conserved glutamic acid residue near the C-terminus of Gluconacetobacter diazotrophicus CowN is necessary for its function. Mutation of the glutamic acid residue abolishes both CowN's protection against CO inhibition and the ability of CowN to bind to nitrogenase. In contrast, a conserved C-terminal cysteine residue is not important for CO protection by CowN. Overall, this work uncovers structural features in CowN that are required for its function and provides new insights into its nitrogenase binding and CO protection mechanism.
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Affiliation(s)
- Dustin
L. Willard
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Joshuah J. Arellano
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Mitch Underdahl
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Terrence M. Lee
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Avinash S. Ramaswamy
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Gabriella Fumes
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Agatha Kliman
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Emily Y. Wong
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
| | - Cedric P. Owens
- Department of Chemistry and
Biochemistry, Schmid College, Chapman University, Orange, California 92866, United States
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3
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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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4
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Dent MR, Weaver BR, Roberts MG, Burstyn JN. Carbon Monoxide-Sensing Transcription Factors: Regulators of Microbial Carbon Monoxide Oxidation Pathway Gene Expression. J Bacteriol 2023; 205:e0033222. [PMID: 37154694 PMCID: PMC10210986 DOI: 10.1128/jb.00332-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Carbon monoxide (CO) serves as a source of energy and carbon for a diverse set of microbes found in anaerobic and aerobic environments. The enzymes that bacteria and archaea use to oxidize CO depend upon complex metallocofactors that require accessory proteins for assembly and proper function. This complexity comes at a high energetic cost and necessitates strict regulation of CO metabolic pathways in facultative CO metabolizers to ensure that gene expression occurs only when CO concentrations and redox conditions are appropriate. In this review, we examine two known heme-dependent transcription factors, CooA and RcoM, that regulate inducible CO metabolism pathways in anaerobic and aerobic microorganisms. We provide an analysis of the known physiological and genomic contexts of these sensors and employ this analysis to contextualize known biochemical properties. In addition, we describe a growing list of putative transcription factors associated with CO metabolism that potentially use cofactors other than heme to sense CO.
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Affiliation(s)
- Matthew R. Dent
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brian R. Weaver
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Madeleine G. Roberts
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Judith N. Burstyn
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
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5
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Cadoux C, Ratcliff D, Maslać N, Gu W, Tsakoumagkos I, Hoogendoorn S, Wagner T, Milton RD. Nitrogen Fixation and Hydrogen Evolution by Sterically Encumbered Mo-Nitrogenase. JACS AU 2023; 3:1521-1533. [PMID: 37234119 PMCID: PMC10207099 DOI: 10.1021/jacsau.3c00165] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/20/2023] [Indexed: 05/27/2023]
Abstract
The substrate-reducing proteins of all nitrogenases (MoFe, VFe, and FeFe) are organized as α2ß2(γ2) multimers with two functional halves. While their dimeric organization could afford improved structural stability of nitrogenases in vivo, previous research has proposed both negative and positive cooperativity contributions with respect to enzymatic activity. Here, a 1.4 kDa peptide was covalently introduced in the proximity of the P cluster, corresponding to the Fe protein docking position. The Strep-tag carried by the added peptide simultaneously sterically inhibits electron delivery to the MoFe protein and allows the isolation of partially inhibited MoFe proteins (where the half-inhibited MoFe protein was targeted). We confirm that the partially functional MoFe protein retains its ability to reduce N2 to NH3, with no significant difference in selectivity over obligatory/parasitic H2 formation. Our experiment concludes that wild-type nitrogenase exhibits negative cooperativity during the steady state regarding H2 and NH3 formation (under Ar or N2), with one-half of the MoFe protein inhibiting turnover in the second half. This emphasizes the presence and importance of long-range (>95 Å) protein-protein communication in biological N2 fixation in Azotobacter vinelandii.
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Affiliation(s)
- Cécile Cadoux
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Daniel Ratcliff
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Nevena Maslać
- Max
Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Wenyu Gu
- Department
of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Ioannis Tsakoumagkos
- Department
of Organic Chemistry, National Center of Competence in Research (NCCR)
Chemical Biology, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Sascha Hoogendoorn
- Department
of Organic Chemistry, National Center of Competence in Research (NCCR)
Chemical Biology, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Tristan Wagner
- Max
Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Ross D. Milton
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
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6
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Rutledge HL, Field MJ, Rittle J, Green MT, Akif Tezcan F. Role of Serine Coordination in the Structural and Functional Protection of the Nitrogenase P-Cluster. J Am Chem Soc 2022; 144:22101-22112. [PMID: 36445204 PMCID: PMC9957664 DOI: 10.1021/jacs.2c09480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Nitrogenase catalyzes the multielectron reduction of dinitrogen to ammonia. Electron transfer in the catalytic protein (MoFeP) proceeds through a unique [8Fe-7S] cluster (P-cluster) to the active site (FeMoco). In the reduced, all-ferrous (PN) state, the P-cluster is coordinated by six cysteine residues. Upon two-electron oxidation to the P2+ state, the P-cluster undergoes conformational changes in which a highly conserved oxygen-based residue (a Ser or a Tyr) and a backbone amide additionally ligate the cluster. Previous studies of Azotobacter vinelandii (Av) MoFeP revealed that when the oxygen-based residue, βSer188, was mutated to a noncoordinating residue, Ala, the P-cluster became redox-labile and reversibly lost two of its eight Fe centers. Surprisingly, the Av strain with a MoFeP variant that lacked the serine ligand (Av βSer188Ala MoFeP) displayed the same diazotrophic growth and in vitro enzyme turnover rates as wild-type Av MoFeP, calling into question the necessity of this conserved ligand for nitrogenase function. Based on these observations, we hypothesized that βSer188 plays a role in protecting the P-cluster under nonideal conditions. Here, we investigated the protective role of βSer188 both in vivo and in vitro by characterizing the ability of Av βSer188Ala cells to grow under suboptimal conditions (high oxidative stress or Fe limitation) and by determining the tendency of βSer188Ala MoFeP to be mismetallated in vitro. Our results demonstrate that βSer188 (1) increases Av cell survival upon exposure to oxidative stress in the form of hydrogen peroxide, (2) is necessary for efficient Av diazotrophic growth under Fe-limiting conditions, and (3) may protect the P-cluster from metal exchange in vitro. Taken together, our findings suggest a structural adaptation of nitrogenase to protect the P-cluster via Ser ligation, which is a previously unidentified functional role of the Ser residue in redox proteins and adds to the expanding functional roles of non-Cys ligands to FeS clusters.
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Affiliation(s)
- Hannah L. Rutledge
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Mackenzie J. Field
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Jonathan Rittle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Michael T. Green
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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7
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Lo Verde C, Pepra-Ameyaw NB, Drucker CT, Okumura TLS, Lyon KA, Muniz JC, Sermet CS, Were Senger L, Owens CP. A highly active esterase from Lactobacillus helveticus hydrolyzes chlorogenic acid in sunflower meal to prevent chlorogenic acid induced greening in sunflower protein isolates. Food Res Int 2022; 162:111996. [PMID: 36461298 DOI: 10.1016/j.foodres.2022.111996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022]
Abstract
Chlorogenic acid (CGA) is an ester between caffeic and quinic acid. It is found in many foods and reacts with free amino groups in proteins at alkaline pH, leading to the formation of an undesirable green pigment in sunflower seed-derived ingredients. This paper presents the biochemical characterization and application of a highly active chlorogenic acid esterase from Lactobacillus helveticus. The enzyme is one of the most active CGA esterases known to date with a Km of 0.090 mM and a kcat of 82.1 s-1. The CGA esterase is easily expressed recombinantly in E. coli in large yields and is stable over a wide range of pH and temperatures. We characterized CGA esterase's kinetic properties in sunflower meal and demonstrated that the enzyme completely hydrolyzes CGA in the meal. Finally, we showed that CGA esterase treatment of sunflower seed meal enables the production of pale brown sunflower protein isolates using alkaline extraction. This work will allow for more widespread use of sunflower-derived products in applications where neutrally-colored food products are desired.
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Affiliation(s)
- Christine Lo Verde
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange CA 92866, USA.
| | - Nana Baah Pepra-Ameyaw
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange CA 92866, USA.
| | - Charles T Drucker
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange CA 92866, USA.
| | - Tracie L S Okumura
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange CA 92866, USA.
| | - Katherine A Lyon
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange CA 92866, USA.
| | - Julia C Muniz
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange CA 92866, USA.
| | - Chloe S Sermet
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange CA 92866, USA.
| | - Lilian Were Senger
- 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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8
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Oehlmann NN, Rebelein JG. The Conversion of Carbon Monoxide and Carbon Dioxide by Nitrogenases. Chembiochem 2022; 23:e202100453. [PMID: 34643977 PMCID: PMC9298215 DOI: 10.1002/cbic.202100453] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/13/2021] [Indexed: 12/02/2022]
Abstract
Nitrogenases are the only known family of enzymes that catalyze the reduction of molecular nitrogen (N2 ) to ammonia (NH3 ). The N2 reduction drives biological nitrogen fixation and the global nitrogen cycle. Besides the conversion of N2 , nitrogenases catalyze a whole range of other reductions, including the reduction of the small gaseous substrates carbon monoxide (CO) and carbon dioxide (CO2 ) to hydrocarbons. However, it remains an open question whether these 'side reactivities' play a role under environmental conditions. Nonetheless, these reactivities and particularly the formation of hydrocarbons have spurred the interest in nitrogenases for biotechnological applications. There are three different isozymes of nitrogenase: the molybdenum and the alternative vanadium and iron-only nitrogenase. The isozymes differ in their metal content, structure, and substrate-dependent activity, despite their homology. This minireview focuses on the conversion of CO and CO2 to methane and higher hydrocarbons and aims to specify the differences in activity between the three nitrogenase isozymes.
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Affiliation(s)
- Niels N. Oehlmann
- Max Planck Institute for Terrestrial MicrobiologyKarl-von-Frisch-Straße 1035043MarburgGermany
| | - Johannes G. Rebelein
- Max Planck Institute for Terrestrial MicrobiologyKarl-von-Frisch-Straße 1035043MarburgGermany
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