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Wannicke N, Stüeken EE, Bauersachs T, Gehringer MM. Exploring the influence of atmospheric CO 2 and O 2 levels on the utility of nitrogen isotopes as proxy for biological N 2 fixation. Appl Environ Microbiol 2024:e0057424. [PMID: 39320082 DOI: 10.1128/aem.00574-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 08/26/2024] [Indexed: 09/26/2024] Open
Abstract
Biological N2 fixation (BNF) is traced to the Archean. The nitrogen isotopic fractionation composition (δ15N) of sedimentary rocks is commonly used to reconstruct the presence of ancient diazotrophic ecosystems. While δ15N has been validated mostly using organisms grown under present-day conditions; it has not under the pre-Cambrian conditions, when atmospheric pO2 was lower and pCO2 was higher. Here, we explore δ15N signatures under three atmospheres with (i) elevated CO2 and no O2 (Archean), (ii) present-day CO2, and O2 and (iii) future elevated CO2, in marine and freshwater, heterocytous cyanobacteria. Additionally, we augment our data set from literature for more generalized dependencies of δ15N and the associated fractionation factor epsilon (ε = δ15Nbiomass - δ15NN2) during BNF in Archaea and Bacteria, including cyanobacteria, and habitats. The ε ranges between 3.70‰ and -4.96‰ with a mean ε value of -1.38 ± 0.95‰, for all bacteria, including cyanobacteria, across all tested conditions. The expanded data set revealed correlations of isotopic fractionation of BNF with CO2 concentrations, toxin production, and light, although within 1‰. Moreover, correlation showed significant dependency of ε to species type, C/N ratios and toxin production in cyanobacteria, albeit it within a small range (-1.44 ± 0.89‰). We therefore conclude that δ15N is likely robust when applied to the pre-Cambrian-like atmosphere, stressing the strong cyanobacterial bias. Interestingly, the increased fractionation (lower ε) observed in the toxin-producing Nodularia and Nostoc spp. suggests a heretofore unknown role of toxins in modulating nitrogen isotopic signals that warrants further investigation.IMPORTANCENitrogen is an essential element of life on Earth; however, despite its abundance, it is not biologically accessible. Biological nitrogen fixation is an essential process whereby microbes fix N2 into biologically usable NH3. During this process, the enzyme nitrogenase preferentially uses light 14N, resulting in 15N depleted biomass. This signature can be traced back in time in sediments on Earth, and possibly other planets. In this paper, we explore the influence of pO2 and pCO2 on this fractionation signal. We find the signal is stable, especially for the primary producers, cyanobacteria, with correlations to CO2, light, and toxin-producing status, within a small range. Unexpectedly, we identified higher fractionation signals in toxin-producing Nodularia and Nostoc species that offer insight into why some organisms produce these N-rich toxic secondary metabolites.
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Affiliation(s)
- Nicola Wannicke
- Leibniz Institute for Plasma Science and Technology e.V., Greifswald, Germany
| | - Eva E Stüeken
- School of Earth & Environmental Sciences, University of St. Andrews, St. Andrews, United Kingdom
| | - Thorsten Bauersachs
- Institute of Organic Biochemistry in Geo-Systems, RWTH Aachen University, Aachen, Germany
| | - Michelle M Gehringer
- Department of Microbiology, University of Kaiserslautern-Landau (RPTU), Kaiserslautern, Germany
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2
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Morimoto Y, Uesaka K, Fujita Y, Yamamoto H. A nitrogenase-like enzyme is involved in the novel anaerobic assimilation pathway of a sulfonate, isethionate, in the photosynthetic bacterium Rhodobacter capsulatus. mSphere 2024; 9:e0049824. [PMID: 39191391 PMCID: PMC11423573 DOI: 10.1128/msphere.00498-24] [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: 07/01/2024] [Accepted: 07/09/2024] [Indexed: 08/29/2024] Open
Abstract
Prokaryotes contribute to the global sulfur cycle by using diverse sulfur compounds as sulfur sources or electron acceptors. In this study, we report that a nitrogenase-like enzyme (NFL) and a radical SAM enzyme (RSE) are involved in the novel anaerobic assimilation pathway of a sulfonate, isethionate, in the photosynthetic bacterium Rhodobacter capsulatus. The nflHDK genes for NFL are localized at a locus containing genes for known sulfonate metabolism in the genome. A gene nflB encoding an RSE is present just upstream of nflH, forming a small gene cluster nflBHDK. Mutants lacking any nflBHDK genes are incapable of growing with isethionate as the sole sulfur source under anaerobic photosynthetic conditions, indicating that all four NflBHDK proteins are essential for the isethionate assimilation pathway. Heterologous expression of the islAB genes encoding a known isethionate lyase that degrades isethionate to sulfite and acetaldehyde restored the isethionate-dependent growth of a mutant lacking nflDK, indicating that the enzyme encoding nflBHDK is involved in an isethionate assimilation reaction to release sulfite. Furthermore, the heterologous expression of nflBHDK and ssuCAB encoding an isethionate transporter in the closely related species R. sphaeroides, which does not have nflBHDK and cannot grow with isethionate as the sole sulfur source, conferred isethionate-dependent growth ability to this species. We propose to rename nflBHDK as isrBHDK (isethionate reductase). The isrBHDK genes are widely distributed among various prokaryote phyla. Discovery of the isethionate assimilation pathway by IsrBHDK provides a missing piece for the anaerobic sulfur cycle and for understanding the evolution of ancient sulfur metabolism.IMPORTANCENitrogenase is an important enzyme found in prokaryotes that reduces atmospheric nitrogen to ammonia and plays a fundamental role in the global nitrogen cycle. It has been noted that nitrogenase-like enzymes (NFLs), which share an evolutionary origin with nitrogenase, have evolved to catalyze diverse reactions such as chlorophyll biosynthesis (photosynthesis), coenzyme F430 biosynthesis (methanogenesis), and methionine biosynthesis. In this study, we discovered that an NFL with unknown function in the photosynthetic bacterium Rhodobacter capsulatus is a novel isethionate reductase (Isr), which catalyzes the assimilatory degradation of isethionate, a sulfonate, releasing sulfite used as the sulfur source under anaerobic conditions. Isr is widely distributed among various bacterial phyla, including intestinal bacteria, and is presumed to play an important role in sulfur metabolism in anaerobic environments such as animal guts and microbial mats. This finding provides a clue for understanding ancient metabolism that evolved under anaerobic environments at the dawn of life.
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Affiliation(s)
- Yoshiki Morimoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kazuma Uesaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yuichi Fujita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Haruki Yamamoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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3
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Lyons TW, Tino CJ, Fournier GP, Anderson RE, Leavitt WD, Konhauser KO, Stüeken EE. Co-evolution of early Earth environments and microbial life. Nat Rev Microbiol 2024; 22:572-586. [PMID: 38811839 DOI: 10.1038/s41579-024-01044-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2024] [Indexed: 05/31/2024]
Abstract
Two records of Earth history capture the evolution of life and its co-evolving ecosystems with interpretable fidelity: the geobiological and geochemical traces preserved in rocks and the evolutionary histories captured within genomes. The earliest vestiges of life are recognized mostly in isotopic fingerprints of specific microbial metabolisms, whereas fossils and organic biomarkers become important later. Molecular biology provides lineages that can be overlayed on geologic and geochemical records of evolving life. All these data lie within a framework of biospheric evolution that is primarily characterized by the transition from an oxygen-poor to an oxygen-rich world. In this Review, we explore the history of microbial life on Earth and the degree to which it shaped, and was shaped by, fundamental transitions in the chemical properties of the oceans, continents and atmosphere. We examine the diversity and evolution of early metabolic processes, their couplings with biogeochemical cycles and their links to the oxygenation of the early biosphere. We discuss the distinction between the beginnings of metabolisms and their subsequent proliferation and their capacity to shape surface environments on a planetary scale. The evolution of microbial life and its ecological impacts directly mirror the Earth's chemical and physical evolution through cause-and-effect relationships.
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Affiliation(s)
- Timothy W Lyons
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA.
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA.
| | - Christopher J Tino
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA.
| | - Gregory P Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rika E Anderson
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
- Biology Department, Carleton College, Northfield, MN, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, USA
- Department of Chemistry, Dartmouth College, Hanover, NH, USA
| | - Kurt O Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Eva E Stüeken
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
- School of Earth and Environmental Sciences, University of St Andrews, St Andrews, UK
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4
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Maslać N, Cadoux C, Bolte P, Murken F, Gu W, Milton RD, Wagner T. Structural comparison of (hyper-)thermophilic nitrogenase reductases from three marine Methanococcales. FEBS J 2024; 291:3454-3480. [PMID: 38696373 DOI: 10.1111/febs.17148] [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: 08/16/2023] [Revised: 01/17/2024] [Accepted: 04/17/2024] [Indexed: 05/04/2024]
Abstract
The nitrogenase reductase NifH catalyses ATP-dependent electron delivery to the Mo-nitrogenase, a reaction central to biological dinitrogen (N2) fixation. While NifHs have been extensively studied in bacteria, structural information about their archaeal counterparts is limited. Archaeal NifHs are considered more ancient, particularly those from Methanococcales, a group of marine hydrogenotrophic methanogens, which includes diazotrophs growing at temperatures near 92 °C. Here, we structurally and biochemically analyse NifHs from three Methanococcales, offering the X-ray crystal structures from meso-, thermo-, and hyperthermophilic methanogens. While NifH from Methanococcus maripaludis (37 °C) was obtained through heterologous recombinant expression, the proteins from Methanothermococcus thermolithotrophicus (65 °C) and Methanocaldococcus infernus (85 °C) were natively purified from the diazotrophic archaea. The structures from M. thermolithotrophicus crystallised as isolated exhibit high flexibility. In contrast, the complexes of NifH with MgADP obtained from the three methanogens are superposable, more rigid, and present remarkable structural conservation with their homologues. They retain key structural features of P-loop NTPases and share similar electrostatic profiles with the counterpart from the bacterial model organism Azotobacter vinelandii. In comparison to the NifH from the phylogenetically distant Methanosarcina acetivorans, these reductases do not cross-react significantly with Mo-nitrogenase from A. vinelandii. However, they associate with bacterial nitrogenase when ADP·AlF 4 - is added to mimic a transient reactive state. Accordingly, detailed surface analyses suggest that subtle substitutions would affect optimal binding during the catalytic cycle between the NifH from Methanococcales and the bacterial nitrogenase, implying differences in the N2-machinery from these ancient archaea.
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Affiliation(s)
- Nevena Maslać
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Cécile Cadoux
- Department of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Switzerland
- National Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Switzerland
| | - Pauline Bolte
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Fenja Murken
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Wenyu Gu
- Laboratory of Microbial Physiology and Resource Biorecovery, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédéral de Lausanne, Switzerland
| | - Ross D Milton
- Department of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Switzerland
- National Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Switzerland
| | - Tristan Wagner
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
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5
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He H, Zheng W, Xiao S, Gong L, Li H, Zhou K, Zhang L, Tu Q, Zhu YZ, Zhang Y. Deciphering the Nitrogen Fixation Gene Cluster in Vibrio natriegens: A Study on Optimized Expression and Application of Nitrogenase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12618-12629. [PMID: 38778776 DOI: 10.1021/acs.jafc.4c01232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Microbial nitrogen fixation presents a viable alternative to chemical fertilizers, yet the limited colonization and specificity of naturally occurring nitrogen-fixing microorganisms present significant challenges to their widespread application. In this study, we identified a nitrogen fixation gene cluster (VNnif) in Vibrio natriegens (VN) and tested its nitrogenase activity through the acetylene reduction assay. We investigated the potential utilization of nitrogenase by incorporating the nitrogenase gene cluster from VN into plant growth-promoting rhizosphere bacteria Pseudomonas protegens CHA0 and enhancing its activity to 48.16 nmol C2H2/mg/h through promoter replacement and cluster rearrangement. The engineered strain CHA0-PVNnif was found to positively impact the growth of Arabidopsis thaliana col-0 and Triticum aestivum L. (wheat). This study expanded the role of plant growth-promoting rhizobacteria (PGPR) and provided a research foundation for enhancing nitrogenase activity.
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Affiliation(s)
- Haocheng He
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Weijin Zheng
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- College of Life and Geographic Sciences, Kashi University, Kashi 844099, China
| | - Shuai Xiao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Liang Gong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - He Li
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR 999078, China
| | - Kexuan Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR 999078, China
| | - Letian Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- State Key Lab of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Qiang Tu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yi Zhun Zhu
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR 999078, China
- State Key Lab of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Youming Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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6
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Rucker HR, Kaçar B. Enigmatic evolution of microbial nitrogen fixation: insights from Earth's past. Trends Microbiol 2024; 32:554-564. [PMID: 37061455 DOI: 10.1016/j.tim.2023.03.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 04/17/2023]
Abstract
The evolution of nitrogen fixation undoubtedly altered nearly all corners of the biosphere, given the essential role of nitrogen in the synthesis of biomass. To date, there is no unified view on what planetary conditions gave rise to nitrogen fixation or how these conditions have sustained it evolutionarily. Intriguingly, the concentrations of metals that nitrogenases require to function have changed throughout Earth's history. In this review, we describe the interconnection of the metal and nitrogen cycles with nitrogenase evolution and the importance of ancient ecology in the formation of the modern nitrogen cycle. We argue that exploration of the nitrogen cycle's deep past will provide insights into humanity's immediate environmental challenges centered on nitrogen availability.
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Affiliation(s)
- Holly R Rucker
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA.
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7
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Bellanger M, Figueroa JL, Tiemann L, Friesen ML, III RW. NF ixDB (Nitrogen Fixation DataBase)-a comprehensive integrated database for robust 'omics analysis of diazotrophs. NAR Genom Bioinform 2024; 6:lqae063. [PMID: 38846350 PMCID: PMC11155484 DOI: 10.1093/nargab/lqae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/16/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
Biological nitrogen fixation is a fundamental biogeochemical process that transforms molecular nitrogen into biologically available nitrogen via diazotrophic microbes. Diazotrophs anaerobically fix nitrogen using the nitrogenase enzyme which is arranged in three different gene clusters: (i) molybdenum nitrogenase (nifHDK) is the most abundant, followed by it's alternatives, (ii) vanadium nitrogenase (vnfHDK) and (iii) iron nitrogenase (anfHDK). Multiple databases have been constructed as resources for diazotrophic 'omics analysis; however, an integrated database based on whole genome references does not exist. Here, we present NFixDB (Nitrogen Fixation DataBase), a comprehensive integrated whole genome based database for diazotrophs, which includes all nitrogenases (nifHDK, vnfHDK, anfHDK) and nitrogenase-like enzymes (e.g. nflHD) linked to ribosomal RNA operons (16S-5S-23S). NFixDB was computed using Hidden Markov Models (HMMs) against the entire whole genome based Genome Taxonomy Database (GTDB R214), providing searchable reference HMMs for all nitrogenase and nitrogenase-like genes, complete ribosomal RNA operons, both GTDB and NCBI/RefSeq taxonomy, and an SQL database for querying matches. We compared NFixDB to nifH databases from Buckley, Zehr, Mise and FunGene finding extensive evidence of nifH, in addition to vnfH and nflH. NFixDB contains >4000 verified nifHDK sequences contained on 50 unique phyla of bacteria and archaea. NFixDB provides the first comprehensive nitrogenase database available to researchers unlocking diazotrophic microbial potential.
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Affiliation(s)
- Madeline Bellanger
- North Carolina Research Campus (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 150 N Research Campus Dr, Kannapolis, NC 28081, USA
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA
| | - Jose L Figueroa
- North Carolina Research Campus (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 150 N Research Campus Dr, Kannapolis, NC 28081, USA
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA
| | - Lisa Tiemann
- Department of Plant, Soil and Microbial Sciences, Michigan State University, Plant and Soil Sciences Building, 1066 Bogue St Room A286, East Lansing, MI 48824, USA
| | - Maren L Friesen
- Department of Plant Pathology, Washington State University, Clark Hall, 2040 Ellis Way, Pullman, WA 99163, USA
| | - Richard Allen White III
- North Carolina Research Campus (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 150 N Research Campus Dr, Kannapolis, NC 28081, USA
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA
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8
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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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9
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Pi HW, Chiang YR, Li WH. Mapping Geological Events and Nitrogen Fixation Evolution Onto the Timetree of the Evolution of Nitrogen-Fixation Genes. Mol Biol Evol 2024; 41:msae023. [PMID: 38319744 PMCID: PMC10881105 DOI: 10.1093/molbev/msae023] [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: 10/09/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 02/08/2024] Open
Abstract
Nitrogen is essential for all organisms, but biological nitrogen fixation (BNF) occurs only in a small fraction of prokaryotes. Previous studies divided nitrogenase-gene-carrying prokaryotes into Groups I to IV and provided evidence that BNF first evolved in bacteria. This study constructed a timetree of the evolution of nitrogen-fixation genes and estimated that archaea evolved BNF much later than bacteria and that nitrogen-fixing cyanobacteria evolved later than 1,900 MYA, considerably younger than the previous estimate of 2,200 MYA. Moreover, Groups III and II/I diverged ∼2,280 MYA, after the Kenorland supercontinent breakup (∼2,500-2,100 MYA) and the Great Oxidation Event (∼2,400-2,100 MYA); Groups III and Vnf/Anf diverged ∼2,086 MYA, after the Yarrabubba impact (∼2,229 MYA); and Groups II and I diverged ∼1,920 MYA, after the Vredefort impact (∼2,023 MYA). In summary, this study provided a timescale of BNF events and discussed the possible effects of geological events on BNF evolution.
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Affiliation(s)
- Hong-Wei Pi
- Biodiversity Research Center, Academia Sinica, Taipei 115201, Taiwan
- Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yin-Ru Chiang
- Biodiversity Research Center, Academia Sinica, Taipei 115201, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei 115201, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
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10
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Payne D, Spietz RL, Newell DL, Dijkstra P, Boyd ES. Influence of sulfide on diazotrophic growth of the methanogen Methanococcus maripaludis and its implications for the origin of nitrogenase. Commun Biol 2023; 6:799. [PMID: 37524775 PMCID: PMC10390477 DOI: 10.1038/s42003-023-05163-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 07/21/2023] [Indexed: 08/02/2023] Open
Abstract
Methanogens inhabit euxinic (sulfide-rich) or ferruginous (iron-rich) environments that promote the precipitation of transition metals as metal sulfides, such as pyrite, reducing metal or sulfur availability. Such environments have been common throughout Earth's history raising the question as to how anaerobes obtain(ed) these elements for the synthesis of enzyme cofactors. Here, we show a methanogen can synthesize molybdenum nitrogenase metallocofactors from pyrite as the source of iron and sulfur, enabling nitrogen fixation. Pyrite-grown, nitrogen-fixing cells grow faster and require 25-fold less molybdenum than cells grown under euxinic conditions. Growth yields are 3 to 8 times higher in cultures grown under ferruginous relative to euxinic conditions. Physiological, transcriptomic, and geochemical data indicate these observations are due to sulfide-promoted metal limitation, in particular molybdenum. These findings suggest that molybdenum nitrogenase may have originated in a ferruginous environment that titrated sulfide to form pyrite, facilitating the availability of sufficient iron, sulfur, and molybdenum for cofactor biosynthesis.
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Affiliation(s)
- Devon Payne
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Rachel L Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Dennis L Newell
- Department of Geosciences, Utah State University, Logan, UT, 84322, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
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11
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Sheng Y, Baars O, Guo D, Whitham J, Srivastava S, Dong H. Mineral-Bound Trace Metals as Cofactors for Anaerobic Biological Nitrogen Fixation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:7206-7216. [PMID: 37116091 DOI: 10.1021/acs.est.3c01371] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nitrogenase is the only known biological enzyme capable of reducing N2 to bioavailable NH3. Most nitrogenases use Mo as a metallocofactor, while alternative cofactors V and Fe are also viable. Both geological and bioinformatic evidence suggest an ancient origin of Mo-based nitrogenase in the Archean, despite the low concentration of dissolved Mo in the Archean oceans. This apparent paradox would be resolvable if mineral-bound Mo were bioavailable for nitrogen fixation by ancient diazotrophs. In this study, the bioavailability of mineral-bound Mo, V, and Fe was determined by incubating an obligately anaerobic diazotroph Clostridium kluyveri with Mo-, V-, and Fe-bearing minerals (molybdenite, cavansite, and ferrihydrite, respectively) and basalt under diazotrophic conditions. The results showed that C. kluyveri utilized mineral-associated metals to express nitrogenase genes and fix nitrogen, as measured by the reverse transcription quantitative polymerase chain reaction and acetylene reduction assay, respectively. C. kluyveri secreted chelating molecules to extract metals from the minerals. As a result of microbial weathering, mineral surface chemistry significantly changed, likely due to surface coating by microbial exudates for metal extraction. These results provide important support for the ancient origin of Mo-based nitrogenase, with profound implications for coevolution of the biosphere and geosphere.
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Affiliation(s)
- Yizhi Sheng
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio 45056, United States
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Oliver Baars
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Dongyi Guo
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio 45056, United States
| | - Jason Whitham
- Department of Plant and Molecular Biology, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Shreya Srivastava
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio 45056, United States
| | - Hailiang Dong
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio 45056, United States
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12
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Martin Del Campo JS, Rigsbee J, Bueno Batista M, Mus F, Rubio LM, Einsle O, Peters JW, Dixon R, Dean DR, Dos Santos PC. Overview of physiological, biochemical, and regulatory aspects of nitrogen fixation in Azotobacter vinelandii. Crit Rev Biochem Mol Biol 2023; 57:492-538. [PMID: 36877487 DOI: 10.1080/10409238.2023.2181309] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Understanding how Nature accomplishes the reduction of inert nitrogen gas to form metabolically tractable ammonia at ambient temperature and pressure has challenged scientists for more than a century. Such an understanding is a key aspect toward accomplishing the transfer of the genetic determinants of biological nitrogen fixation to crop plants as well as for the development of improved synthetic catalysts based on the biological mechanism. Over the past 30 years, the free-living nitrogen-fixing bacterium Azotobacter vinelandii emerged as a preferred model organism for mechanistic, structural, genetic, and physiological studies aimed at understanding biological nitrogen fixation. This review provides a contemporary overview of these studies and places them within the context of their historical development.
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Affiliation(s)
| | - Jack Rigsbee
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA
| | | | - Florence Mus
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
| | - Oliver Einsle
- Department of Biochemistry, University of Freiburg, Freiburg, Germany
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Dennis R Dean
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
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13
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Garcia AK, Harris DF, Rivier AJ, Carruthers BM, Pinochet-Barros A, Seefeldt LC, Kaçar B. Nitrogenase resurrection and the evolution of a singular enzymatic mechanism. eLife 2023; 12:e85003. [PMID: 36799917 PMCID: PMC9977276 DOI: 10.7554/elife.85003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/16/2023] [Indexed: 02/18/2023] Open
Abstract
The planetary biosphere is powered by a suite of key metabolic innovations that emerged early in the history of life. However, it is unknown whether life has always followed the same set of strategies for performing these critical tasks. Today, microbes access atmospheric sources of bioessential nitrogen through the activities of just one family of enzymes, nitrogenases. Here, we show that the only dinitrogen reduction mechanism known to date is an ancient feature conserved from nitrogenase ancestors. We designed a paleomolecular engineering approach wherein ancestral nitrogenase genes were phylogenetically reconstructed and inserted into the genome of the diazotrophic bacterial model, Azotobacter vinelandii, enabling an integrated assessment of both in vivo functionality and purified nitrogenase biochemistry. Nitrogenase ancestors are active and robust to variable incorporation of one or more ancestral protein subunits. Further, we find that all ancestors exhibit the reversible enzymatic mechanism for dinitrogen reduction, specifically evidenced by hydrogen inhibition, which is also exhibited by extant A. vinelandii nitrogenase isozymes. Our results suggest that life may have been constrained in its sampling of protein sequence space to catalyze one of the most energetically challenging biochemical reactions in nature. The experimental framework established here is essential for probing how nitrogenase functionality has been shaped within a dynamic, cellular context to sustain a globally consequential metabolism.
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Affiliation(s)
- Amanda K Garcia
- Department of Bacteriology, University of Wisconsin–MadisonMadisonUnited States
| | - Derek F Harris
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUnited States
| | - Alex J Rivier
- Department of Bacteriology, University of Wisconsin–MadisonMadisonUnited States
| | - Brooke M Carruthers
- Department of Bacteriology, University of Wisconsin–MadisonMadisonUnited States
| | | | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUnited States
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin–MadisonMadisonUnited States
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14
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Bennett EM, Murray JW, Isalan M. Engineering Nitrogenases for Synthetic Nitrogen Fixation: From Pathway Engineering to Directed Evolution. BIODESIGN RESEARCH 2023; 5:0005. [PMID: 37849466 PMCID: PMC10521693 DOI: 10.34133/bdr.0005] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 12/24/2022] [Indexed: 10/19/2023] Open
Abstract
Globally, agriculture depends on industrial nitrogen fertilizer to improve crop growth. Fertilizer production consumes fossil fuels and contributes to environmental nitrogen pollution. A potential solution would be to harness nitrogenases-enzymes capable of converting atmospheric nitrogen N2 to NH3 in ambient conditions. It is therefore a major goal of synthetic biology to engineer functional nitrogenases into crop plants, or bacteria that form symbiotic relationships with crops, to support growth and reduce dependence on industrially produced fertilizer. This review paper highlights recent work toward understanding the functional requirements for nitrogenase expression and manipulating nitrogenase gene expression in heterologous hosts to improve activity and oxygen tolerance and potentially to engineer synthetic symbiotic relationships with plants.
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Affiliation(s)
- Emily M. Bennett
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - James W. Murray
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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15
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Boyd ES, Spietz RL, Kour M, Colman DR. A naturalist perspective of microbiology: Examples from methanogenic archaea. Environ Microbiol 2023; 25:184-198. [PMID: 36367391 DOI: 10.1111/1462-2920.16285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
Abstract
Storytelling has been the primary means of knowledge transfer over human history. The effectiveness and reach of stories are improved when the message is appropriate for the target audience. Oftentimes, the stories that are most well received and recounted are those that have a clear purpose and that are told from a variety of perspectives that touch on the varied interests of the target audience. Whether scientists realize or not, they are accustomed to telling stories of their own scientific discoveries through the preparation of manuscripts, presentations, and lectures. Perhaps less frequently, scientists prepare review articles or book chapters that summarize a body of knowledge on a given subject matter, meant to be more holistic recounts of a body of literature. Yet, by necessity, such summaries are often still narrow in their scope and are told from the perspective of a particular discipline. In other words, interdisciplinary reviews or book chapters tend to be the rarity rather than the norm. Here, we advocate for and highlight the benefits of interdisciplinary perspectives on microbiological subjects.
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Affiliation(s)
- Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Rachel L Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Manjinder Kour
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
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16
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Comparative Transcriptomics Sheds Light on Remodeling of Gene Expression during Diazotrophy in the Thermophilic Methanogen Methanothermococcus thermolithotrophicus. mBio 2022; 13:e0244322. [PMID: 36409126 PMCID: PMC9765008 DOI: 10.1128/mbio.02443-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Some marine thermophilic methanogens are able to perform energy-consuming nitrogen fixation despite deriving only little energy from hydrogenotrophic methanogenesis. We studied this process in Methanothermococcus thermolithotrophicus DSM 2095, a methanogenic archaeon of the order Methanococcales that contributes to the nitrogen pool in some marine environments. We successfully grew this archaeon under diazotrophic conditions in both batch and fermenter cultures, reaching the highest cell density reported so far. Diazotrophic growth depended strictly on molybdenum and, in contrast to other diazotrophs, was not inhibited by tungstate or vanadium. This suggests an elaborate control of metal uptake and a specific metal recognition system for the insertion into the nitrogenase cofactor. Differential transcriptomics of M. thermolithotrophicus grown under diazotrophic conditions with ammonium-fed cultures as controls revealed upregulation of the nitrogenase machinery, including chaperones, regulators, and molybdate importers, as well as simultaneous upregulation of an ammonium transporter and a putative pathway for nitrate and nitrite utilization. The organism thus employs multiple synergistic strategies for uptake of nitrogen nutrients during the early exponential growth phase without altering transcription levels for genes involved in methanogenesis. As a counterpart, genes coding for transcription and translation processes were downregulated, highlighting the maintenance of an intricate metabolic balance to deal with energy constraints and nutrient limitations imposed by diazotrophy. This switch in the metabolic balance included unexpected processes, such as upregulation of the CRISPR-Cas system, probably caused by drastic changes in transcription levels of putative mobile and virus-like elements. IMPORTANCE The thermophilic anaerobic archaeon M. thermolithotrophicus is a particularly suitable model organism to study the coupling of methanogenesis to diazotrophy. Likewise, its capability of simultaneously reducing N2 and CO2 into NH3 and CH4 with H2 makes it a viable target for biofuel production. We optimized M. thermolithotrophicus cultivation, resulting in considerably higher cell yields and enabling the successful establishment of N2-fixing bioreactors. Improved understanding of the N2 fixation process would provide novel insights into metabolic adaptations that allow this energy-limited extremophile to thrive under diazotrophy, for instance, by investigating its physiology and uncharacterized nitrogenase. We demonstrated that diazotrophic growth of M. thermolithotrophicus is exclusively dependent on molybdenum, and complementary transcriptomics corroborated the expression of the molybdenum nitrogenase system. Further analyses of differentially expressed genes during diazotrophy across three cultivation time points revealed insights into the response to nitrogen limitation and the coordination of core metabolic processes.
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17
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Gluconacetobacter diazotrophicus Gene Fitness during Diazotrophic Growth. Appl Environ Microbiol 2022; 88:e0124122. [PMID: 36374093 PMCID: PMC9746312 DOI: 10.1128/aem.01241-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Plant growth-promoting (PGP) bacteria are important to the development of sustainable agricultural systems. PGP microbes that fix atmospheric nitrogen (diazotrophs) could minimize the application of industrially derived fertilizers and function as a biofertilizer. The bacterium Gluconacetobacter diazotrophicus is a nitrogen-fixing PGP microbe originally discovered in association with sugarcane plants, where it functions as an endophyte. It also forms endophyte associations with a range of other agriculturally relevant crop plants. G. diazotrophicus requires microaerobic conditions for diazotrophic growth. We generated a transposon library for G. diazotrophicus and cultured the library under various growth conditions and culture medium compositions to measure fitness defects associated with individual transposon inserts (transposon insertion sequencing [Tn-seq]). Using this library, we probed more than 3,200 genes and ascertained the importance of various genes for diazotrophic growth of this microaerobic endophyte. We also identified a set of essential genes. IMPORTANCE Our results demonstrate a succinct set of genes involved in diazotrophic growth for G. diazotrophicus, with a lower degree of redundancy than what is found in other model diazotrophs. The results will serve as a valuable resource for those interested in biological nitrogen fixation and will establish a baseline data set for plant free growth, which could complement future studies related to the endophyte relationship.
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18
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Spietz RL, Payne D, Szilagyi R, Boyd ES. Reductive biomining of pyrite by methanogens. Trends Microbiol 2022; 30:1072-1083. [PMID: 35624031 DOI: 10.1016/j.tim.2022.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 01/13/2023]
Abstract
Pyrite (FeS2) is the most abundant iron sulfide mineral in Earth's crust. Until recently, FeS2 has been considered a sink for iron (Fe) and sulfur (S) at low temperature in the absence of oxygen or oxidative weathering, making these elements unavailable to biology. However, anaerobic methanogens can transfer electrons extracellularly to reduce FeS2 via direct contact with the mineral. Reduction of FeS2 occurs through a multistep process that generates aqueous sulfide (HS-) and FeS2-associated pyrrhotite (Fe1-xS). Subsequent dissolution of Fe1-xS provides Fe(II)(aq), but not HS-, that rapidly complexes with HS-(aq) generated from FeS2 reduction to form soluble iron sulfur clusters [nFeS(aq)]. Cells assimilate nFeS(aq) to meet Fe/S nutritional demands by mobilizing and hyperaccumulating Fe and S from FeS2. As such, reductive dissolution of FeS2 by methanogens has important implications for element cycling in anoxic habitats, both today and in the geologic past.
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Affiliation(s)
- Rachel L Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Devon Payne
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Robert Szilagyi
- Department of Chemistry, University of British Columbia - Okanagan, Kelowna, BC V1V 1V7, Canada
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA.
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19
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He W, Burén S, Baysal C, Jiang X, Capell T, Christou P, Rubio LM. Nitrogenase Cofactor Maturase NifB Isolated from Transgenic Rice is Active in FeMo-co Synthesis. ACS Synth Biol 2022; 11:3028-3036. [PMID: 35998307 PMCID: PMC9486962 DOI: 10.1021/acssynbio.2c00194] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The engineering of nitrogen fixation in plants requires assembly of an active prokaryotic nitrogenase complex, which is yet to be achieved. Nitrogenase biogenesis relies on NifB, which catalyzes the formation of the [8Fe-9S-C] metal cluster NifB-co. This is the first committed step in the biosynthesis of the iron-molybdenum cofactor (FeMo-co) found at the nitrogenase active site. The production of NifB in plants is challenging because this protein is often insoluble in eukaryotic cells, and its [Fe-S] clusters are extremely unstable and sensitive to O2. As a first step to address this challenge, we generated transgenic rice plants expressing NifB from the Archaea Methanocaldococcus infernus and Methanothermobacter thermautotrophicus. The recombinant proteins were targeted to the mitochondria to limit exposure to O2 and to have access to essential [4Fe-4S] clusters required for NifB-co biosynthesis. M. infernus and M. thermautotrophicus NifB accumulated as soluble proteins in planta, and the purified proteins were functional in the in vitro FeMo-co synthesis assay. We thus report NifB protein expression and purification from an engineered staple crop, representing a first step in the biosynthesis of a functional NifDK complex, as required for independent biological nitrogen fixation in cereals.
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Affiliation(s)
- Wenshu He
- Department
of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain
| | - Stefan Burén
- Centro
de Biotecnología y Genómica de Plantas, Universidad
Politécnica de Madrid (UPM), Instituto
Nacional de Investigación y Tecnología Agraria y Alimentaria
(INIA), Campus Montegancedo
UPM, Pozuelo de Alarcón, 28223 , Madrid, Spain,Departamento
de Biotecnología-Biología Vegetal, Escuela Técnica
Superior de Ingeniería Agronómica, Alimentaria y de
Biosistemas, Universidad Politécnica
de Madrid, 28040 Madrid, Spain
| | - Can Baysal
- Department
of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain
| | - Xi Jiang
- Centro
de Biotecnología y Genómica de Plantas, Universidad
Politécnica de Madrid (UPM), Instituto
Nacional de Investigación y Tecnología Agraria y Alimentaria
(INIA), Campus Montegancedo
UPM, Pozuelo de Alarcón, 28223 , Madrid, Spain,Departamento
de Biotecnología-Biología Vegetal, Escuela Técnica
Superior de Ingeniería Agronómica, Alimentaria y de
Biosistemas, Universidad Politécnica
de Madrid, 28040 Madrid, Spain
| | - Teresa Capell
- Department
of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain
| | - Paul Christou
- Department
of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Av. Alcalde Rovira Roure, 191, 25198 Lleida, Spain,ICREA,
Catalan Institute for Research and Advanced Studies, Passeig Lluís Companys 23, 08010 Barcelona, Spain,
| | - Luis M. Rubio
- Centro
de Biotecnología y Genómica de Plantas, Universidad
Politécnica de Madrid (UPM), Instituto
Nacional de Investigación y Tecnología Agraria y Alimentaria
(INIA), Campus Montegancedo
UPM, Pozuelo de Alarcón, 28223 , Madrid, Spain,Departamento
de Biotecnología-Biología Vegetal, Escuela Técnica
Superior de Ingeniería Agronómica, Alimentaria y de
Biosistemas, Universidad Politécnica
de Madrid, 28040 Madrid, Spain,
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20
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Pi HW, Lin JJ, Chen CA, Wang PH, Chiang YR, Huang CC, Young CC, Li WH. Origin and evolution of nitrogen fixation in prokaryotes. Mol Biol Evol 2022; 39:6673025. [PMID: 35993177 PMCID: PMC9447857 DOI: 10.1093/molbev/msac181] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The origin of nitrogen fixation is an important issue in evolutionary biology. While nitrogen is required by all living organisms, only a small fraction of bacteria and archaea can fix nitrogen. The prevailing view is that nitrogen fixation first evolved in archaea and was later transferred to bacteria. However, nitrogen-fixing (Nif) bacteria are far larger in number and far more diverse in ecological niches than Nif archaea. We, therefore, propose the bacteria-first hypothesis, which postulates that nitrogen fixation first evolved in bacteria and was later transferred to archaea. As >30,000 prokaryotic genomes have been sequenced, we conduct an in-depth comparison of the two hypotheses. We first identify the six genes involved in nitrogen fixation in all sequenced prokaryotic genomes and then reconstruct phylogenetic trees using the six Nif proteins individually or in combination. In each of these trees, the earliest lineages are bacterial Nif protein sequences and in the oldest clade (group) the archaeal sequences are all nested inside bacterial sequences, suggesting that the Nif proteins first evolved in bacteria. The bacteria-first hypothesis is further supported by the observation that the majority of Nif archaea carry the major bacterial Mo (molybdenum) transporter (ModABC) rather than the archaeal Mo transporter (WtpABC). Moreover, in our phylogeny of all available ModA and WtpA protein sequences, the earliest lineages are bacterial sequences while archaeal sequences are nested inside bacterial sequences. Furthermore, the bacteria-first hypothesis is supported by available isotopic data. In conclusion, our study strongly supports the bacteria-first hypothesis.
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Affiliation(s)
- Hong Wei Pi
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Jinn Jy Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Chi An Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529.,Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - Po Hsiang Wang
- Graduate Institute of Environmental Engineering, National Central University, Taoyuan, Taiwan 32001.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan 145-0061
| | - Yin Ru Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Chieh Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan 402
| | - Chiu Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan 402
| | - Wen Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529.,Department of Ecology and Evolution, University of Chicago, Chicago 60637, USA
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21
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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22
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Bennett AC, Murugapiran SK, Kees ED, Sauer HM, Hamilton TL. Temperature and Geographic Location Impact the Distribution and Diversity of Photoautotrophic Gene Variants in Alkaline Yellowstone Hot Springs. Microbiol Spectr 2022; 10:e0146521. [PMID: 35575591 PMCID: PMC9241655 DOI: 10.1128/spectrum.01465-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/21/2022] [Indexed: 11/20/2022] Open
Abstract
Alkaline hot springs in Yellowstone National Park (YNP) provide a framework to study the relationship between photoautotrophs and temperature. Previous work has focused on studying how cyanobacteria (oxygenic phototrophs) vary with temperature, sulfide, and pH, but many questions remain regarding the ecophysiology of anoxygenic photosynthesis due to the taxonomic and metabolic diversity of these taxa. To this end, we examined the distribution of genes involved in phototrophy, carbon fixation, and nitrogen fixation in eight alkaline (pH 7.3-9.4) hot spring sites near the upper temperature limit of photosynthesis (71ºC) in YNP using metagenome sequencing. Based on genes encoding key reaction center proteins, geographic isolation plays a larger role than temperature in selecting for distinct phototrophic Chloroflexi, while genes typically associated with autotrophy in anoxygenic phototrophs, did not have distinct distributions with temperature. Additionally, we recovered Calvin cycle gene variants associated with Chloroflexi, an alternative carbon fixation pathway in anoxygenic photoautotrophs. Lastly, we recovered several abundant nitrogen fixation gene sequences associated with Roseiflexus, providing further evidence that genes involved in nitrogen fixation in Chloroflexi are more common than previously assumed. Together, our results add to the body of work on the distribution and functional potential of phototrophic bacteria in Yellowstone National Park hot springs and support the hypothesis that a combination of abiotic and biotic factors impact the distribution of phototrophic bacteria in hot springs. Future studies of isolates and metagenome assembled genomes (MAGs) from these data and others will further our understanding of the ecology and evolution of hot spring anoxygenic phototrophs. IMPORTANCE Photosynthetic bacteria in hot springs are of great importance to both microbial evolution and ecology. While a large body of work has focused on oxygenic photosynthesis in cyanobacteria in Mushroom and Octopus Springs in Yellowstone National Park, many questions remain regarding the metabolic potential and ecology of hot spring anoxygenic phototrophs. Anoxygenic phototrophs are metabolically and taxonomically diverse, and further investigations into their physiology will lead to a deeper understanding of microbial evolution and ecology of these taxa. Here, we have quantified the distribution of key genes involved in carbon and nitrogen metabolism in both oxygenic and anoxygenic phototrophs. Our results suggest that temperature >68ºC selects for distinct groups of cyanobacteria and that carbon fixation pathways associated with these taxa are likely subject to the same selective pressure. Additionally, our data suggest that phototrophic Chloroflexi genes and carbon fixation genes are largely influenced by local conditions as evidenced by our gene variant analysis. Lastly, we recovered several genes associated with potentially novel phototrophic Chloroflexi. Together, our results add to the body of work on hot springs in Yellowstone National Park and set the stage for future work on metagenome assembled genomes.
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Affiliation(s)
- Annastacia C. Bennett
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Senthil K. Murugapiran
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Eric D. Kees
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Hailey M. Sauer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Trinity L. Hamilton
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
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Jiang X, Coroian D, Barahona E, Echavarri-Erasun C, Castellanos-Rueda R, Eseverri Á, Aznar-Moreno JA, Burén S, Rubio LM. Functional Nitrogenase Cofactor Maturase NifB in Mitochondria and Chloroplasts of Nicotiana benthamiana. mBio 2022; 13:e0026822. [PMID: 35695456 PMCID: PMC9239050 DOI: 10.1128/mbio.00268-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022] Open
Abstract
Engineering plants to synthesize nitrogenase and assimilate atmospheric N2 will reduce crop dependency on industrial N fertilizers. This technology can be achieved by expressing prokaryotic nitrogen fixation gene products for the assembly of a functional nitrogenase in plants. NifB is a critical nitrogenase component since it catalyzes the first committed step in the biosynthesis of all types of nitrogenase active-site cofactors. Here, we used a library of 30 distinct nifB sequences originating from different phyla and ecological niches to restore diazotrophic growth of an Azotobacter vinelandii nifB mutant. Twenty of these variants rescued the nifB mutant phenotype despite their phylogenetic distance to A. vinelandii. Because multiple protein interactions are required in the iron-molybdenum cofactor (FeMo-co) biosynthetic pathway, the maturation of nitrogenase in a heterologous host can be divided in independent modules containing interacting proteins that function together to produce a specific intermediate. Therefore, nifB functional modules composed of a nifB variant, together with the A. vinelandii NifS and NifU proteins (for biosynthesis of NifB [Fe4S4] clusters) and the FdxN ferredoxin (for NifB function), were expressed in Nicotiana benthamiana chloroplasts and mitochondria. Three archaeal NifB proteins accumulated at high levels in soluble fractions of chloroplasts (Methanosarcina acetivorans and Methanocaldococcus infernus) or mitochondria (M. infernus and Methanothermobacter thermautotrophicus). These NifB proteins were shown to accept [Fe4S4] clusters from NifU and were functional in FeMo-co synthesis in vitro. The accumulation of significant levels of soluble and functional NifB proteins in chloroplasts and mitochondria is critical to engineering biological nitrogen fixation in plants. IMPORTANCE Biological nitrogen fixation is the conversion of inert atmospheric dinitrogen gas into nitrogen-reactive ammonia, a reaction catalyzed by the nitrogenase enzyme of diazotrophic bacteria and archaea. Because plants cannot fix their own nitrogen, introducing functional nitrogenase in cereals and other crop plants would reduce our strong dependency on N fertilizers. NifB is required for the biosynthesis of the active site cofactors of all nitrogenases, which arguably makes it the most important protein in global nitrogen fixation. NifB functionality is therefore a requisite to engineer a plant nitrogenase. The expression of nifB genes from a wide range of prokaryotes into the model diazotroph Azotobacter vinelandii shows a surprising level of genetic complementation suggestive of plasticity in the nitrogenase biosynthetic pathway. In addition, we obtained NifB proteins from both mitochondria and chloroplasts of tobacco that are functional in vitro after reconstitution by providing [Fe4S4] clusters from NifU, paving the way to nitrogenase cofactor biosynthesis in plants.
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Affiliation(s)
- Xi Jiang
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Diana Coroian
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
| | - Emma Barahona
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
| | - Carlos Echavarri-Erasun
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Rocío Castellanos-Rueda
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
| | - Álvaro Eseverri
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
| | - Jose A. Aznar-Moreno
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
| | - Stefan Burén
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Luis M. Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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24
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Bender KS, Madigan MT, Williamson KL, Mayer MH, Parenteau MN, Jahnke LL, Welander PV, Sanguedolce SA, Brown AC, Sattley WM. Genomic Features of the Bundle-Forming Heliobacterium Heliophilum fasciatum. Microorganisms 2022; 10:microorganisms10050869. [PMID: 35630314 PMCID: PMC9147875 DOI: 10.3390/microorganisms10050869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 02/01/2023] Open
Abstract
Eight species of heliobacteria have had their genomes sequenced. However, only two of these genomes have been analyzed in detail, those from the thermophilic Heliomicrobium (Hmi.) modesticaldum and the alkaliphilic Heliorestis (Hrs.) convoluta. Here we present analyses of the draft genome sequence of a species of heliobacterium that grows optimally at a moderate temperature and neutral pH. The organism, Heliophilum (Hph.) fasciatum, is phylogenetically unique among cultured heliobacteria and was isolated from rice soil, a common habitat for heliobacteria. The Hph. fasciatum genome contains 3.14 Mbp—similar to that of other reported heliobacteria—but has a G+C base ratio that lies between that of Hmi. modesticaldum and Hrs. convoluta. Many of the genomic features of Hmi. modesticaldum and Hrs. convoluta, such as the absence of genes encoding autotrophic pathways, the presence of a superoperonal cluster of photosynthesis-related genes, and genes encoding endospore-specific proteins, are also characteristic of the Hph. fasciatum genome. However, despite the fact that Hph. fasciatum is diazotrophic, classical nif genes encoding the alpha and beta subunits of dinitrogenase (nifDK) present in other heliobacteria could not be identified. Instead, genes encoding several highly divergent NifDK homologs were present, at least one of which likely encodes a functional dinitrogenase and another a methylthio-alkane reductase (MarDK) for sulfur assimilation. A classical NifH (dinitrogenase reductase) homolog was also absent in Hph. fasciatum, but a related protein was identified that likely carries out this function as well as electron delivery to MarDK. The N2-fixing system of Hph. fasciatum is therefore distinct from that of other heliobacteria and may have unusual properties.
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Affiliation(s)
- Kelly S. Bender
- Microbiology Program, School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (K.S.B.); (M.T.M.); (K.L.W.)
| | - Michael T. Madigan
- Microbiology Program, School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (K.S.B.); (M.T.M.); (K.L.W.)
| | - Kyleigh L. Williamson
- Microbiology Program, School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (K.S.B.); (M.T.M.); (K.L.W.)
| | - Marisa H. Mayer
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA 94035, USA; (M.H.M.); (M.N.P.); (L.L.J.)
| | - Mary N. Parenteau
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA 94035, USA; (M.H.M.); (M.N.P.); (L.L.J.)
| | - Linda L. Jahnke
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA 94035, USA; (M.H.M.); (M.N.P.); (L.L.J.)
| | - Paula V. Welander
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA;
| | - Sophia A. Sanguedolce
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN 46953, USA; (S.A.S.); (A.C.B.)
| | - Abigail C. Brown
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN 46953, USA; (S.A.S.); (A.C.B.)
| | - W. Matthew Sattley
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN 46953, USA; (S.A.S.); (A.C.B.)
- Correspondence: ; Tel.: +1-765-677-2128
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25
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Genomic and Experimental Analysis of the Biostimulant and Antagonistic Properties of Phytopathogens of Bacillus safensis and Bacillus siamensis. Microorganisms 2022; 10:microorganisms10040670. [PMID: 35456723 PMCID: PMC9024481 DOI: 10.3390/microorganisms10040670] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/21/2022] Open
Abstract
The B. safensis RGM 2450 and B. siamensis RGM 2529 strains were isolated from the rhizosphere of plants presenting resilience to abiotic and biotic stress conditions. To understand the implications of bacteria in resilience, a genomic and experimental analysis was carried out on their biostimulant and phytopathogenic antagonist properties. Genome analyses of both strains indicated that they have the potential to synthesize bioactive compounds such as the battery of non-ribosomal peptides, polyketides, extracellular enzymes and phytohormones. These results were consistent with the antagonistic activities of both strains against the phytopathogens Botrytis cinerea, Colletotrichum acutatum, Fusarium oxysporum and Phytophtora cinnamomi. They also showed the capacity to solubilize phosphorus, fix nitrogen and produce indole acetic acid. This was observed in tomato seedlings grown from seeds inoculated with the mixture of strains which presented significantly greater length as well as wet and dry weight in comparison with the treatments individually inoculated with each strain and the control. Accordingly, the combination of B. safensis RGM 2450 and B. siamensis RGM 2529 showed synergistic biostimulant activity. These findings contribute new knowledge of the genomic and metabolomic properties taking part in the symbiotic interactions between these strains and the plants and uphold the combined use of both strains as a biostimulant.
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26
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Garcia AK, Kolaczkowski B, Kaçar B. Reconstruction of nitrogenase predecessors suggests origin from maturase-like proteins. Genome Biol Evol 2022; 14:6531971. [PMID: 35179578 PMCID: PMC8890362 DOI: 10.1093/gbe/evac031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2022] [Indexed: 11/17/2022] Open
Abstract
The evolution of biological nitrogen fixation, uniquely catalyzed by nitrogenase enzymes, has been one of the most consequential biogeochemical innovations over life’s history. Though understanding the early evolution of nitrogen fixation has been a longstanding goal from molecular, biogeochemical, and planetary perspectives, its origins remain enigmatic. In this study, we reconstructed the evolutionary histories of nitrogenases, as well as homologous maturase proteins that participate in the assembly of the nitrogenase active-site cofactor but are not able to fix nitrogen. We combined phylogenetic and ancestral sequence inference with an analysis of predicted functionally divergent sites between nitrogenases and maturases to infer the nitrogen-fixing capabilities of their shared ancestors. Our results provide phylogenetic constraints to the emergence of nitrogen fixation and are consistent with a model wherein nitrogenases emerged from maturase-like predecessors. Though the precise functional role of such a predecessor protein remains speculative, our results highlight evolutionary contingency as a significant factor shaping the evolution of a biogeochemically essential enzyme.
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Affiliation(s)
- Amanda K Garcia
- Department of Bacteriology, University of Wisconsin - Madison, USA
| | - Bryan Kolaczkowski
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin - Madison, USA
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27
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Pathways of Iron and Sulfur Acquisition, Cofactor Assembly, Destination, and Storage in Diverse Archaeal Methanogens and Alkanotrophs. J Bacteriol 2021; 203:e0011721. [PMID: 34124941 PMCID: PMC8351635 DOI: 10.1128/jb.00117-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Archaeal methanogens, methanotrophs, and alkanotrophs have a high demand for iron (Fe) and sulfur (S); however, little is known of how they acquire, traffic, deploy, and store these elements. Here, we examined the distribution of homologs of proteins mediating key steps in Fe/S metabolism in model microorganisms, including iron(II) sensing/uptake (FeoAB), sulfide extraction from cysteine (SufS), and the biosynthesis of iron-sulfur [Fe-S] clusters (SufBCDE), siroheme (Pch2 dehydrogenase), protoheme (AhbABCD), cytochrome c (Cyt c) (CcmCF), and iron storage/detoxification (Bfr, FtrA, and IssA), among 326 publicly available, complete or metagenome-assembled genomes of archaeal methanogens/methanotrophs/alkanotrophs. The results indicate several prevalent but nonuniversal features, including FeoB, SufBC, and the biosynthetic apparatus for the basic tetrapyrrole scaffold, as well as its siroheme (and F430) derivatives. However, several early-diverging genomes lacked SufS and pathways to synthesize and deploy heme. Genomes encoding complete versus incomplete heme biosynthetic pathways exhibited equivalent prevalences of [Fe-S] cluster binding proteins, suggesting an expansion of catalytic capabilities rather than substitution of heme for [Fe-S] in the former group. Several strains with heme binding proteins lacked heme biosynthesis capabilities, while other strains with siroheme biosynthesis capability lacked homologs of known siroheme binding proteins, indicating heme auxotrophy and unknown siroheme biochemistry, respectively. While ferritin proteins involved in ferric oxide storage were widespread, those involved in storing Fe as thioferrate were unevenly distributed. Collectively, the results suggest that differences in the mechanisms of Fe and S acquisition, deployment, and storage have accompanied the diversification of methanogens/methanotrophs/alkanotrophs, possibly in response to differential availability of these elements as these organisms evolved. IMPORTANCE Archaeal methanogens, methanotrophs, and alkanotrophs, argued to be among the most ancient forms of life, have a high demand for iron (Fe) and sulfur (S) for cofactor biosynthesis, among other uses. Here, using comparative bioinformatic approaches applied to 326 genomes, we show that major differences in Fe/S acquisition, trafficking, deployment, and storage exist in this group. Variation in these characters was generally congruent with the phylogenetic placement of these genomes, indicating that variation in Fe/S usage and deployment has contributed to the diversification and ecology of these organisms. However, incongruency was observed among the distribution of cofactor biosynthesis pathways and known protein destinations for those cofactors, suggesting auxotrophy or yet-to-be-discovered pathways for cofactor biosynthesis.
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28
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Philippi M, Kitzinger K, Berg JS, Tschitschko B, Kidane AT, Littmann S, Marchant HK, Storelli N, Winkel LHE, Schubert CJ, Mohr W, Kuypers MMM. Purple sulfur bacteria fix N 2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue. Nat Commun 2021; 12:4774. [PMID: 34362886 PMCID: PMC8346585 DOI: 10.1038/s41467-021-25000-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/15/2021] [Indexed: 01/04/2023] Open
Abstract
Biological N2 fixation was key to the expansion of life on early Earth. The N2-fixing microorganisms and the nitrogenase type used in the Proterozoic are unknown, although it has been proposed that the canonical molybdenum-nitrogenase was not used due to low molybdenum availability. We investigate N2 fixation in Lake Cadagno, an analogue system to the sulfidic Proterozoic continental margins, using a combination of biogeochemical, molecular and single cell techniques. In Lake Cadagno, purple sulfur bacteria (PSB) are responsible for high N2 fixation rates, to our knowledge providing the first direct evidence for PSB in situ N2 fixation. Surprisingly, no alternative nitrogenases are detectable, and N2 fixation is exclusively catalyzed by molybdenum-nitrogenase. Our results show that molybdenum-nitrogenase is functional at low molybdenum conditions in situ and that in contrast to previous beliefs, PSB may have driven N2 fixation in the Proterozoic ocean.
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Affiliation(s)
- Miriam Philippi
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katharina Kitzinger
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Jasmine S Berg
- Department of Environmental Systems Science, ETH-Zurich, Zurich, Switzerland
| | - Bernhard Tschitschko
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Abiel T Kidane
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sten Littmann
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Hannah K Marchant
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Nicola Storelli
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
| | - Lenny H E Winkel
- Department of Environmental Systems Science, ETH-Zurich, Zurich, Switzerland.,Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Carsten J Schubert
- Department of Environmental Systems Science, ETH-Zurich, Zurich, Switzerland.,Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Wiebke Mohr
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marcel M M Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
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29
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Li Q, Zhang H, Zhang L, Chen S. Functional analysis of multiple nifB genes of Paenibacillus strains in synthesis of Mo-, Fe- and V-nitrogenases. Microb Cell Fact 2021; 20:139. [PMID: 34281551 PMCID: PMC8287671 DOI: 10.1186/s12934-021-01629-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/10/2021] [Indexed: 12/16/2022] Open
Abstract
Background Biological nitrogen fixation is catalyzed by Mo-, V- and Fe-nitrogenases that are encoded by nif, vnf and anf genes, respectively. NifB is the key protein in synthesis of the cofactors of all nitrogenases. Most diazotrophic Paenibacillus strains have only one nifB gene located in a compact nif gene cluster (nifBHDKENX(orf1)hesAnifV). But some Paenibacillus strains have multiple nifB genes and their functions are not known. Results A total of 138 nifB genes are found in the 116 diazotrophic Paenibacillus strains. Phylogeny analysis shows that these nifB genes fall into 4 classes: nifBI class including the genes (named as nifB1 genes) that are the first gene within the compact nif gene cluster, nifBII class including the genes (named as nifB2 genes) that are adjacent to anf or vnf genes, nifBIII class whose members are designated as nifB3 genes and nifBIV class whose members are named as nifB4 genes are scattered on genomes. Functional analysis by complementation of the ∆nifB mutant of P. polymyxa which has only one nifB gene has shown that both nifB1 and nifB2 are active in synthesis of Mo-nitrogenase, while nifB3 and nifB4 genes are not. Deletion analysis also has revealed that nifB1 of Paenibacillus sabinae T27 is involved in synthesis of Mo-nitrogenase, while nifB3 and nifB4 genes are not. Complementation of the P. polymyxa ∆nifBHDK mutant with the four reconstituted operons: nifB1anfHDGK, nifB2anfHDGK, nifB1vnfHDGK and nifB2vnfHDGK, has shown both that nifB1 and nifB2 were able to support synthesis of Fe- or V-nitrogenases. Transcriptional results obtained in the original Paenibacillus strains are consistent with the complementation results. Conclusions The multiple nifB genes of the diazotrophic Paenibacillus strains are divided into 4 classes. The nifB1 located in a compact nif gene cluster (nifBHDKENX(orf1)hesAnifV) and the nifB2 genes being adjacent to nif or anf or vnf genes are active in synthesis of Mo-, Fe and V-nitrogenases, but nifB3 and nifB4 are not. The reconstituted anf system comprising 8 genes (nifBanfHDGK and nifXhesAnifV) and vnf system comprising 10 genes (nifBvnfHDGKEN and nifXhesAnifV) support synthesis of Fe-nitrogenase and V-nitrogenase in Paenibacillus background, respectively. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01629-9.
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Affiliation(s)
- Qin Li
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China.,Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture and Rural Affairs, and College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Haowei Zhang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Liqun Zhang
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture and Rural Affairs, and College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Sanfeng Chen
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China.
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30
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Berkemer SJ, McGlynn SE. A New Analysis of Archaea-Bacteria Domain Separation: Variable Phylogenetic Distance and the Tempo of Early Evolution. Mol Biol Evol 2021; 37:2332-2340. [PMID: 32316034 PMCID: PMC7403611 DOI: 10.1093/molbev/msaa089] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Comparative genomics and molecular phylogenetics are foundational for understanding biological evolution. Although many studies have been made with the aim of understanding the genomic contents of early life, uncertainty remains. A study by Weiss et al. (Weiss MC, Sousa FL, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S, Martin WF. 2016. The physiology and habitat of the last universal common ancestor. Nat Microbiol. 1(9):16116.) identified a number of protein families in the last universal common ancestor of archaea and bacteria (LUCA) which were not found in previous works. Here, we report new research that suggests the clustering approaches used in this previous study undersampled protein families, resulting in incomplete phylogenetic trees which do not reflect protein family evolution. Phylogenetic analysis of protein families which include more sequence homologs rejects a simple LUCA hypothesis based on phylogenetic separation of the bacterial and archaeal domains for a majority of the previously identified LUCA proteins (∼82%). To supplement limitations of phylogenetic inference derived from incompletely populated orthologous groups and to test the hypothesis of a period of rapid evolution preceding the separation of the domains, we compared phylogenetic distances both within and between domains, for thousands of orthologous groups. We find a substantial diversity of interdomain versus intradomain branch lengths, even among protein families which exhibit a single domain separating branch and are thought to be associated with the LUCA. Additionally, phylogenetic trees with long interdomain branches relative to intradomain branches are enriched in information categories of protein families in comparison to those associated with metabolic functions. These results provide a new view of protein family evolution and temper claims about the phenotype and habitat of the LUCA.
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Affiliation(s)
- Sarah J Berkemer
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig, Germany.,Competence Center for Scalable Data Services and Solutions, Dresden/Leipzig, Germany
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo, Japan.,Blue Marble Space Institute of Science, Seattle, WA.,RIKEN Center for Sustainable Resource Science (CSRS), Saitama, Japan
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31
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Kapili BJ, Dekas AE. PPIT: an R package for inferring microbial taxonomy from nifH sequences. Bioinformatics 2021; 37:2289-2298. [PMID: 33580675 DOI: 10.1093/bioinformatics/btab100] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/22/2020] [Accepted: 02/11/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Linking microbial community members to their ecological functions is a central goal of environmental microbiology. When assigned taxonomy, amplicon sequences of metabolic marker genes can suggest such links, thereby offering an overview of the phylogenetic structure underpinning particular ecosystem functions. However, inferring microbial taxonomy from metabolic marker gene sequences remains a challenge, particularly for the frequently sequenced nitrogen fixation marker gene, nitrogenase reductase (nifH). Horizontal gene transfer in recent nifH evolutionary history can confound taxonomic inferences drawn from the pairwise identity methods used in existing software. Other methods for inferring taxonomy are not standardized and require manual inspection that is difficult to scale. RESULTS We present Phylogenetic Placement for Inferring Taxonomy (PPIT), an R package that infers microbial taxonomy from nifH amplicons using both phylogenetic and sequence identity approaches. After users place query sequences on a reference nifH gene tree provided by PPIT (n = 6317 full-length nifH sequences), PPIT searches the phylogenetic neighborhood of each query sequence and attempts to infer microbial taxonomy. An inference is drawn only if references in the phylogenetic neighborhood are: (1) taxonomically consistent and (2) share sufficient pairwise identity with the query, thereby avoiding erroneous inferences due to known horizontal gene transfer events. We find that PPIT returns a higher proportion of correct taxonomic inferences than BLAST-based approaches at the cost of fewer total inferences. We demonstrate PPIT on deep-sea sediment and find that Deltaproteobacteria are the most abundant potential diazotrophs. Using this dataset we show that emending PPIT inferences based on visual inspection of query sequence placement can achieve taxonomic inferences for nearly all sequences in a query set. We additionally discuss how users can apply PPIT to the analysis of other marker genes. AVAILABILITY PPIT is freely available to non-commercial users at https://github.com/bkapili/ppit. Installation includes a vignette that demonstrates package use and reproduces the nifH amplicon analysis discussed here. The raw nifH amplicon sequence data have been deposited in the GenBank, EMBL, and DDBJ databases under BioProject number PRJEB37167. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Bennett J Kapili
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
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32
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Parison K, Gies-Elterlein J, Trncik C, Einsle O. Expression, Isolation, and Characterization of Vanadium Nitrogenase from Azotobacter vinelandii. Methods Mol Biol 2021; 2353:97-121. [PMID: 34292546 DOI: 10.1007/978-1-0716-1605-5_6] [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] [Indexed: 12/12/2022]
Abstract
Nitrogenases are the sole enzymes known to mediate biological nitrogen fixation, an essential process for sustaining life on earth. Among the three known variants, molybdenum nitrogenase is the best-studied to date. Recent work on the alternative vanadium nitrogenase provided important insights into the mechanism of nitrogen fixation since this enzyme differs from its molybdenum counterpart in some important aspects. Here, we present a protocol to obtain unmodified vanadium nitrogenase in high yield and purity from the paradigmatic diazotroph Azotobacter vinelandii, including procedures for cell cultivation, purification, and protein characterization.
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Affiliation(s)
- Katharina Parison
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | | | - Christian Trncik
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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33
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Parsons C, Stüeken EE, Rosen CJ, Mateos K, Anderson RE. Radiation of nitrogen-metabolizing enzymes across the tree of life tracks environmental transitions in Earth history. GEOBIOLOGY 2021; 19:18-34. [PMID: 33108025 PMCID: PMC7894544 DOI: 10.1111/gbi.12419] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 09/28/2020] [Accepted: 10/05/2020] [Indexed: 05/03/2023]
Abstract
Nitrogen is an essential element to life and exerts a strong control on global biological productivity. The rise and spread of nitrogen-utilizing microbial metabolisms profoundly shaped the biosphere on the early Earth. Here, we reconciled gene and species trees to identify birth and horizontal gene transfer events for key nitrogen-cycling genes, dated with a time-calibrated tree of life, in order to examine the timing of the proliferation of these metabolisms across the tree of life. Our results provide new insights into the evolution of the early nitrogen cycle that expand on geochemical reconstructions. We observed widespread horizontal gene transfer of molybdenum-based nitrogenase back to the Archean, minor horizontal transfer of genes for nitrate reduction in the Archean, and an increase in the proliferation of genes metabolizing nitrite around the time of the Mesoproterozoic (~1.5 Ga). The latter coincides with recent geochemical evidence for a mid-Proterozoic rise in oxygen levels. Geochemical evidence of biological nitrate utilization in the Archean and early Proterozoic may reflect at least some contribution of dissimilatory nitrate reduction to ammonium (DNRA) rather than pure denitrification to N2 . Our results thus help unravel the relative dominance of two metabolic pathways that are not distinguishable with current geochemical tools. Overall, our findings thus provide novel constraints for understanding the evolution of the nitrogen cycle over time and provide insights into the bioavailability of various nitrogen sources in the early Earth with possible implications for the emergence of eukaryotic life.
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Affiliation(s)
- Chris Parsons
- Carleton CollegeNorthfieldMNUSA
- Massachusetts Institute of TechnologyCambridgeMAUSA
| | | | | | | | - Rika E. Anderson
- Carleton CollegeNorthfieldMNUSA
- NASA NExSS Virtual Planetary LaboratoryUniversity of WashingtonSeattleWAUSA
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34
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Chen Y, Nishihara A, Haruta S. Nitrogen-fixing Ability and Nitrogen Fixation-related Genes of Thermophilic Fermentative Bacteria in the Genus Caldicellulosiruptor. Microbes Environ 2021; 36. [PMID: 34108360 PMCID: PMC8209448 DOI: 10.1264/jsme2.me21018] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Fermentative nitrogen-fixing bacteria have not yet been examined in detail in thermal environments. In the present study, we isolated the thermophilic fermentative bacterium, strain YA01 from a hot spring. This strain grew at temperatures up to 78°C. A phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain YA01 belonged to the genus Caldicellulosiruptor, which are fermentative bacteria in the phylum Firmicutes, with 97.7–98.0% sequence identity to its closest relatives. Strain YA01 clearly exhibited N2-dependent growth at 70°C. We also confirmed N2-dependent growth in the relatives of strain YA01, Caldicellulosiruptor hydrothermalis 108 and Caldicellulosiruptor kronotskyensis 2002. The nitrogenase activities of these three strains were examined using the acetylene reduction assay. Similar activities were detected for all tested strains, and were slightly suppressed by the addition of ammonium. A genome analysis revealed that strain YA01, as well as other Caldicellulosiruptor, possessed a gene set for nitrogen fixation, but lacked the nifN gene, which encodes a nitrogenase iron-molybdenum cofactor biosynthesis protein that is commonly detected in nitrogen-fixing bacteria. The amino acid sequences of nitrogenase encoded by nifH, nifD, and nifK shared 92–98% similarity in Caldicellulosiruptor. A phylogenetic tree of concatenated NifHDK sequences showed that NifHDK of Caldicellulosiruptor was in the deepest clade. To the best of our knowledge, this is the first study to demonstrate the nitrogen-fixing ability of fermentative bacteria at 70°C. Caldicellulosiruptor may have retained an ancient nitrogen-fixing enzyme system.
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Affiliation(s)
- Yuxin Chen
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
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35
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Kacar B, Garcia AK, Anbar AD. Evolutionary History of Bioessential Elements Can Guide the Search for Life in the Universe. Chembiochem 2020; 22:114-119. [PMID: 33136319 DOI: 10.1002/cbic.202000500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/29/2020] [Indexed: 11/10/2022]
Abstract
Our understanding of life in the universe comes from one sample, life on Earth. Current and next-generation space missions will target exoplanets as well as planets and moons in our own solar system with the primary goal of detecting, interpreting and characterizing indications of possible biological activity. Thus, understanding life's fundamental characteristics is increasingly critical for detecting and interpreting potential biological signatures elsewhere in the universe. Astrobiologists have outlined the essential roles of carbon and water for life, but we have yet to decipher the rules governing the evolution of how living organisms use bioessential elements. Does the suite of life's essential chemical elements on Earth constitute only one possible evolutionary outcome? Are some elements so essential for biological functions that evolution will select for them despite low availability? How would this play out on other worlds that have different relative element abundances? When we look for life in the universe, or the conditions that could give rise to life, we must learn how to recognize it in extremely different chemical and environmental conditions from those on Earth. We argue that by exposing self-organizing biotic chemistries to different combinations of abiotic materials, and by mapping the evolutionary history of metalloenzyme biochemistry onto geological availabilities of metals, alternative element choices that are very different from life's present-day molecular structure might result. A greater understanding of the paleomolecular evolutionary history of life on Earth will create a predictive capacity for detecting and assessing life's existence on worlds where alternate evolutionary paths might have been taken.
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Affiliation(s)
- Betul Kacar
- Department of Molecular and Cellular Biology, University of Arizona, 1007 E Lowell St, Tucson, AZ, 85721, USA.,Department of Astronomy and Steward Observatory, University of Arizona, 933 N Cherry Ave, Tucson, AZ, 85719, USA.,Lunar and Planetary Laboratory, University of Arizona, 1629 E University Blvd, Tucson, AZ, 85721, USA.,Earth-Life Science Institute, Tokyo Institute of Technology, 1 Chome-31 Ishikawacho, Ota City, Tokyo, Japan
| | - Amanda K Garcia
- Department of Molecular and Cellular Biology, University of Arizona, 1007 E Lowell St, Tucson, AZ, 85721, USA
| | - Ariel D Anbar
- School of Earth and Space Exploration, Arizona State University, E Tyler Mall, Tempe, AZ, 85281, USA
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36
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Jasniewski AJ, Lee CC, Ribbe MW, Hu Y. Reactivity, Mechanism, and Assembly of the Alternative Nitrogenases. Chem Rev 2020; 120:5107-5157. [PMID: 32129988 PMCID: PMC7491575 DOI: 10.1021/acs.chemrev.9b00704] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological nitrogen fixation is catalyzed by the enzyme nitrogenase, which facilitates the cleavage of the relatively inert triple bond of N2. Nitrogenase is most commonly associated with the molybdenum-iron cofactor called FeMoco or the M-cluster, and it has been the subject of extensive structural and spectroscopic characterization over the past 60 years. In the late 1980s and early 1990s, two "alternative nitrogenase" systems were discovered, isolated, and found to incorporate V or Fe in place of Mo. These systems are regulated by separate gene clusters; however, there is a high degree of structural and functional similarity between each nitrogenase. Limited studies with the V- and Fe-nitrogenases initially demonstrated that these enzymes were analogously active as the Mo-nitrogenase, but more recent investigations have found capabilities that are unique to the alternative systems. In this review, we will discuss the reactivity, biosynthetic, and mechanistic proposals for the alternative nitrogenases as well as their electronic and structural properties in comparison to the well-characterized Mo-dependent system. Studies over the past 10 years have been particularly fruitful, though key aspects about V- and Fe-nitrogenases remain unexplored.
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Affiliation(s)
- Andrew J Jasniewski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
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37
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Van Stappen C, Decamps L, Cutsail GE, Bjornsson R, Henthorn JT, Birrell JA, DeBeer S. The Spectroscopy of Nitrogenases. Chem Rev 2020; 120:5005-5081. [PMID: 32237739 PMCID: PMC7318057 DOI: 10.1021/acs.chemrev.9b00650] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Indexed: 01/08/2023]
Abstract
Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.
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Affiliation(s)
- Casey Van Stappen
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Laure Decamps
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - George E. Cutsail
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Justin T. Henthorn
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - James A. Birrell
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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38
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Li Q, Chen S. Transfer of Nitrogen Fixation (nif) Genes to Non-diazotrophic Hosts. Chembiochem 2020; 21:1717-1722. [PMID: 32009294 DOI: 10.1002/cbic.201900784] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Indexed: 12/20/2022]
Abstract
Nitrogen is one of the most important nutrients for plant growth. To enhance crop productivity, chemical nitrogen fertilizer is commonly applied in agriculture. Biological nitrogen fixation, the conversion of atmospheric N2 to NH3 , is an important source of nitrogen input in agriculture and represents a promising substitute for chemical nitrogen fertilizers. However, nitrogen fixation is only sporadically distributed within bacteria and archaea (diazotrophs). Thus, many biologists hope to reconstitute a nitrogenase biosynthetic pathway in a eukaryotic host, with the final aim of developing N2 -fixing cereal crops. With the advent of synthetic biology and a deep understanding of the fundamental genetic determinants necessary to sustain nitrogen fixation in bacteria, much progress has been made toward this goal. Transfer of native and refactored nif (nitrogen fixation) genes to non-diazotrophs has been attempted in model bacteria, yeast, and plants. Specifically, nif genes from Klebsiella oxytoca, Azotobacter vinelandii, and Paenibacillus polymyxa have been successfully transferred and expressed in Escherichia coli, Saccharomyces cerevisiae, and even in the tobacco plant. These advances have laid the groundwork to enable cereal crops to "fix" nitrogen themselves to sustain their growth and yield.
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Affiliation(s)
- Qin Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology of Agriculture Ministry and, College of Biological Sciences, China Agricultural University, Haidian District Yuanmingyuan West Road No.2, Beijing, P. R. China
| | - Sanfeng Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology of Agriculture Ministry and, College of Biological Sciences, China Agricultural University, Haidian District Yuanmingyuan West Road No.2, Beijing, P. R. China
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39
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020. [PMID: 31900730 DOI: 10.1007/s00709-019-01442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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40
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Garcia AK, McShea H, Kolaczkowski B, Kaçar B. Reconstructing the evolutionary history of nitrogenases: Evidence for ancestral molybdenum-cofactor utilization. GEOBIOLOGY 2020; 18:394-411. [PMID: 32065506 PMCID: PMC7216921 DOI: 10.1111/gbi.12381] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/23/2019] [Accepted: 01/22/2020] [Indexed: 05/08/2023]
Abstract
The nitrogenase metalloenzyme family, essential for supplying fixed nitrogen to the biosphere, is one of life's key biogeochemical innovations. The three forms of nitrogenase differ in their metal dependence, each binding either a FeMo-, FeV-, or FeFe-cofactor where the reduction of dinitrogen takes place. The history of nitrogenase metal dependence has been of particular interest due to the possible implication that ancient marine metal availabilities have significantly constrained nitrogenase evolution over geologic time. Here, we reconstructed the evolutionary history of nitrogenases, and combined phylogenetic reconstruction, ancestral sequence inference, and structural homology modeling to evaluate the potential metal dependence of ancient nitrogenases. We find that active-site sequence features can reliably distinguish extant Mo-nitrogenases from V- and Fe-nitrogenases and that inferred ancestral sequences at the deepest nodes of the phylogeny suggest these ancient proteins most resemble modern Mo-nitrogenases. Taxa representing early-branching nitrogenase lineages lack one or more biosynthetic nifE and nifN genes that both contribute to the assembly of the FeMo-cofactor in studied organisms, suggesting that early Mo-nitrogenases may have utilized an alternate and/or simplified pathway for cofactor biosynthesis. Our results underscore the profound impacts that protein-level innovations likely had on shaping global biogeochemical cycles throughout the Precambrian, in contrast to organism-level innovations that characterize the Phanerozoic Eon.
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Affiliation(s)
- Amanda K. Garcia
- Department of Molecular and Cellular BiologyUniversity of ArizonaTucsonArizona
| | - Hanon McShea
- Department of Earth System ScienceStanford UniversityStanfordCalifornia
| | - Bryan Kolaczkowski
- Department of Microbiology and Cell ScienceUniversity of FloridaGainesvilleFlorida
| | - Betül Kaçar
- Department of Molecular and Cellular BiologyUniversity of ArizonaTucsonArizona
- Steward Observatory and the Lunar and Planetary LaboratoryUniversity of ArizonaTucsonArizona
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41
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020; 257:621-753. [PMID: 31900730 PMCID: PMC7203096 DOI: 10.1007/s00709-019-01442-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/19/2019] [Indexed: 05/02/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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42
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Van Stappen C, Davydov R, Yang ZY, Fan R, Guo Y, Bill E, Seefeldt LC, Hoffman BM, DeBeer S. Spectroscopic Description of the E 1 State of Mo Nitrogenase Based on Mo and Fe X-ray Absorption and Mössbauer Studies. Inorg Chem 2019; 58:12365-12376. [PMID: 31441651 PMCID: PMC6751781 DOI: 10.1021/acs.inorgchem.9b01951] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Indexed: 11/29/2022]
Abstract
Mo nitrogenase (N2ase) utilizes a two-component protein system, the catalytic MoFe and its electron-transfer partner FeP, to reduce atmospheric dinitrogen (N2) to ammonia (NH3). The FeMo cofactor contained in the MoFe protein serves as the catalytic center for this reaction and has long inspired model chemistry oriented toward activating N2. This field of chemistry has relied heavily on the detailed characterization of how Mo N2ase accomplishes this feat. Understanding the reaction mechanism of Mo N2ase itself has presented one of the most challenging problems in bioinorganic chemistry because of the ephemeral nature of its catalytic intermediates, which are difficult, if not impossible, to singly isolate. This is further exacerbated by the near necessity of FeP to reduce native MoFe, rendering most traditional means of selective reduction inept. We have now investigated the first fundamental intermediate of the MoFe catalytic cycle, E1, as prepared both by low-flux turnover and radiolytic cryoreduction, using a combination of Mo Kα high-energy-resolution fluorescence detection and Fe K-edge partial-fluorescence-yield X-ray absorption spectroscopy techniques. The results demonstrate that the formation of this state is the result of an Fe-centered reduction and that Mo remains redox-innocent. Furthermore, using Fe X-ray absorption and 57Fe Mössbauer spectroscopies, we correlate a previously reported unique species formed under cryoreducing conditions to the natively formed E1 state through annealing, demonstrating the viability of cryoreduction in studying the catalytic intermediates of MoFe.
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Affiliation(s)
- Casey Van Stappen
- Max Planck Institute
for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Roman Davydov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Ruixi Fan
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Eckhard Bill
- Max Planck Institute
for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Lance C. Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Serena DeBeer
- Max Planck Institute
for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
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43
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Mus F, Colman DR, Peters JW, Boyd ES. Geobiological feedbacks, oxygen, and the evolution of nitrogenase. Free Radic Biol Med 2019; 140:250-259. [PMID: 30735835 DOI: 10.1016/j.freeradbiomed.2019.01.050] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/31/2019] [Indexed: 12/21/2022]
Abstract
Biological nitrogen fixation via the activity of nitrogenase is one of the most important biological innovations, allowing for an increase in global productivity that eventually permitted the emergence of higher forms of life. The complex metalloenzyme termed nitrogenase contains complex iron-sulfur cofactors. Three versions of nitrogenase exist that differ mainly by the presence or absence of a heterometal at the active site metal cluster (either Mo or V). Mo-dependent nitrogenase is the most common while V-dependent or heterometal independent (Fe-only) versions are often termed alternative nitrogenases since they have apparent lower activities for N2 reduction and are expressed in the absence of Mo. Phylogenetic data indicates that biological nitrogen fixation emerged in an anaerobic, thermophilic ancestor of hydrogenotrophic methanogens and later diversified via lateral gene transfer into anaerobic bacteria, and eventually aerobic bacteria including Cyanobacteria. Isotopic evidence suggests that nitrogenase activity existed at 3.2 Ga, prior to the advent of oxygenic photosynthesis and rise of oxygen in the atmosphere, implying the presence of favorable environmental conditions for oxygen-sensitive nitrogenase to evolve. Following the proliferation of oxygenic phototrophs, diazotrophic organisms had to develop strategies to protect nitrogenase from oxygen inactivation and generate the right balance of low potential reducing equivalents and cellular energy for growth and nitrogen fixation activity. Here we review the fundamental advances in our understanding of biological nitrogen fixation in the context of the emergence, evolution, and taxonomic distribution of nitrogenase, with an emphasis placed on key events associated with its emergence and diversification from anoxic to oxic environments.
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Affiliation(s)
- Florence Mus
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA.
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA.
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44
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Garcia AK, Kaçar B. How to resurrect ancestral proteins as proxies for ancient biogeochemistry. Free Radic Biol Med 2019; 140:260-269. [PMID: 30951835 DOI: 10.1016/j.freeradbiomed.2019.03.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/11/2019] [Accepted: 03/26/2019] [Indexed: 10/27/2022]
Abstract
Throughout the history of life, enzymes have served as the primary molecular mediators of biogeochemical cycles by catalyzing the metabolic pathways that interact with geochemical substrates. The byproducts of enzymatic activities have been preserved as chemical and isotopic signatures in the geologic record. However, interpretations of these signatures are limited by the assumption that such enzymes have remained functionally conserved over billions of years of molecular evolution. By reconstructing ancient genetic sequences in conjunction with laboratory enzyme resurrection, preserved biogeochemical signatures can instead be related to experimentally constrained, ancestral enzymatic properties. We may thereby investigate instances within molecular evolutionary trajectories potentially tied to significant biogeochemical transitions evidenced in the geologic record. Here, we survey recent enzyme resurrection studies to provide a reasoned assessment of areas of success and common pitfalls relevant to ancient biogeochemical applications. We conclude by considering the Great Oxidation Event, which provides a constructive example of a significant biogeochemical transition that warrants investigation with ancestral enzyme resurrection. This event also serves to highlight the pitfalls of facile interpretation of paleophenotype models and data, as applied to two examples of enzymes that likely both influenced and were influenced by the rise of atmospheric oxygen - RuBisCO and nitrogenase.
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Affiliation(s)
- Amanda K Garcia
- Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Betül Kaçar
- Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA; Department of Astronomy and Steward Observatory, University of Arizona, Tucson, AZ, 85721, USA.
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45
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Liu X, Wang M, Song Y, Li Y, Liu P, Shi H, Li Y, Hao T, Zhang H, Jiang W, Chen S, Li J. Combined Assembly and Targeted Integration of Multigene for Nitrogenase Biosynthetic Pathway in Saccharomyces cerevisiae. ACS Synth Biol 2019; 8:1766-1775. [PMID: 31117360 DOI: 10.1021/acssynbio.9b00060] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biological nitrogen fixation, a process unique to diazotrophic prokaryote, is catalyzed by the nitrogenase complex. There has been a long-standing interest in reconstituting a nitrogenase biosynthetic pathway in a eukaryotic host with the final aim of developing N2-fixing cereal crops. In this study, we report that a nitrogenase biosynthetic pathway (∼38 kb containing 15 genes) was assembled in two individual one-step methods via in vivo assembly and integrated at δ and HO sites in Saccharomyces cerevisiae chromosome. Of the 15 genes, 11 genes (nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA, nifV, groES, groEL) were from Paenibacillus polymyxa WLY78 and 4 genes (nifS, nifU, nifF, nifJ) were from Klebsiella oxytoca. The 15-gene nitrogenase biosynthetic pathway was correctly assembled and transcribed in the recombinant S. cerevisiae. The NifDK tetramer with an identical molecular weight as that of P. polymyxa was formed in yeast and the expressed NifH exhibited the activity of Fe protein. This study demonstrates that it will be possible to produce active nitrogenase in eukaryotic hosts.
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Affiliation(s)
- Xiaomeng Liu
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Beijing, P. R. China
| | - Minyang Wang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Beijing, P. R. China
| | - Yi Song
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Beijing, P. R. China
| | - Yongbin Li
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Beijing, P. R. China
| | - Pengxi Liu
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Beijing, P. R. China
| | - Haowen Shi
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Beijing, P. R. China
| | - Yunlong Li
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Beijing, P. R. China
| | - Tianyi Hao
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Beijing, P. R. China
| | - Haowei Zhang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Beijing, P. R. China
| | - Wei Jiang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Beijing, P. R. China
| | - Sanfeng Chen
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Beijing, P. R. China
| | - Jilun Li
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Beijing, P. R. China
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46
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Cardona T, Sánchez‐Baracaldo P, Rutherford AW, Larkum AW. Early Archean origin of Photosystem II. GEOBIOLOGY 2019; 17:127-150. [PMID: 30411862 PMCID: PMC6492235 DOI: 10.1111/gbi.12322] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/03/2018] [Accepted: 10/11/2018] [Indexed: 05/09/2023]
Abstract
Photosystem II is a photochemical reaction center that catalyzes the light-driven oxidation of water to molecular oxygen. Water oxidation is the distinctive photochemical reaction that permitted the evolution of oxygenic photosynthesis and the eventual rise of eukaryotes. At what point during the history of life an ancestral photosystem evolved the capacity to oxidize water still remains unknown. Here, we study the evolution of the core reaction center proteins of Photosystem II using sequence and structural comparisons in combination with Bayesian relaxed molecular clocks. Our results indicate that a homodimeric photosystem with sufficient oxidizing power to split water had already appeared in the early Archean about a billion years before the most recent common ancestor of all described Cyanobacteria capable of oxygenic photosynthesis, and well before the diversification of some of the known groups of anoxygenic photosynthetic bacteria. Based on a structural and functional rationale, we hypothesize that this early Archean photosystem was capable of water oxidation to oxygen and had already evolved protection mechanisms against the formation of reactive oxygen species. This would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.
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Affiliation(s)
- Tanai Cardona
- Department of Life SciencesImperial College LondonLondonUK
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47
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Nishihara A, Thiel V, Matsuura K, McGlynn SE, Haruta S. Phylogenetic Diversity of Nitrogenase Reductase Genes and Possible Nitrogen-Fixing Bacteria in Thermophilic Chemosynthetic Microbial Communities in Nakabusa Hot Springs. Microbes Environ 2018; 33:357-365. [PMID: 30404970 PMCID: PMC6307998 DOI: 10.1264/jsme2.me18030] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chemosynthetic microbial communities develop and form dense cell aggregates in slightly alkaline sulfidic hot springs in the temperature range of 70–86°C at Nakabusa, Japan. Nitrogenase activity has recently been detected in the microbial communities collected. To identify possible members capable of nitrogen fixation, we examined the diversities of 16S rRNA and nitrogenase reductase (NifH) gene sequences in four types of chemosynthetic communities with visually different colors and thicknesses. The results of a 16S rRNA gene analysis indicated that all four microbial communities had similar bacterial constituents; the phylum Aquificae was the dominant member, followed in abundance by Thermodesulfobacteria, Firmicutes, and Thermotogae. Most of the NifH sequences were related to sequences reported in hydrothermal vents and terrestrial hot springs. The results of a phylogenetic analysis of NifH sequences revealed diversity in this gene among the communities collected, distributed within 7 phylogenetic groups. NifH sequences affiliated with Aquificae (Hydrogenobacter/Thermocrinis) and Firmicutes (Caldicellulosiruptor) were abundant. At least two different energy metabolic pathways appeared to be related to nitrogen fixation in the communities analyzed; aerobic sulfur/hydrogen-oxidizing bacteria in Aquificae and fermentative bacteria in Firmicutes. The metabolic characteristics of these two dominant phyla differed from those previously inferred from nitrogenase activity assays on chemosynthetic communities, which were associated with hydrogen-dependent autotrophic sulfate reduction. These assays may correspond to the observed NifH sequences that are distantly related to the known species of Thermodesulfovibrio sp. (Nitrospirae) detected in the present study. The activities of nitrogen-fixing organisms in communities may depend on redox states as well as the availability of electron donors, acceptors, and carbon sources.
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Affiliation(s)
- Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shawn E McGlynn
- Department of Biological Sciences, Tokyo Metropolitan University.,Earth-Life Science Institute, Tokyo Institute of Technology.,Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science.,Blue Marble Space Institute of Science
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
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48
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Stanton CL, Reinhard CT, Kasting JF, Ostrom NE, Haslun JA, Lyons TW, Glass JB. Nitrous oxide from chemodenitrification: A possible missing link in the Proterozoic greenhouse and the evolution of aerobic respiration. GEOBIOLOGY 2018; 16:597-609. [PMID: 30133143 DOI: 10.1111/gbi.12311] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/23/2018] [Accepted: 07/02/2018] [Indexed: 05/26/2023]
Abstract
The potent greenhouse gas nitrous oxide (N2 O) may have been an important constituent of Earth's atmosphere during Proterozoic (~2.5-0.5 Ga). Here, we tested the hypothesis that chemodenitrification, the rapid reduction of nitric oxide by ferrous iron, would have enhanced the flux of N2 O from ferruginous Proterozoic seas. We empirically derived a rate law, d N 2 O d t = 7.2 × 10 - 5 [ Fe 2 + ] 0.3 [ NO ] 1 , and measured an isotopic site preference of +16‰ for the reaction. Using this empirical rate law, and integrating across an oceanwide oxycline, we found that low nM NO and μM-low mM Fe2+ concentrations could have sustained a sea-air flux of 100-200 Tg N2 O-N year-1 , if N2 fixation rates were near-modern and all fixed N2 was emitted as N2 O. A 1D photochemical model was used to obtain steady-state atmospheric N2 O concentrations as a function of sea-air N2 O flux across the wide range of possible pO2 values (0.001-1 PAL). At 100-200 Tg N2 O-N year-1 and >0.1 PAL O2 , this model yielded low-ppmv N2 O, which would produce several degrees of greenhouse warming at 1.6 ppmv CH4 and 320 ppmv CO2 . These results suggest that enhanced N2 O production in ferruginous seawater via a previously unconsidered chemodenitrification pathway may have helped to fill a Proterozoic "greenhouse gap," reconciling an ice-free Mesoproterozoic Earth with a less luminous early Sun. A particularly notable result was that high N2 O fluxes at intermediate O2 concentrations (0.01-0.1 PAL) would have enhanced ozone screening of solar UV radiation. Due to rapid photolysis in the absence of an ozone shield, N2 O is unlikely to have been an important greenhouse gas if Mesoproterozoic O2 was 0.001 PAL. At low O2 , N2 O might have played a more important role as life's primary terminal electron acceptor during the transition from an anoxic to oxic surface Earth, and correspondingly, from anaerobic to aerobic metabolisms.
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Affiliation(s)
- Chloe L Stanton
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia
- Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania
| | - Christopher T Reinhard
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - James F Kasting
- Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania
| | - Nathaniel E Ostrom
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan
- DOE Great Lakes Bioenergy Research Institute, Michigan State University, East Lansing, Michigan
| | - Joshua A Haslun
- Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Timothy W Lyons
- Department of Earth Sciences, University of California, Riverside, California
| | - Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia
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49
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Qin H, Ji B, Zhang S, Kong Z. Study on the bacterial and archaeal community structure and diversity of activated sludge from three wastewater treatment plants. MARINE POLLUTION BULLETIN 2018; 135:801-807. [PMID: 30301100 DOI: 10.1016/j.marpolbul.2018.08.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
In this study, the bacterial and archaeal communities along with their functions of activated sludge from three wastewater treatment plants were investigated by Illumina MiSeq Platform. The treatment processes were modified A/A/O, DE oxidation ditch and pre-anaerobic carrousel oxidation ditch, respectively. The taxonomic analyses showed that Proteobacteria was the predominant bacterial phylum, and Nitrosospira was the dominant nitrification genus. Candidatus Accumulibacter was abundant in DE oxidation ditch process, and the main archaea communities were methanosaeta-like species which had the capability to anaerobic ammonia oxidation. The results illustrated that anaerobic ammonium oxidation played an important role in the nitrogen metabolism and there might be other unknown phosphate-accumulating organisms (PAOs) performing phosphorus removal in activated sludge. The predicted function analyses indicated that both bacteria and archaea were involved in nitrification, denitrification, ammonification and phosphorus removal processes, and their relative abundance varied metabolic modules differed from each other.
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Affiliation(s)
- Hui Qin
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Bin Ji
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China.
| | - Shufei Zhang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Zehua Kong
- Department of Civil and Structural Engineering, Sir Frederick Mappin Building, Mappin Street, Sheffield S1 3JD, UK
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50
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Poudel S, Dunham EC, Lindsay MR, Amenabar MJ, Fones EM, Colman DR, Boyd ES. Origin and Evolution of Flavin-Based Electron Bifurcating Enzymes. Front Microbiol 2018; 9:1762. [PMID: 30123204 PMCID: PMC6085437 DOI: 10.3389/fmicb.2018.01762] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/13/2018] [Indexed: 12/31/2022] Open
Abstract
Twelve evolutionarily unrelated oxidoreductases form enzyme complexes that catalyze the simultaneous coupling of exergonic and endergonic oxidation–reduction reactions to circumvent thermodynamic barriers and minimize free energy loss in a process known as flavin-based electron bifurcation. Common to these 12 bifurcating (Bf) enzymes are protein-bound flavin, the proposed site of bifurcation, and the electron carrier ferredoxin. Despite the documented role of Bf enzymes in balancing the redox state of intracellular electron carriers and in improving the efficiency of cellular metabolism, a comprehensive description of the diversity and evolutionary history of Bf enzymes is lacking. Here, we report the taxonomic distribution, functional diversity, and evolutionary history of Bf enzyme homologs in 4,588 archaeal, bacterial, and eukaryal genomes and 3,136 community metagenomes. Bf homologs were primarily detected in the genomes of anaerobes, including those of sulfate-reducers, acetogens, fermenters, and methanogens. Phylogenetic analyses of Bf enzyme catalytic subunits (oxidoreductases) suggest they were not a property of the Last Universal Common Ancestor of Archaea and Bacteria, which is consistent with the limited and unique taxonomic distributions of enzyme homologs among genomes. Further, phylogenetic analyses of oxidoreductase subunits reveal that non-Bf homologs predate Bf homologs. These observations indicate that multiple independent recruitments of flavoproteins to existing oxidoreductases enabled coupling of numerous new electron Bf reactions. Consistent with the role of these enzymes in the energy metabolism of anaerobes, homologs of Bf enzymes were enriched in metagenomes from subsurface environments relative to those from surface environments. Phylogenetic analyses of homologs from metagenomes reveal that the earliest evolving homologs of most Bf enzymes are from subsurface environments, including fluids from subsurface rock fractures and hydrothermal systems. Collectively, these data suggest strong selective pressures drove the emergence of Bf enzyme complexes via recruitment of flavoproteins that allowed for an increase in the efficiency of cellular metabolism and improvement in energy capture in anaerobes inhabiting a variety of subsurface anoxic habitats where the energy yield of oxidation-reduction reactions is generally low.
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Affiliation(s)
- Saroj Poudel
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Eric C Dunham
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Melody R Lindsay
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Maximiliano J Amenabar
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Elizabeth M Fones
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
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