1
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Osorio-Rodriguez D, Metcalfe KS, McGlynn SE, Yu H, Dekas AE, Ellisman M, Deerinck T, Aristilde L, Grotzinger JP, Orphan VJ. Microbially induced precipitation of silica by anaerobic methane-oxidizing consortia and implications for microbial fossil preservation. Proc Natl Acad Sci U S A 2023; 120:e2302156120. [PMID: 38079551 PMCID: PMC10743459 DOI: 10.1073/pnas.2302156120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Authigenic carbonate minerals can preserve biosignatures of microbial anaerobic oxidation of methane (AOM) in the rock record. It is not currently known whether the microorganisms that mediate sulfate-coupled AOM-often occurring as multicelled consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB)-are preserved as microfossils. Electron microscopy of ANME-SRB consortia in methane seep sediments has shown that these microorganisms can be associated with silicate minerals such as clays [Chen et al., Sci. Rep. 4, 1-9 (2014)], but the biogenicity of these phases, their geochemical composition, and their potential preservation in the rock record is poorly constrained. Long-term laboratory AOM enrichment cultures in sediment-free artificial seawater [Yu et al., Appl. Environ. Microbiol. 88, e02109-21 (2022)] resulted in precipitation of amorphous silicate particles (~200 nm) within clusters of exopolymer-rich AOM consortia from media undersaturated with respect to silica, suggestive of a microbially mediated process. The use of techniques like correlative fluorescence in situ hybridization (FISH), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDS), and nanoscale secondary ion mass spectrometry (nanoSIMS) on AOM consortia from methane seep authigenic carbonates and sediments further revealed that they are enveloped in a silica-rich phase similar to the mineral phase on ANME-SRB consortia in enrichment cultures. Like in cyanobacteria [Moore et al., Geology 48, 862-866 (2020)], the Si-rich phases on ANME-SRB consortia identified here may enhance their preservation as microfossils. The morphology of these silica-rich precipitates, consistent with amorphous-type clay-like spheroids formed within organic assemblages, provides an additional mineralogical signature that may assist in the search for structural remnants of microbial consortia in rocks which formed in methane-rich environments from Earth and other planetary bodies.
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Affiliation(s)
- Daniela Osorio-Rodriguez
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Kyle S. Metcalfe
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Shawn E. McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo152-8550, Japan
| | - Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
- College of Urban and Environmental Sciences, Peking University, Beijing100871, China
| | - Anne E. Dekas
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
- Department of Earth System Science, Stanford University, Stanford, CA94305
| | - Mark Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, School of Medicine, La Jolla, CA92093
| | - Tom Deerinck
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, School of Medicine, La Jolla, CA92093
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL60208
| | - John P. Grotzinger
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
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2
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Castro Garcia A, Cheng S, McGlynn SE, Cross JS. Machine Learning Model Insights into Base-Catalyzed Hydrothermal Lignin Depolymerization. ACS Omega 2023; 8:32078-32089. [PMID: 37692207 PMCID: PMC10483646 DOI: 10.1021/acsomega.3c04168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/11/2023] [Indexed: 09/12/2023]
Abstract
Lignin, an abundant component of plant matter, can be depolymerized into renewable aromatic chemicals and biofuels but remains underutilized. Homogeneously catalyzed depolymerization in water has gained attention due to its economic feasibility and performance but suffers from inconsistently reported yields of bio-oil and solid residues. In this study, machine learning methods were used to develop predictive models for bio-oil and solid residue yields by using a few reaction variables and were subsequently validated by doing experimental work and comparing the predictions to the results. The models achieved a coefficient of determination (R2) score of 0.83 and 0.76, respectively, for bio-oil yield and solid residue. Variable importance for each model was calculated by two different methodologies and was tied to existing studies to explain the model predictive behavior. Based on the outcome of the study, the creation of concrete guidelines for reporting in lignin depolymerization studies was recommended. Shapley additive explanation value analysis reveals that temperature and reaction time are generally the strongest predictors of experimental outcomes compared to the rest.
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Affiliation(s)
- Abraham Castro Garcia
- Department
of Transdisciplinary Science and Engineering, School of Environment
and Society, Tokyo Institute of Technology, 2-12-1 S6-10, Ookayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Shuo Cheng
- Department
of Transdisciplinary Science and Engineering, School of Environment
and Society, Tokyo Institute of Technology, 2-12-1 S6-10, Ookayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Shawn E. McGlynn
- Earth-Life
Science Institute, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
- Blue
Marble Space Institute of Science, Seattle, Washington 98101, United States
| | - Jeffrey S. Cross
- Department
of Transdisciplinary Science and Engineering, School of Environment
and Society, Tokyo Institute of Technology, 2-12-1 S6-10, Ookayama, Meguro-ku, Tokyo 152-8552, Japan
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3
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Twing KI, Ward LM, Kane ZK, Sanders A, Price RE, Pendleton HL, Giovannelli D, Brazelton WJ, McGlynn SE. Microbial ecology of a shallow alkaline hydrothermal vent: Strýtan Hydrothermal Field, Eyjafördur, northern Iceland. Front Microbiol 2022; 13:960335. [PMID: 36466646 PMCID: PMC9713835 DOI: 10.3389/fmicb.2022.960335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/05/2022] [Indexed: 10/20/2023] Open
Abstract
Strýtan Hydrothermal Field (SHF) is a submarine system located in Eyjafördur in northern Iceland composed of two main vents: Big Strýtan and Arnarnesstrýtan. The vents are shallow, ranging from 16 to 70 m water depth, and vent high pH (up to 10.2), moderate temperature (T max ∼70°C), anoxic, fresh fluids elevated in dissolved silica, with slightly elevated concentrations of hydrogen and methane. In contrast to other alkaline hydrothermal vents, SHF is unique because it is hosted in basalt and therefore the high pH is not created by serpentinization. While previous studies have assessed the geology and geochemistry of this site, the microbial diversity of SHF has not been explored in detail. Here we present a microbial diversity survey of the actively venting fluids and chimneys from Big Strýtan and Arnarnesstrýtan, using 16S rRNA gene amplicon sequencing. Community members from the vent fluids are mostly aerobic heterotrophic bacteria; however, within the chimneys oxic, low oxygen, and anoxic habitats could be distinguished, where taxa putatively capable of acetogenesis, sulfur-cycling, and hydrogen metabolism were observed. Very few archaea were observed in the samples. The inhabitants of SHF are more similar to terrestrial hot spring samples than other marine sites. It has been hypothesized that life on Earth (and elsewhere in the solar system) could have originated in an alkaline hydrothermal system, however all other studied alkaline submarine hydrothermal systems to date are fueled by serpentinization. SHF adds to our understandings of hydrothermal vents in relationship to microbial diversity, evolution, and possibly the origin of life.
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Affiliation(s)
- Katrina I. Twing
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - L. M. Ward
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Department of Geosciences, Smith College, Northampton, MA, United States
| | - Zachary K. Kane
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Alexa Sanders
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Roy Edward Price
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - H. Lizethe Pendleton
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
| | - Donato Giovannelli
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - William J. Brazelton
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
| | - Shawn E. McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Center for Sustainable Resource Science, RIKEN, Saitama, Japan
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4
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Longo LM, Hirai H, McGlynn SE. An Evolutionary History of the CoA-Binding Protein Nat/Ivy. Protein Sci 2022; 31:e4463. [PMID: 36192822 DOI: 10.1002/pro.4463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 11/11/2022]
Abstract
Nat/Ivy is a diverse and ubiquitous CoA-binding evolutionary lineage that catalyzes acyltransferase reactions, primarily converting thioesters into amides. At the heart of the Nat/Ivy fold is a phosphate-binding loop that bears a striking resemblance to that of P-loop NTPases - both are extended, glycine-rich loops situated between a β-strand and an α-helix. Nat/Ivy, therefore, represents an intriguing intersection between thioester chemistry, a putative primitive energy currency, and an ancient mode of phospho-ligand binding. Current evidence suggests that Nat/Ivy emerged independently of other cofactor-utilizing enzymes, and that the observed structural similarity - particularly of the cofactor binding site - is the product of shared constraints instead of shared ancestry. The reliance of Nat/Ivy on a β-α-β motif for CoA binding highlights the extent to which this simple structural motif may have been a fundamental evolutionary 'nucleus' around which modern cofactor-binding domains condensed, as has been suggested for HUP domains, Rossmanns, and P-loop NTPases. Finally, by dissecting the patterns of conserved interactions between Nat/Ivy families and CoA, the coevolution of the enzyme and the cofactor was analyzed. As with the Rossmann, it appears that the pyrophosphate moiety at the center of the cofactor predates the enzyme, suggesting that Nat/Ivy emerged sometime after the metabolite dephospho-CoA. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Liam M Longo
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Hayate Hirai
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Blue Marble Space Institute of Science, Seattle, Washington, USA.,School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan.,Biofunctional Catalyst Research 82 Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan
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5
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Longo LM, Kolodny R, McGlynn SE. Evidence for the emergence of β-trefoils by 'Peptide Budding' from an IgG-like β-sandwich. PLoS Comput Biol 2022; 18:e1009833. [PMID: 35157697 PMCID: PMC8880906 DOI: 10.1371/journal.pcbi.1009833] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/25/2022] [Accepted: 01/13/2022] [Indexed: 12/02/2022] Open
Abstract
As sequence and structure comparison algorithms gain sensitivity, the intrinsic interconnectedness of the protein universe has become increasingly apparent. Despite this general trend, β-trefoils have emerged as an uncommon counterexample: They are an isolated protein lineage for which few, if any, sequence or structure associations to other lineages have been identified. If β-trefoils are, in fact, remote islands in sequence-structure space, it implies that the oligomerizing peptide that founded the β-trefoil lineage itself arose de novo. To better understand β-trefoil evolution, and to probe the limits of fragment sharing across the protein universe, we identified both 'β-trefoil bridging themes' (evolutionarily-related sequence segments) and 'β-trefoil-like motifs' (structure motifs with a hallmark feature of the β-trefoil architecture) in multiple, ostensibly unrelated, protein lineages. The success of the present approach stems, in part, from considering β-trefoil sequence segments or structure motifs rather than the β-trefoil architecture as a whole, as has been done previously. The newly uncovered inter-lineage connections presented here suggest a novel hypothesis about the origins of the β-trefoil fold itself-namely, that it is a derived fold formed by 'budding' from an Immunoglobulin-like β-sandwich protein. These results demonstrate how the evolution of a folded domain from a peptide need not be a signature of antiquity and underpin an emerging truth: few protein lineages escape nature's sewing table.
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Affiliation(s)
- Liam M. Longo
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Blue Marble Space Institute of Science, Seattle, Washington, United States of America
| | - Rachel Kolodny
- Department of Computer Science, University of Haifa, Haifa, Israel
| | - Shawn E. McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Blue Marble Space Institute of Science, Seattle, Washington, United States of America
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6
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Sanden SA, Szilagyi RK, Li Y, Kitadai N, Webb SM, Yano T, Nakamura R, Hara M, McGlynn SE. Electrochemically induced metal- vs. ligand-based redox changes in mackinawite: identification of a Fe 3+- and polysulfide-containing intermediate. Dalton Trans 2021; 50:11763-11774. [PMID: 34346451 PMCID: PMC8553345 DOI: 10.1039/d1dt01684a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Under anaerobic conditions, ferrous iron reacts with sulfide producing FeS, which can then undergo a temperature, redox potential, and pH dependent maturation process resulting in the formation of oxidized mineral phases, such as greigite or pyrite. A greater understanding of this maturation process holds promise for the development of iron-sulfide catalysts, which are known to promote diverse chemical reactions, such as H+, CO2 and NO3- reduction processes. Hampering the full realization of the catalytic potential of FeS, however, is an incomplete knowledge of the molecular and redox processess ocurring between mineral and nanoparticulate phases. Here, we investigated the chemical properties of iron-sulfide by cyclic voltammetry, Raman and X-ray absorption spectroscopic techniques. Tracing oxidative maturation pathways by varying electrode potential, nanoparticulate n(Fe2+S2-)(s) was found to oxidize to a Fe3+ containing FeS phase at -0.5 V vs. Ag/AgCl (pH = 7). In a subsequent oxidation, polysulfides are proposed to give a material that is composed of Fe2+, Fe3+, S2- and polysulfide (Sn2-) species, with its composition described as Fe2+1-3xFe3+2xS2-1-y(Sn2-)y. Thermodynamic properties of model compounds calculated by density functional theory indicate that ligand oxidation occurs in conjunction with structural rearrangements, whereas metal oxidation may occur prior to structural rearrangement. These findings together point to the existence of a metastable FeS phase located at the junction of a metal-based oxidation path between FeS and greigite (Fe2+Fe3+2S2-4) and a ligand-based oxidation path between FeS and pyrite (Fe2+(S2)2-).
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Affiliation(s)
- Sebastian A. Sanden
- Earth Life Science Institute, Tokyo Institute of Technology 2-21-1 IE-1 Ookayama, Meguro, Tokyo 152-8550, Japan
- School of Materials and Chemical Technology, Tokyo Institute of Technology 4259 G1-7 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Robert K. Szilagyi
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Yamei Li
- Earth Life Science Institute, Tokyo Institute of Technology 2-21-1 IE-1 Ookayama, Meguro, Tokyo 152-8550, Japan
| | - Norio Kitadai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Samuel M. Webb
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Takaaki Yano
- Institute of Post-LED Photonics, Tokushima University, Minami-Jyosanjima, Tokushima 770-8506, Japan
| | - Ryuhei Nakamura
- Earth Life Science Institute, Tokyo Institute of Technology 2-21-1 IE-1 Ookayama, Meguro, Tokyo 152-8550, Japan
- Center for Sustainable Resource Science, RIKEN 2-1 Hirosawa. Wako, Saitama 351-0198, Japan
| | - Masahiko Hara
- Earth Life Science Institute, Tokyo Institute of Technology 2-21-1 IE-1 Ookayama, Meguro, Tokyo 152-8550, Japan
- School of Materials and Chemical Technology, Tokyo Institute of Technology 4259 G1-7 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Shawn E. McGlynn
- Earth Life Science Institute, Tokyo Institute of Technology 2-21-1 IE-1 Ookayama, Meguro, Tokyo 152-8550, Japan
- Center for Sustainable Resource Science, RIKEN 2-1 Hirosawa. Wako, Saitama 351-0198, Japan
- Blue Marble Space Institute of Science, Seattle, Washington 98154, USA
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7
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Ward LM, Li-Hau F, Kakegawa T, McGlynn SE. Complex History of Aerobic Respiration and Phototrophy in the Chloroflexota Class Anaerolineae Revealed by High-Quality Draft Genome of Ca. Roseilinea mizusawaensis AA3_104. Microbes Environ 2021; 36. [PMID: 34470945 PMCID: PMC8446752 DOI: 10.1264/jsme2.me21020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Roseilinea is a novel lineage of Chloroflexota known only from incomplete metagenome-assembled genomes (MAGs) and preliminary enrichments. Roseilinea is notable for appearing capable of anoxygenic photoheterotrophy despite being only distantly related to well-known phototrophs in the Chloroflexia class such as Chloroflexus and Roseiflexus. Here, we present a high-quality MAG of a member of Roseilinea, improving our understanding of the metabolic capacity and phylogeny of this genus, and resolving the multiple instances of horizontal gene transfer that have led to its metabolic potential. These data allow us to propose a candidate family for these organisms, Roseilineaceae, within the Anaerolineae class.
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Affiliation(s)
- Lewis M Ward
- Department of Earth and Planetary Sciences, Harvard University.,Earth-Life Science Institute, Tokyo Institute of Technology
| | - Fátima Li-Hau
- Earth-Life Science Institute, Tokyo Institute of Technology
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8
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Shepard EM, Impano S, Duffus BR, Pagnier A, Duschene KS, Betz JN, Byer AS, Galambas A, McDaniel EC, Watts H, McGlynn SE, Peters JW, Broderick WE, Broderick JB. HydG, the "dangler" iron, and catalytic production of free CO and CN -: implications for [FeFe]-hydrogenase maturation. Dalton Trans 2021; 50:10405-10422. [PMID: 34240096 DOI: 10.1039/d1dt01359a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The organometallic H-cluster of the [FeFe]-hydrogenase consists of a [4Fe-4S] cubane bridged via a cysteinyl thiolate to a 2Fe subcluster ([2Fe]H) containing CO, CN-, and dithiomethylamine (DTMA) ligands. The H-cluster is synthesized by three dedicated maturation proteins: the radical SAM enzymes HydE and HydG synthesize the non-protein ligands, while the GTPase HydF serves as a scaffold for assembly of [2Fe]H prior to its delivery to the [FeFe]-hydrogenase containing the [4Fe-4S] cubane. HydG uses l-tyrosine as a substrate, cleaving it to produce p-cresol as well as the CO and CN- ligands to the H-cluster, although there is some question as to whether these are formed as free diatomics or as part of a [Fe(CO)2(CN)] synthon. Here we show that Clostridium acetobutylicum (C.a.) HydG catalyzes formation of multiple equivalents of free CO at rates comparable to those for CN- formation. Free CN- is also formed in excess molar equivalents over protein. A g = 8.9 EPR signal is observed for C.a. HydG reconstituted to load the 5th "dangler" iron of the auxiliary [4Fe-4S][FeCys] cluster and is assigned to this "dangler-loaded" cluster state. Free CO and CN- formation and the degree of activation of [FeFe]-hydrogenase all occur regardless of dangler loading, but are increased 10-35% in the dangler-loaded HydG; this indicates the dangler iron is not essential to this process but may affect relevant catalysis. During HydG turnover in the presence of myoglobin, the g = 8.9 signal remains unchanged, indicating that a [Fe(CO)2(CN)(Cys)] synthon is not formed at the dangler iron. Mutation of the only protein ligand to the dangler iron, H272, to alanine nearly completely abolishes both free CO formation and hydrogenase activation, however results show this is not due solely to the loss of the dangler iron. In experiments with wild type and H272A HydG, and with different degrees of dangler loading, we observe a consistent correlation between free CO/CN- formation and hydrogenase activation. Taken in full, our results point to free CO/CN-, but not an [Fe(CO)2(CN)(Cys)] synthon, as essential species in hydrogenase maturation.
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Affiliation(s)
- Eric M Shepard
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Stella Impano
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Benjamin R Duffus
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Adrien Pagnier
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Kaitlin S Duschene
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Jeremiah N Betz
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Amanda S Byer
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Amanda Galambas
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Elizabeth C McDaniel
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Hope Watts
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99163, USA
| | - William E Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Joan B Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
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9
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Abstract
Cyanobacteria thrive in diverse environments. However, questions remain about possible growth limitations in ancient environmental conditions. As a single genus, the Thermosynechococcus are cosmopolitan and live in chemically diverse habitats. To understand the genetic basis for this, we compared the protein coding component of Thermosynechococcus genomes. Supplementing the known genetic diversity of Thermosynechococcus, we report draft metagenome-assembled genomes of two Thermosynechococcus recovered from ferrous carbonate hot springs in Japan. We find that as a genus, Thermosynechococcus is genomically conserved, having a small pan-genome with few accessory genes per individual strain as well as few genes that are unique to the genus. Furthermore, by comparing orthologous protein groups, including an analysis of genes encoding proteins with an iron related function (uptake, storage or utilization), no clear differences in genetic content, or adaptive mechanisms could be detected between genus members, despite the range of environments they inhabit. Overall, our results highlight a seemingly innate ability for Thermosynechococcus to inhabit diverse habitats without having undergone substantial genomic adaptation to accommodate this. The finding of Thermosynechococcus in both hot and high iron environments without adaptation recognizable from the perspective of the proteome has implications for understanding the basis of thermophily within this clade, and also for understanding the possible genetic basis for high iron tolerance in cyanobacteria on early Earth. The conserved core genome may be indicative of an allopatric lifestyle-or reduced genetic complexity of hot spring habitats relative to other environments.
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Affiliation(s)
- Paula Prondzinsky
- Department of Chemical Science and Engineering, Tokyo Institute of Technology.,Earth-Life Science Institute, Tokyo Institute of Technology
| | - Sarah J Berkemer
- Bioinformatics Group, Department of Computer Science, University Leipzig.,Competence Center for Scalable Data Services and Solutions
| | - Lewis M Ward
- Earth-Life Science Institute, Tokyo Institute of Technology.,Department of Earth and Planetary Sciences, Harvard University
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10
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Gastoldi L, Ward LM, Nakagawa M, Giordano M, McGlynn SE. Changes in ATP Sulfurylase Activity in Response to Altered Cyanobacteria Growth Conditions. Microbes Environ 2021; 36. [PMID: 34039816 PMCID: PMC8209453 DOI: 10.1264/jsme2.me20145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We investigated variations in cell growth and ATP Sulfurylase (ATPS) activity when two cyanobacterial strains-Synechocystis sp. PCC6803 and Synechococcus sp. WH7803-were grown in conventional media, and media with low ammonium, low sulfate and a high CO2/low O2 atmosphere. In both organisms, a transition and adaptation to the reconstructed environmental media resulted in a decrease in ATPS activity. This variation appears to be decoupled from growth rate, suggesting the enzyme is not rate-limiting in S assimilation and raising questions about the role of ATPS redox regulation in cell physiology and throughout Earth history.
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Affiliation(s)
- Lucia Gastoldi
- Laboratory of Algal and Plant Physiology, Department of Life and Environmental Sciences (DISVA), Università Politecnica delle Marche (UNIVPM)
| | - Lewis M Ward
- Department of Earth and Planetary Sciences, Harvard University.,Earth-Life Science Institute, Tokyo Institute of Technology
| | | | - Mario Giordano
- Laboratory of Algal and Plant Physiology, Department of Life and Environmental Sciences (DISVA), Università Politecnica delle Marche (UNIVPM)
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11
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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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12
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Linard B, Ebersberger I, McGlynn SE, Glover N, Mochizuki T, Patricio M, Lecompte O, Nevers Y, Thomas PD, Gabaldón T, Sonnhammer E, Dessimoz C, Uchiyama I. Ten Years of Collaborative Progress in the Quest for Orthologs. Mol Biol Evol 2021; 38:3033-3045. [PMID: 33822172 PMCID: PMC8321534 DOI: 10.1093/molbev/msab098] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/07/2021] [Accepted: 04/01/2021] [Indexed: 12/19/2022] Open
Abstract
Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology-evolutionary relatedness-is in many cases readily determined based on sequence similarity analysis. By contrast, whether or not two genes directly descended from a common ancestor by a speciation event (orthologs) or duplication event (paralogs) is more challenging, yet provides critical information on the history of a gene. Since 2009, this task has been the focus of the Quest for Orthologs (QFO) Consortium. The sixth QFO meeting took place in Okazaki, Japan in conjunction with the 67th National Institute for Basic Biology conference. Here, we report recent advances, applications, and oncoming challenges that were discussed during the conference. Steady progress has been made toward standardization and scalability of new and existing tools. A feature of the conference was the presentation of a panel of accessible tools for phylogenetic profiling and several developments to bring orthology beyond the gene unit-from domains to networks. This meeting brought into light several challenges to come: leveraging orthology computations to get the most of the incoming avalanche of genomic data, integrating orthology from domain to biological network levels, building better gene models, and adapting orthology approaches to the broad evolutionary and genomic diversity recognized in different forms of life and viruses.
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Affiliation(s)
- Benjamin Linard
- LIRMM, University of Montpellier, CNRS, Montpellier, France.,SPYGEN, Le Bourget-du-Lac, France
| | - Ingo Ebersberger
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany.,Senckenberg Biodiversity and Climate Research Centre (S-BIKF), Frankfurt, Germany.,LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt, Germany
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo, Japan.,Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Natasha Glover
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Tomohiro Mochizuki
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo, Japan
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Yannis Nevers
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Paul D Thomas
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BCS-CNS), Jordi Girona, Barcelona, Spain.,Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Erik Sonnhammer
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Christophe Dessimoz
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Department of Computer Science, University College London, London, United Kingdom.,Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Ikuo Uchiyama
- Department of Theoretical Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
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13
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Shimizu T, Hayashi Y, Arai M, McGlynn SE, Masuda T, Masuda S. Repressor Activity of SqrR, a Master Regulator of Persulfide-Responsive Genes, Is Regulated by Heme Coordination. Plant Cell Physiol 2021; 62:100-110. [PMID: 33169162 DOI: 10.1093/pcp/pcaa144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
Reactive sulfur species (RSS) are involved in bioactive regulation via persulfidation of proteins. However, how cells regulate RSS-based signaling and RSS metabolism is poorly understood, despite the importance of universal regulation systems in biology. We previously showed that the persulfide-responsive transcriptional factor SqrR acts as a master regulator of sulfide-dependent photosynthesis in proteobacteria. Here, we demonstrated that SqrR also binds heme at a near one-to-one ratio with a binding constant similar to other heme-binding proteins. Heme does not change the DNA-binding pattern of SqrR to the target gene promoter region; however, DNA-binding affinity of SqrR is reduced by the binding of heme, altering its regulatory activity. Circular dichroism spectroscopy clearly showed secondary structural changes in SqrR by the heme binding. Incremental change in the intracellular heme concentration is associated with small, but significant reduction in the transcriptional repression by SqrR. Overall, these results indicate that SqrR has an ability to bind heme to modulate its DNA-binding activity, which may be important for the precise regulation of RSS metabolism in vivo.
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Affiliation(s)
- Takayuki Shimizu
- Department of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuuki Hayashi
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Munehito Arai
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
- Department of Physics, The University of Tokyo, Tokyo, Japan
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Tatsuru Masuda
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Shinji Masuda
- Department of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
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14
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Ward LM, Fischer WW, McGlynn SE. Candidatus Anthektikosiphon siderophilum OHK22, a New Member of the Chloroflexi Family Herpetosiphonaceae from Oku-okuhachikurou Onsen. Microbes Environ 2021; 35. [PMID: 32727976 PMCID: PMC7511795 DOI: 10.1264/jsme2.me20030] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We report the draft metagenome-assembled genome of a member of the Chloroflexi family Herpetosiphonaceae from microbial biofilms developed in a circumneutral, iron-rich hot spring in Japan. This taxon represents a novel genus and species—here proposed as Candidatus Anthektikosiphon siderophilum—that expands the known taxonomic and genetic diversity of the Herpetosiphonaceae and helps orient the evolutionary history of key traits like photosynthesis and aerobic respiration in the Chloroflexi.
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Affiliation(s)
- Lewis M Ward
- Department of Earth & Planetary Sciences, Harvard University.,Earth-Life Science Institute, Tokyo Institute of Technology
| | - Woodward W Fischer
- Division of Geological & Planetary Sciences, California Institute of Technology
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15
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Merino N, Kawai M, Boyd ES, Colman DR, McGlynn SE, Nealson KH, Kurokawa K, Hongoh Y. Single-Cell Genomics of Novel Actinobacteria With the Wood-Ljungdahl Pathway Discovered in a Serpentinizing System. Front Microbiol 2020; 11:1031. [PMID: 32655506 PMCID: PMC7325909 DOI: 10.3389/fmicb.2020.01031] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/27/2020] [Indexed: 01/04/2023] Open
Abstract
Serpentinite-hosted systems represent modern-day analogs of early Earth environments. In these systems, water-rock interactions generate highly alkaline and reducing fluids that can contain hydrogen, methane, and low-molecular-weight hydrocarbons-potent reductants capable of fueling microbial metabolism. In this study, we investigated the microbiota of Hakuba Happo hot springs (∼50°C; pH∼10.5-11), located in Nagano (Japan), which are impacted by the serpentinization process. Analysis of the 16S rRNA gene amplicon sequences revealed that the bacterial community comprises Nitrospirae (47%), "Parcubacteria" (19%), Deinococcus-Thermus (16%), and Actinobacteria (9%), among others. Notably, only 57 amplicon sequence variants (ASV) were detected, and fifteen of these accounted for 90% of the amplicons. Among the abundant ASVs, an early-branching, uncultivated actinobacterial clade identified as RBG-16-55-12 in the SILVA database was detected. Ten single-cell genomes (average pairwise nucleotide identity: 0.98-1.00; estimated completeness: 33-93%; estimated genome size: ∼2.3 Mb) that affiliated with this clade were obtained. Taxonomic classification using single copy genes indicates that the genomes belong to the actinobacterial class-level clade UBA1414 in the Genome Taxonomy Database. Based on metabolic pathway predictions, these actinobacteria are anaerobes, capable of glycolysis, dissimilatory nitrate reduction and CO2 fixation via the Wood-Ljungdahl (WL) pathway. Several other genomes within UBA1414 and two related class-level clades also encode the WL pathway, which has not yet been reported for the Actinobacteria phylum. For the Hakuba actinobacterium, the energy metabolism related to the WL pathway is likely supported by a combination of the Rnf complex, group 3b and 3d [NiFe]-hydrogenases, [FeFe]-hydrogenases, and V-type (H+/Na+ pump) ATPase. The genomes also harbor a form IV ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, also known as a RubisCO-like protein, and contain signatures of interactions with viruses, including clustered regularly interspaced short palindromic repeat (CRISPR) regions and several phage integrases. This is the first report and detailed genome analysis of a bacterium within the Actinobacteria phylum capable of utilizing the WL pathway. The Hakuba actinobacterium is a member of the clade UBA1414/RBG-16-55-12, formerly within the group "OPB41." We propose to name this bacterium 'Candidatus Hakubanella thermoalkaliphilus.'
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Affiliation(s)
- Nancy Merino
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Mikihiko Kawai
- School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan.,Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Eric S Boyd
- 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
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan.,Blue Marble Space Institute of Science, Seattle, WA, United States
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Ken Kurokawa
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Informatics, National Institute of Genetics, Shizuoka, Japan
| | - Yuichi Hongoh
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan
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16
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Wang PH, Fujishima K, Berhanu S, Kuruma Y, Jia TZ, Khusnutdinova AN, Yakunin AF, McGlynn SE. A Bifunctional Polyphosphate Kinase Driving the Regeneration of Nucleoside Triphosphate and Reconstituted Cell-Free Protein Synthesis. ACS Synth Biol 2020; 9:36-42. [PMID: 31829622 DOI: 10.1021/acssynbio.9b00456] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reconstituted cell-free protein synthesis systems (e.g., the PURE system) allow the expression of toxic proteins, hetero-oligomeric protein subunits, and proteins with noncanonical amino acids with high levels of homogeneity. In these systems, an artificial ATP/GTP regeneration system is required to drive protein synthesis, which is accomplished using three kinases and phosphocreatine. Here, we demonstrate the replacement of these three kinases with one bifunctional Cytophaga hutchinsonii polyphosphate kinase that phosphorylates nucleosides in an exchange reaction from polyphosphate. The optimized single-kinase system produced a final sfGFP concentration (∼530 μg/mL) beyond that of the three-kinase system (∼400 μg/mL), with a 5-fold faster mRNA translation rate in the first 90 min. The single-kinase system is also compatible with the expression of heat-sensitive firefly luciferase at 37 °C. Potentially, the single-kinase nucleoside triphosphate regeneration approach developed herein could expand future applications of cell-free protein synthesis systems and could be used to drive other biochemical processes in synthetic biology which require both ATP and GTP.
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Affiliation(s)
- Po-Hsiang Wang
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa, 108-8345, Japan
| | - Samuel Berhanu
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Yutetsu Kuruma
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
- JST, PRESTO, Saitama, 102-0076, Japan
| | - Tony Z. Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
- Blue Marble Space Institute of Science, Seattle, Washington 98154, United States
| | - Anna N. Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario ON M5S, Canada
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario ON M5S, Canada
- Centre for Environmental Biotechnology, Bangor University, Bangor, Wales LL57 2DG, United Kingdom
| | - Shawn E. McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
- Blue Marble Space Institute of Science, Seattle, Washington 98154, United States
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17
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Sanden SA, Yi R, Hara M, McGlynn SE. Correction: Simultaneous synthesis of thioesters and iron–sulfur clusters in water: two universal components of energy metabolism. Chem Commun (Camb) 2020; 56:14920. [DOI: 10.1039/d0cc90485f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Correction for ‘Simultaneous synthesis of thioesters and iron–sulfur clusters in water: two universal components of energy metabolism’ by Sebastian A. Sanden et al., Chem. Commun., 2020, 56, 11989–11992, DOI: 10.1039/D0CC07078A.
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Affiliation(s)
- Sebastian A. Sanden
- Earth Life Science Institute
- Tokyo Institute of Technology
- Meguro
- Japan
- School of Materials and Chemical Technology
| | - Ruiqin Yi
- Earth Life Science Institute
- Tokyo Institute of Technology
- Meguro
- Japan
| | - Masahiko Hara
- Earth Life Science Institute
- Tokyo Institute of Technology
- Meguro
- Japan
- School of Materials and Chemical Technology
| | - Shawn E. McGlynn
- Earth Life Science Institute
- Tokyo Institute of Technology
- Meguro
- Japan
- Center for Sustainable Resource Science
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18
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Sanden SA, Yi R, Hara M, McGlynn SE. Simultaneous synthesis of thioesters and iron–sulfur clusters in water: two universal components of energy metabolism. Chem Commun (Camb) 2020; 56:11989-11992. [DOI: 10.1039/d0cc04078a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Thioesters and peptide ligated [Fe–S] clusters can be synthesized simultaneously from thioacetic acid in an aqueous one-pot reaction.
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Affiliation(s)
- Sebastian A. Sanden
- Earth Life Science Institute
- Tokyo Institute of Technology
- Meguro
- Japan
- School of Materials and Chemical Technology
| | - Ruiqin Yi
- Earth Life Science Institute
- Tokyo Institute of Technology
- Meguro
- Japan
| | - Masahiko Hara
- Earth Life Science Institute
- Tokyo Institute of Technology
- Meguro
- Japan
- School of Materials and Chemical Technology
| | - Shawn E. McGlynn
- Earth Life Science Institute
- Tokyo Institute of Technology
- Meguro
- Japan
- Center for Sustainable Resource Science
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19
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Szilagyi RK, Hanscam R, Shepard EM, McGlynn SE. Natural selection based on coordination chemistry: computational assessment of [4Fe-4S]-maquettes with non-coded amino acids. Interface Focus 2019; 9:20190071. [PMID: 31641437 DOI: 10.1098/rsfs.2019.0071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/27/2019] [Indexed: 12/21/2022] Open
Abstract
Cysteine is the only coded amino acid in biology that contains a thiol functional group. Deprotonated thiolate is essential for anchoring iron-sulfur ([Fe-S]) clusters, as prosthetic groups to the protein matrix. [Fe-S] metalloproteins and metalloenzymes are involved in biological electron transfer, radical chemistry, small molecule activation and signalling. These are key metabolic and regulatory processes that would likely have been present in the earliest organisms. In the context of emergence of life theories, the selection and evolution of the cysteine-specific R-CH2-SH side chain is a fascinating question to confront. We undertook a computational [4Fe-4S]-maquette modelling approach to evaluate how side chain length can influence [Fe-S] cluster binding and stability in short 7-mer and long 16-mer peptides, which contained either thioglycine, cysteine or homocysteine. Force field-based molecular dynamics simulations for [4Fe-4S] cluster nest formation were supplemented with density functional theory calculations of a ligand-exchange reaction between a preassembled cluster and the peptide. Secondary structure analysis revealed that peptides with cysteine are found with greater frequency nested to bind preformed [4Fe-4S] clusters. Additionally, the presence of the single methylene group in cysteine ligands mitigates the steric bulk, maintains the H-bonding and dipole network, and provides covalent Fe-S(thiolate) bonds that together create the optimal electronic and geometric structural conditions for [4Fe-4S] cluster binding compared to thioglycine or homocysteine ligands. Our theoretical work forms an experimentally testable hypothesis of the natural selection of cysteine through coordination chemistry.
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Affiliation(s)
- Robert K Szilagyi
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Rebecca Hanscam
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Eric M Shepard
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Blue Marble Space Institute of Science, Seattle, WA 98154, USA.,Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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20
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Ward LM, Idei A, Nakagawa M, Ueno Y, Fischer WW, McGlynn SE. Geochemical and Metagenomic Characterization of Jinata Onsen, a Proterozoic-Analog Hot Spring, Reveals Novel Microbial Diversity including Iron-Tolerant Phototrophs and Thermophilic Lithotrophs. Microbes Environ 2019; 34:278-292. [PMID: 31413226 PMCID: PMC6759342 DOI: 10.1264/jsme2.me19017] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hydrothermal systems, including terrestrial hot springs, contain diverse geochemical conditions that vary over short spatial scales due to progressive interactions between reducing hydrothermal fluids, the oxygenated atmosphere, and, in some cases, seawater. At Jinata Onsen on Shikinejima Island, Japan, an intertidal, anoxic, iron-rich hot spring mixes with the oxygenated atmosphere and seawater over short spatial scales, creating diverse chemical potentials and redox pairs over a distance of ~10 m. We characterized geochemical conditions along the outflow of Jinata Onsen as well as the microbial communities present in biofilms, mats, and mineral crusts along its traverse using 16S rRNA gene amplicon and genome-resolved shotgun metagenomic sequencing. Microbial communities significantly changed downstream as temperatures and dissolved iron concentrations decreased and dissolved oxygen increased. Biomass was more limited near the spring source than downstream, and primary productivity appeared to be fueled by the oxidation of ferrous iron and molecular hydrogen by members of Zetaproteobacteria and Aquificae. The microbial community downstream was dominated by oxygenic Cyanobacteria. Cyanobacteria are abundant and active even at ferrous iron concentrations of ~150 μM, which challenges the idea that iron toxicity limited cyanobacterial expansion in Precambrian oceans. Several novel lineages of Bacteria are also present at Jinata Onsen, including previously uncharacterized members of the phyla Chloroflexi and Calditrichaeota, positioning Jinata Onsen as a valuable site for the future characterization of these clades.
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Affiliation(s)
- Lewis M Ward
- Department of Earth and Planetary Sciences, Harvard University.,Earth-Life Science Institute, Tokyo Institute of Technology.,Division of Geological and Planetary Sciences, California Institute of Technology
| | - Airi Idei
- Department of Biological Sciences, Tokyo Metropolitan University
| | | | - Yuichiro Ueno
- Earth-Life Science Institute, Tokyo Institute of Technology.,Department of Earth and Planetary Sciences, Tokyo Institute of Technology.,Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology
| | - Woodward W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology
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21
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Ooka H, McGlynn SE, Nakamura R. Cover Feature: Electrochemistry at Deep‐Sea Hydrothermal Vents: Utilization of the Thermodynamic Driving Force towards the Autotrophic Origin of Life (ChemElectroChem 5/2019). ChemElectroChem 2019. [DOI: 10.1002/celc.201900134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Hideshi Ooka
- Biofunctional Catalyst Research TeamRIKEN Center for Sustainable Resource Science (CSRS) 2-1, Hirosawa, Wako Saitama 351-0198 Japan
| | - Shawn E. McGlynn
- Biofunctional Catalyst Research TeamRIKEN Center for Sustainable Resource Science (CSRS) 2-1, Hirosawa, Wako Saitama 351-0198 Japan
- Earth-Life Science Institute (ELSI)Tokyo Institute of Technology 2-12-1-1E-1 Ookayama, Meguro-ku Tokyo 152-8550 Japan
- Blue Marble Space Institute of Science Seattle, WA USA
| | - Ryuhei Nakamura
- Biofunctional Catalyst Research TeamRIKEN Center for Sustainable Resource Science (CSRS) 2-1, Hirosawa, Wako Saitama 351-0198 Japan
- Earth-Life Science Institute (ELSI)Tokyo Institute of Technology 2-12-1-1E-1 Ookayama, Meguro-ku Tokyo 152-8550 Japan
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22
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Sojo V, Ohno A, McGlynn SE, Yamada YMA, Nakamura R. Microfluidic Reactors for Carbon Fixation under Ambient-Pressure Alkaline-Hydrothermal-Vent Conditions. Life (Basel) 2019; 9:life9010016. [PMID: 30717250 PMCID: PMC6463036 DOI: 10.3390/life9010016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/22/2019] [Accepted: 01/25/2019] [Indexed: 12/13/2022] Open
Abstract
The alkaline-hydrothermal-vent theory for the origin of life predicts the spontaneous reduction of CO₂, dissolved in acidic ocean waters, with H₂ from the alkaline vent effluent. This reaction would be catalyzed by Fe(Ni)S clusters precipitated at the interface, which effectively separate the two fluids into an electrochemical cell. Using microfluidic reactors, we set out to test this concept. We produced thin, long Fe(Ni)S precipitates of less than 10 µm thickness. Mixing simplified analogs of the acidic-ocean and alkaline-vent fluids, we then tested for the reduction of CO₂. We were unable to detect reduced carbon products under a number of conditions. As all of our reactions were performed at atmospheric pressure, the lack of reduced carbon products may simply be attributable to the low concentration of hydrogen in our system, suggesting that high-pressure reactors may be a necessity.
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Affiliation(s)
- Victor Sojo
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
- Systems Biophysics, Ludwig-Maximilian University of Munich, Munich 80799, Germany.
- Institute for Advanced Study, Berlin. Wallotstr. 19, Berlin 14193, Germany.
| | - Aya Ohno
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Shawn E McGlynn
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
- Blue Marble Space Institute of Science, Seattle, WA 98154, USA.
| | - Yoichi M A Yamada
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Ryuhei Nakamura
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
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23
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Ooka H, McGlynn SE, Nakamura R. Electrochemistry at Deep‐Sea Hydrothermal Vents: Utilization of the Thermodynamic Driving Force towards the Autotrophic Origin of Life. ChemElectroChem 2019. [DOI: 10.1002/celc.201801432] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Hideshi Ooka
- Biofunctional Catalyst Research TeamRIKEN Center for Sustainable Resource Science (CSRS) 2-1, Hirosawa, Wako Saitama 351-0198 Japan
| | - Shawn E. McGlynn
- Biofunctional Catalyst Research TeamRIKEN Center for Sustainable Resource Science (CSRS) 2-1, Hirosawa, Wako Saitama 351-0198 Japan
- Earth-Life Science Institute (ELSI)Tokyo Institute of Technology 2-12-1-1E-1 Ookayama, Meguro-ku Tokyo 152-8550 Japan
- Blue Marble Space Institute of Science Seattle, WA USA
| | - Ryuhei Nakamura
- Biofunctional Catalyst Research TeamRIKEN Center for Sustainable Resource Science (CSRS) 2-1, Hirosawa, Wako Saitama 351-0198 Japan
- Earth-Life Science Institute (ELSI)Tokyo Institute of Technology 2-12-1-1E-1 Ookayama, Meguro-ku Tokyo 152-8550 Japan
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24
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Sim MS, Ogata H, Lubitz W, Adkins JF, Sessions AL, Orphan VJ, McGlynn SE. Role of APS reductase in biogeochemical sulfur isotope fractionation. Nat Commun 2019; 10:44. [PMID: 30626879 PMCID: PMC6327049 DOI: 10.1038/s41467-018-07878-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/29/2018] [Indexed: 11/09/2022] Open
Abstract
Sulfur isotope fractionation resulting from microbial sulfate reduction (MSR) provides some of the earliest evidence of life, and secular variations in fractionation values reflect changes in biogeochemical cycles. Here we determine the sulfur isotope effect of the enzyme adenosine phosphosulfate reductase (Apr), which is present in all known organisms conducting MSR and catalyzes the first reductive step in the pathway and reinterpret the sedimentary sulfur isotope record over geological time. Small fractionations may be attributed to low sulfate concentrations and/or high respiration rates, whereas fractionations greater than that of Apr require a low chemical potential at that metabolic step. Since Archean sediments lack fractionation exceeding the Apr value of 20‰, they are indicative of sulfate reducers having had access to ample electron donors to drive their metabolisms. Large fractionations in post-Archean sediments are congruent with a decline of favorable electron donors as aerobic and other high potential metabolic competitors evolved.
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Affiliation(s)
- Min Sub Sim
- School of Earth and Environmental Sciences, Seoul National University, Seoul, 08826, South Korea. .,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470, Mülheim an der Ruhr, Germany.,Institute of Low Temperature Science, Hokkaido University, Sapporo, 060-0819, Japan
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470, Mülheim an der Ruhr, Germany
| | - Jess F Adkins
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Alex L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Shawn E McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA. .,Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Tokyo, 152-8550, Japan.
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25
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Yu H, Susanti D, McGlynn SE, Skennerton CT, Chourey K, Iyer R, Scheller S, Tavormina PL, Hettich RL, Mukhopadhyay B, Orphan VJ. Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea. Front Microbiol 2018; 9:2917. [PMID: 30559729 PMCID: PMC6286981 DOI: 10.3389/fmicb.2018.02917] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 11/13/2018] [Indexed: 01/17/2023] Open
Abstract
Sulfate is the predominant electron acceptor for anaerobic oxidation of methane (AOM) in marine sediments. This process is carried out by a syntrophic consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria (SRB) through an energy conservation mechanism that is still poorly understood. It was previously hypothesized that ANME alone could couple methane oxidation to dissimilatory sulfate reduction, but a genetic and biochemical basis for this proposal has not been identified. Using comparative genomic and phylogenetic analyses, we found the genetic capacity in ANME and related methanogenic archaea for sulfate reduction, including sulfate adenylyltransferase, APS kinase, APS/PAPS reductase and two different sulfite reductases. Based on characterized homologs and the lack of associated energy conserving complexes, the sulfate reduction pathways in ANME are likely used for assimilation but not dissimilation of sulfate. Environmental metaproteomic analysis confirmed the expression of 6 proteins in the sulfate assimilation pathway of ANME. The highest expressed proteins related to sulfate assimilation were two sulfite reductases, namely assimilatory-type low-molecular-weight sulfite reductase (alSir) and a divergent group of coenzyme F420-dependent sulfite reductase (Group II Fsr). In methane seep sediment microcosm experiments, however, sulfite and zero-valent sulfur amendments were inhibitory to ANME-2a/2c while growth in their syntrophic SRB partner was not observed. Combined with our genomic and metaproteomic results, the passage of sulfur species by ANME as metabolic intermediates for their SRB partners is unlikely. Instead, our findings point to a possible niche for ANME to assimilate inorganic sulfur compounds more oxidized than sulfide in anoxic marine environments.
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Affiliation(s)
- Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States.,Ronald and Maxine Linde Center for Global Environmental Science, California Institute of Technology, Pasadena, CA, United States
| | - Dwi Susanti
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
| | - Shawn E McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Connor T Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Karuna Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Ramsunder Iyer
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Silvan Scheller
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Patricia L Tavormina
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Biswarup Mukhopadhyay
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States.,Biocomplexity Institute, Virginia Tech, Blacksburg, VA, United States.,Virginia Tech Carilion School of Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
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26
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Nishihara A, Matsuura K, Tank M, McGlynn SE, Thiel V, Haruta S. Nitrogenase Activity in Thermophilic Chemolithoautotrophic Bacteria in the Phylum Aquificae Isolated under Nitrogen-Fixing Conditions from Nakabusa Hot Springs. Microbes Environ 2018; 33:394-401. [PMID: 30473565 PMCID: PMC6307999 DOI: 10.1264/jsme2.me18041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The phylum Aquificae comprises chemolithoautotrophic thermophilic to hyperthermophilic bacteria, in which the nitrogenase reductase gene (nifH) has been reported. However, nitrogen-fixing activity has not yet been demonstrated in members of this deeply branching bacterial phylum. We isolated two thermophilic diazotrophic strains from chemosynthetic microbial communities in slightly alkaline hot springs (≥70°C) in Nakabusa, Nagano Prefecture, Japan. A phylogenetic analysis based on 16S rRNA genes identified these strains as members of the genus Hydrogenobacter within Aquificae. Their NifH sequences showed 96.5 and 97.4% amino acid sequence identities to that from Hydrogenobacter thermophilus TK-6. Nitrogenase activity, measured by acetylene reduction, was confirmed in both strains at 70°C. These novel strains grew under semi-aerobic conditions by using CO2 as the sole carbon source and N2 as the sole nitrogen source in media containing hydrogen and/or thiosulfate. To the best of our knowledge, this is the first demonstration of active nitrogen fixation in thermophilic bacteria at 70°C and in the phylum Aquificae.
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Affiliation(s)
- Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Marcus Tank
- 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
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
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27
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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28
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Nishihara A, Haruta S, McGlynn SE, Thiel V, Matsuura K. Nitrogen Fixation in Thermophilic Chemosynthetic Microbial Communities Depending on Hydrogen, Sulfate, and Carbon Dioxide. Microbes Environ 2018; 33:10-18. [PMID: 29367473 PMCID: PMC5877335 DOI: 10.1264/jsme2.me17134] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/28/2017] [Indexed: 12/20/2022] Open
Abstract
The activity of nitrogen fixation measured by acetylene reduction was examined in chemosynthetic microbial mats at 72-75°C in slightly-alkaline sulfidic hot springs in Nakabusa, Japan. Nitrogenase activity markedly varied from sampling to sampling. Nitrogenase activity did not correlate with methane production, but was detected in samples showing methane production levels less than the maximum amount, indicating a possible redox dependency of nitrogenase activity. Nitrogenase activity was not affected by 2-bromo-ethane sulfonate, an inhibitor of methanogenesis. However, it was inhibited by the addition of molybdate, an inhibitor of sulfate reduction and sulfur disproportionation, suggesting the involvement of sulfate-reducing or sulfur-disproportionating organisms. Nitrogenase activity was affected by different O2 concentrations in the gas phase, again supporting the hypothesis of a redox potential dependency, and was decreased by the dispersion of mats with a homogenizer. The loss of activity that occurred from dispersion was partially recovered by the addition of H2, sulfate, and carbon dioxide. These results suggested that the observed activity of nitrogen fixation was related to chemoautotrophic sulfate reducers, and fixation may be active in a limited range of ambient redox potential. Since thermophilic chemosynthetic communities may resemble ancient microbial communities before the appearance of photosynthesis, the present results may be useful when considering the ancient nitrogen cycle on earth.
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Affiliation(s)
- Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
| | - Shawn E. McGlynn
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
- Earth-Life Science Institute, Tokyo Institute of TechnologyOokayama, Meguro-ku, Tokyo 152–8551Japan
- Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource ScienceWako-shi 351–0198Japan
- Blue Marble Space Institute of ScienceSeattle, WA 98145–1561USA
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
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29
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Abstract
The evolutionary mechanisms behind the extant distribution of photosynthesis is a point of substantial contention. Hypotheses range from the presence of phototrophy in the last universal common ancestor and massive gene loss in most lineages, to a later origin in Cyanobacteria followed by extensive horizontal gene transfer into the extant phototrophic clades, with intermediate scenarios that incorporate aspects of both end-members. Here, we report draft genomes of 11 Chloroflexi: the phototrophic Chloroflexia isolate Kouleothrix aurantiaca as well as 10 genome bins recovered from metagenomic sequencing of microbial mats found in Japanese hot springs. Two of these metagenome bins encode photrophic reaction centers and several of these bins form a metabolically diverse, monophyletic clade sister to the Anaerolineae class that we term Candidatus Thermofonsia. Comparisons of organismal (based on conserved ribosomal) and phototrophy (reaction center and bacteriochlorophyll synthesis) protein phylogenies throughout the Chloroflexi demonstrate that two new lineages acquired phototrophy independently via horizontal gene transfer (HGT) from different ancestral donors within the classically phototrophic Chloroflexia class. These results illustrate a complex history of phototrophy within this group, with metabolic innovation tied to HGT. These observations do not support simple hypotheses for the evolution of photosynthesis that require massive character loss from many clades; rather, HGT appears to be the defining mechanic for the distribution of phototrophy in many of the extant clades in which it appears.
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Affiliation(s)
- Lewis M Ward
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - James Hemp
- Department of Gastroenterology, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Patrick M Shih
- Department of Energy, Joint BioEnergy Institute, Emeryville, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Japan
| | - Woodward W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
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30
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Kawaichi S, Yamada T, Umezawa A, McGlynn SE, Suzuki T, Dohmae N, Yoshida T, Sako Y, Matsushita N, Hashimoto K, Nakamura R. Anodic and Cathodic Extracellular Electron Transfer by the Filamentous Bacterium Ardenticatena maritima 110S. Front Microbiol 2018; 9:68. [PMID: 29467724 PMCID: PMC5808234 DOI: 10.3389/fmicb.2018.00068] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/11/2018] [Indexed: 11/13/2022] Open
Abstract
Ardenticatena maritima strain 110S is a filamentous bacterium isolated from an iron-rich coastal hydrothermal field, and it is a unique isolate capable of dissimilatory iron or nitrate reduction among the members of the bacterial phylum Chloroflexi. Here, we report the ability of A. maritima strain 110S to utilize electrodes as a sole electron acceptor and donor when coupled with the oxidation of organic compounds and nitrate reduction, respectively. In addition, multicellular filaments with hundreds of cells arranged end-to-end increased the extracellular electron transfer (EET) ability to electrodes by organizing filaments into bundled structures, with the aid of microbially reduced iron oxide minerals on the cell surface of strain 110S. Based on these findings, together with the attempt to detect surface-localized cytochromes in the genome sequence and the demonstration of redox-dependent staining and immunostaining of the cell surface, we propose a model of bidirectional electron transport by A. maritima strain 110S, in which surface-localized multiheme cytochromes and surface-associated iron minerals serve as a conduit of bidirectional EET in multicellular filaments.
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Affiliation(s)
- Satoshi Kawaichi
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, RIKEN, Saitama, Japan
| | - Tetsuya Yamada
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, RIKEN, Saitama, Japan.,Department of Electronic Chemistry, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo, Japan
| | - Akio Umezawa
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, RIKEN, Saitama, Japan
| | - Shawn E McGlynn
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, RIKEN, Saitama, Japan.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Center for Sustainable Resource Science, RIKEN, Wako, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Center for Sustainable Resource Science, RIKEN, Wako, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Nobuhiro Matsushita
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Tokyo, Japan
| | | | - Ryuhei Nakamura
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, RIKEN, Saitama, Japan.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
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31
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Ward LM, Idei A, Terajima S, Kakegawa T, Fischer WW, McGlynn SE. Microbial diversity and iron oxidation at Okuoku-hachikurou Onsen, a Japanese hot spring analog of Precambrian iron formations. Geobiology 2017; 15:817-835. [PMID: 29035022 DOI: 10.1111/gbi.12266] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 09/21/2017] [Indexed: 06/07/2023]
Abstract
Banded iron formations (BIFs) are rock deposits common in the Archean and Paleoproterozoic (and regionally Neoproterozoic) sedimentary successions. Multiple hypotheses for their deposition exist, principally invoking the precipitation of iron via the metabolic activities of oxygenic, photoferrotrophic, and/or aerobic iron-oxidizing bacteria. Some isolated environments support chemistry and mineralogy analogous to processes involved in BIF deposition, and their study can aid in untangling the factors that lead to iron precipitation. One such process analog system occurs at Okuoku-hachikurou (OHK) Onsen in Akita Prefecture, Japan. OHK is an iron- and CO2 -rich, circumneutral hot spring that produces a range of precipitated mineral textures containing fine laminae of aragonite and iron oxides that resemble BIF fabrics. Here, we have performed 16S rRNA gene amplicon sequencing of microbial communities across the range of microenvironments in OHK to describe the microbial diversity present and to gain insight into the cycling of iron, oxygen, and carbon in this ecosystem. These analyses suggest that productivity at OHK is based on aerobic iron-oxidizing Gallionellaceae. In contrast to other BIF analog sites, Cyanobacteria, anoxygenic phototrophs, and iron-reducing micro-organisms are present at only low abundances. These observations support a hypothesis where low growth yields and the high stoichiometry of iron oxidized per carbon fixed by aerobic iron-oxidizing chemoautotrophs like Gallionellaceae result in accumulation of iron oxide phases without stoichiometric buildup of organic matter. This system supports little dissimilatory iron reduction, further setting OHK apart from other process analog sites where iron oxidation is primarily driven by phototrophic organisms. This positions OHK as a study area where the controls on primary productivity in iron-rich environments can be further elucidated. When compared with geological data, the metabolisms and mineralogy at OHK are most similar to specific BIF occurrences deposited after the Great Oxygenation Event, and generally discordant with those that accumulated before it.
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Affiliation(s)
- L M Ward
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - A Idei
- Department of Biology, Tokyo Metropolitan University, Tokyo, Japan
| | - S Terajima
- Department of Geosciences, Tohoku University, Sendai City, Japan
| | - T Kakegawa
- Department of Geosciences, Tohoku University, Sendai City, Japan
| | - W W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - S E McGlynn
- Department of Biology, Tokyo Metropolitan University, Tokyo, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Blue Marble Space Institute of Science, Seattle, WA, USA
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32
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Abstract
Anaerobic methane oxidation in archaea is often presented to operate via a pathway of “reverse methanogenesis”. However, if the cumulative reactions of a methanogen are run in reverse there is no apparent way to conserve energy. Recent findings suggest that chemiosmotic coupling enzymes known from their use in methylotrophic and acetoclastic methanogens—in addition to unique terminal reductases—biochemically facilitate energy conservation during complete CH4 oxidation to CO2. The apparent enzyme modularity of these organisms highlights how microbes can arrange their energy metabolisms to accommodate diverse chemical potentials in various ecological niches, even in the extreme case of utilizing “reverse” thermodynamic potentials.
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33
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McGlynn SE, Chadwick GL, Kempes CP, Orphan VJ. Single cell activity reveals direct electron transfer in methanotrophic consortia. Nature 2015; 526:531-5. [PMID: 26375009 DOI: 10.1038/nature15512] [Citation(s) in RCA: 327] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/10/2015] [Indexed: 11/09/2022]
Abstract
Multicellular assemblages of microorganisms are ubiquitous in nature, and the proximity afforded by aggregation is thought to permit intercellular metabolic coupling that can accommodate otherwise unfavourable reactions. Consortia of methane-oxidizing archaea and sulphate-reducing bacteria are a well-known environmental example of microbial co-aggregation; however, the coupling mechanisms between these paired organisms is not well understood, despite the attention given them because of the global significance of anaerobic methane oxidation. Here we examined the influence of interspecies spatial positioning as it relates to biosynthetic activity within structurally diverse uncultured methane-oxidizing consortia by measuring stable isotope incorporation for individual archaeal and bacterial cells to constrain their potential metabolic interactions. In contrast to conventional models of syntrophy based on the passage of molecular intermediates, cellular activities were found to be independent of both species intermixing and distance between syntrophic partners within consortia. A generalized model of electric conductivity between co-associated archaea and bacteria best fit the empirical data. Combined with the detection of large multi-haem cytochromes in the genomes of methanotrophic archaea and the demonstration of redox-dependent staining of the matrix between cells in consortia, these results provide evidence for syntrophic coupling through direct electron transfer.
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Affiliation(s)
- Shawn E McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California 91125, USA
| | - Grayson L Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California 91125, USA
| | - Christopher P Kempes
- Exobiology Branch, National Aeronautics and Space Administration Ames Research Center, Moffett Field, California 94035, USA.,Control and Dynamical Systems, California Institute of Technology, Pasadena, California 91125, USA.,SETI Institute, Mountain View, California 94034, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California 91125, USA
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34
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Abstract
Biomineralization plays a fundamental role in the global silicon cycle. Grasses are known to mobilize significant quantities of Si in the form of silica biominerals and dominate the terrestrial realm today, but they have relatively recent origins and only rose to taxonomic and ecological prominence within the Cenozoic Era. This raises questions regarding when and how the biological silica cycle evolved. To address these questions, we examined silica abundances of extant members of early-diverging land plant clades, which show that silica biomineralization is widespread across terrestrial plant linages. Particularly high silica abundances are observed in lycophytes and early-diverging ferns. However, silica biomineralization is rare within later-evolving gymnosperms, implying a complex evolutionary history within the seed plants. Electron microscopy and X-ray spectroscopy show that the most common silica-mineralized tissues include the vascular system, epidermal cells, and stomata, which is consistent with the hypothesis that biomineralization in plants is frequently coupled to transpiration. Furthermore, sequence, phylogenetic, and structural analysis of nodulin 26-like intrinsic proteins from diverse plant genomes points to a plastic and ancient capacity for silica accumulation within terrestrial plants. The integration of these two comparative biology approaches demonstrates that silica biomineralization has been an important process for land plants over the course of their >400 My evolutionary history.
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Affiliation(s)
| | | | - Shawn E McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125; Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Woodward W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
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Kopf SH, McGlynn SE, Green-Saxena A, Guan Y, Newman DK, Orphan VJ. Heavy water and (15) N labelling with NanoSIMS analysis reveals growth rate-dependent metabolic heterogeneity in chemostats. Environ Microbiol 2015; 17:2542-56. [PMID: 25655651 DOI: 10.1111/1462-2920.12752] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/11/2014] [Accepted: 12/12/2014] [Indexed: 11/30/2022]
Abstract
To measure single-cell microbial activity and substrate utilization patterns in environmental systems, we employ a new technique using stable isotope labelling of microbial populations with heavy water (a passive tracer) and (15) N ammonium in combination with multi-isotope imaging mass spectrometry. We demonstrate simultaneous NanoSIMS analysis of hydrogen, carbon and nitrogen at high spatial and mass resolution, and report calibration data linking single-cell isotopic compositions to the corresponding bulk isotopic equivalents for Pseudomonas aeruginosa and Staphylococcus aureus. Our results show that heavy water is capable of quantifying in situ single-cell microbial activities ranging from generational time scales of minutes to years, with only light isotopic incorporation (∼0.1 atom % (2) H). Applying this approach to study the rates of fatty acid biosynthesis by single cells of S. aureus growing at different rates in chemostat culture (∼6 h, 1 day and 2 week generation times), we observe the greatest anabolic activity diversity in the slowest growing populations. By using heavy water to constrain cellular growth activity, we can further infer the relative contributions of ammonium versus amino acid assimilation to the cellular nitrogen pool. The approach described here can be applied to disentangle individual cell activities even in nutritionally complex environments.
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Affiliation(s)
- Sebastian H Kopf
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Shawn E McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Abigail Green-Saxena
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yunbin Guan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Dianne K Newman
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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Nitschke W, McGlynn SE, Milner-White EJ, Russell MJ. On the antiquity of metalloenzymes and their substrates in bioenergetics. Biochim Biophys Acta 2013; 1827:871-81. [PMID: 23454059 DOI: 10.1016/j.bbabio.2013.02.008] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/15/2013] [Accepted: 02/18/2013] [Indexed: 02/07/2023]
Abstract
Many metalloenzymes that inject and extract reducing equivalents at the beginning and the end of electron transport chains involved in chemiosmosis are suggested, through phylogenetic analysis, to have been present in the Last Universal Common Ancestor (LUCA). Their active centres are affine with the structures of minerals presumed to contribute to precipitate membranes produced on the mixing of hydrothermal solutions with the Hadean Ocean ~4 billion years ago. These mineral precipitates consist of transition element sulphides and oxides such as nickelian mackinawite ([Fe>Ni]2S2), a nickel-bearing greigite (~FeSS[Fe3NiS4]SSFe), violarite (~NiSS[Fe2Ni2S4]SSNi), a molybdenum bearing complex (~Mo(IV/VI)2Fe3S(0/2-)9) and green rust or fougerite (~[Fe(II)Fe(III)(OH)4](+)[OH](-)). They may be respectively compared with the active centres of Ni-Fe hydrogenase, carbon monoxide dehydrogenase (CODH), acetyl coenzyme-A synthase (ACS), the complex iron-sulphur molybdoenzyme (CISM) superfamily and methane monooxygenase (MMO). With the look of good catalysts - a suggestion that gathers some support from prebiotic hydrothermal experimentation - and sequestered by short peptides, they could be thought of as the original building blocks of proto-enzyme active centres. This convergence of the makeup of the LUCA-metalloenzymes with mineral structure and composition of hydrothermal precipitates adds credence to the alkaline hydrothermal (chemiosmotic) theory for the emergence of life, specifically to the possibility that the first metabolic pathway - the acetyl CoA pathway - was initially driven from either end, reductively from CO2 to CO and oxidatively and reductively from CH4 through to a methane thiol group, the two entities assembled with the help of a further thiol on a violarite cluster sequestered by peptides. By contrast, the organic coenzymes were entirely a product of the first metabolic pathways. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Wolfgang Nitschke
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille Cedex 20, France
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Abstract
Nitrogenase enzymes have evolved complex iron–sulfur (Fe–S) containing cofactors that most commonly contain molybdenum (MoFe, Nif) as a heterometal but also exist as vanadium (VFe, Vnf) and heterometal-independent (Fe-only, Anf) forms. All three varieties are capable of the reduction of dinitrogen (N2) to ammonia (NH3) but exhibit differences in catalytic rates and substrate specificity unique to metal type. Recently, N2 reduction activity was observed in archaeal methanotrophs and methanogens that encode for nitrogenase homologs which do not cluster phylogenetically with previously characterized nitrogenases. To gain insight into the metal cofactors of these uncharacterized nitrogenase homologs, predicted three-dimensional structures of the nitrogenase active site metal-cofactor binding subunits NifD, VnfD, and AnfD were generated and compared. Dendrograms based on structural similarity indicate nitrogenase homologs cluster based on heterometal content and that uncharacterized nitrogenase D homologs cluster with NifD, providing evidence that the structure of the enzyme has evolved in response to metal utilization. Characterization of the structural environment of the nitrogenase active site revealed amino acid variations that are unique to each class of nitrogenase as defined by heterometal cofactor content; uncharacterized nitrogenases contain amino acids near the active site most similar to NifD. Together, these results suggest that uncharacterized nitrogenase homologs present in numerous anaerobic methanogens, archaeal methanotrophs, and firmicutes bind FeMo-co in their active site, and add to growing evidence that diversification of metal utilization likely occurred in an anoxic habitat.
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Affiliation(s)
- Shawn E McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
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McGlynn SE, Kanik I, Russell MJ. Peptide and RNA contributions to iron-sulphur chemical gardens as life's first inorganic compartments, catalysts, capacitors and condensers. Philos Trans A Math Phys Eng Sci 2012; 370:3007-3022. [PMID: 22615473 DOI: 10.1098/rsta.2011.0211] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Hydrothermal chimneys and compartments comprising transition metal sulphides and associated minerals have been proposed as likely locations for the beginnings of life. In laboratory simulations of off-axis alkaline springs, it is shown that the interaction of a simulated alkaline sulphide-bearing submarine vent solution with a primeval anoxic iron-bearing ocean leads to the formation of chimney structures reminiscent of chemical gardens. These chimneys display periodicity in their deposition and exhibit diverse morphologies and mineralogies, affording the possibilities of catalysis and molecular sequestration. The addition of peptides and RNA to the alkaline solution modifies the elemental stoichiometry of the chimneys-perhaps indicating the very initial stage of the organic takeover on the way to living cells by charged organic polymers potentially synthesized in this same environment.
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Affiliation(s)
- Shawn E McGlynn
- Planetary Science Section 3220, MS:183-301, Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109-8099, USA
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Mielke RE, Robinson KJ, White LM, McGlynn SE, McEachern K, Bhartia R, Kanik I, Russell MJ. Iron-sulfide-bearing chimneys as potential catalytic energy traps at life's emergence. Astrobiology 2011; 11:933-950. [PMID: 22111762 DOI: 10.1089/ast.2011.0667] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The concept that life emerged where alkaline hydrogen-bearing submarine hot springs exhaled into the most ancient acidulous ocean was used as a working hypothesis to investigate the nature of precipitate membranes. Alkaline solutions at 25-70°C and pH between 8 and 12, bearing HS(-)±silicate, were injected slowly into visi-jars containing ferrous chloride to partially simulate the early ocean on this or any other wet and icy, geologically active rocky world. Dependent on pH and sulfide content, fine tubular chimneys and geodal bubbles were generated with semipermeable walls 4-100 μm thick that comprised radial platelets of nanometric mackinawite [FeS]±ferrous hydroxide [∼Fe(OH)(2)], accompanied by silica and, at the higher temperature, greigite [Fe(3)S(4)]. Within the chimney walls, these platelets define a myriad of micropores. The interior walls of the chimneys host iron sulfide framboids, while, in cases where the alkaline solution has a pH>11 or relatively low sulfide content, their exteriors exhibit radial flanges with a spacing of ∼4 μm that comprise microdendrites of ferrous hydroxide. We speculate that this pattern results from outward and inward radial flow through the chimney walls. The outer Fe(OH)(2) flanges perhaps precipitate where the highly alkaline flow meets the ambient ferrous iron-bearing fluid, while the intervening troughs signal where the acidulous iron-bearing solutions could gain access to the sulfidic and alkaline interior of the chimneys, thereby leading to the precipitation of the framboids. Addition of soluble pentameric peptides enhances membrane durability and accentuates the crenulations on the chimney exteriors. These dynamic patterns may have implications for acid-base catalysis and the natural proton motive force acting through the matrix of the porous inorganic membrane. Thus, within such membranes, steep redox and pH gradients would bear across the nanometric platelets and separate the two counter-flowing solutions, a condition that may have led to the onset of an autotrophic metabolism through the reduction of carbon dioxide.
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Affiliation(s)
- Randall E Mielke
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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Haydon N, McGlynn SE, Robus O. Speculation on quantum mechanics and the operation of life giving catalysts. ORIGINS LIFE EVOL B 2011; 41:35-50. [PMID: 20407928 DOI: 10.1007/s11084-010-9210-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 03/15/2010] [Indexed: 11/30/2022]
Abstract
The origin of life necessitated the formation of catalytic functionalities in order to realize a number of those capable of supporting reactions that led to the proliferation of biologically accessible molecules and the formation of a proto-metabolic network. Here, the discussion of the significance of quantum behavior on biological systems is extended from recent hypotheses exploring brain function and DNA mutation to include origins of life considerations in light of the concept of quantum decoherence and the transition from the quantum to the classical. Current understandings of quantum systems indicate that in the context of catalysis, substrate-catalyst interaction may be considered as a quantum measurement problem. Exploration of catalytic functionality necessary for life's emergence may have been accommodated by quantum searches within metal sulfide compartments, where catalyst and substrate wave function interaction may allow for quantum based searches of catalytic phase space. Considering the degree of entanglement experienced by catalytic and non catalytic outcomes of superimposed states, quantum contributions are postulated to have played an important role in the operation of efficient catalysts that would provide for the kinetic basis for the emergence of life.
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Affiliation(s)
- Nathan Haydon
- NASA NAI Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, MT 59717, USA.
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Mielke RE, Russell MJ, Wilson PR, McGlynn SE, Coleman M, Kidd R, Kanik I. Design, fabrication, and test of a hydrothermal reactor for origin-of-life experiments. Astrobiology 2010; 10:799-810. [PMID: 21087160 DOI: 10.1089/ast.2009.0456] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We describe a continuous high-pressure flow reactor designed to simulate the unforced convective interaction of hydrothermal solutions and ocean waters with submarine crust on early Earth-conditions appropriate to those that may have led to the onset of life. The experimental operating conditions are appropriate for investigating kinetic hydrothermal processes in the early history of any sizable wet, rocky planet. Beyond the description of the fabrication, we report an initial experiment that tested the design and investigated the feasibility of sulfide and silica dissolution in alkaline solution from iron sulfide and basaltic rock, and their possible subsequent transport as HS(-) and H(2)SiO(2-)(4) in hot alkaline solutions. Delivery of hydrogen sulfide and dihydrogen silicate ions would have led to the precipitation of ferrous hydroxide, hydroxysilicates, and iron sulfides as integral mineral components of an off-ridge compartmentalized hydrothermal mound in the Hadean. Such a mound could, we contend, have acted as a natural chemical and electrochemical reactor and, ultimately, as the source of all biochemistry on our planet. In the event, we show that an average of ∼1 mM/kg of both sulfide and silica were released throughout, though over 10 mM/kg of HS(-) was recorded for ∼100 minutes in the early stages of the experiment. This alkaline effluent from the reactor was injected into a reservoir of a simulacrum of ferrous iron-bearing "Hadean Ocean" water in an experiment that demonstrated the capacity of such fluids to generate hydrothermal chimneys and a variety of contiguous inorganic microgeode precipitates bearing disseminations of discrete metal sulfides. Comparable natural composite structures may have acted as hatcheries for emergent life in the Hadean.
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Affiliation(s)
- Randall E Mielke
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109-8099, USA
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Shepard EM, Duffus BR, George SJ, McGlynn SE, Challand MR, Swanson KD, Roach PL, Cramer SP, Peters JW, Broderick JB. [FeFe]-Hydrogenase Maturation: HydG-Catalyzed Synthesis of Carbon Monoxide. J Am Chem Soc 2010; 132:9247-9. [DOI: 10.1021/ja1012273] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eric M. Shepard
- Department of Chemistry & Biochemistry and Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, Montana 59717, Department of Applied Science, University of California—Davis, Davis, California 95616, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Benjamin R. Duffus
- Department of Chemistry & Biochemistry and Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, Montana 59717, Department of Applied Science, University of California—Davis, Davis, California 95616, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Simon J. George
- Department of Chemistry & Biochemistry and Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, Montana 59717, Department of Applied Science, University of California—Davis, Davis, California 95616, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Shawn E. McGlynn
- Department of Chemistry & Biochemistry and Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, Montana 59717, Department of Applied Science, University of California—Davis, Davis, California 95616, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Martin R. Challand
- Department of Chemistry & Biochemistry and Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, Montana 59717, Department of Applied Science, University of California—Davis, Davis, California 95616, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Kevin D. Swanson
- Department of Chemistry & Biochemistry and Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, Montana 59717, Department of Applied Science, University of California—Davis, Davis, California 95616, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Peter L. Roach
- Department of Chemistry & Biochemistry and Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, Montana 59717, Department of Applied Science, University of California—Davis, Davis, California 95616, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Stephen P. Cramer
- Department of Chemistry & Biochemistry and Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, Montana 59717, Department of Applied Science, University of California—Davis, Davis, California 95616, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - John W. Peters
- Department of Chemistry & Biochemistry and Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, Montana 59717, Department of Applied Science, University of California—Davis, Davis, California 95616, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Joan B. Broderick
- Department of Chemistry & Biochemistry and Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, Montana 59717, Department of Applied Science, University of California—Davis, Davis, California 95616, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
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Driesener RC, Challand MR, McGlynn SE, Shepard EM, Boyd ES, Broderick JB, Peters JW, Roach PL. [FeFe]-hydrogenase cyanide ligands derived from S-adenosylmethionine-dependent cleavage of tyrosine. Angew Chem Int Ed Engl 2010; 49:1687-90. [PMID: 20108298 DOI: 10.1002/anie.200907047] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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McGlynn SE, Mulder DW, Shepard EM, Broderick JB, Peters JW. Hydrogenase cluster biosynthesis: organometallic chemistry nature's way. Dalton Trans 2009:4274-85. [PMID: 19662302 DOI: 10.1039/b821432h] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It has been over a decade now since it was revealed that the metal containing active sites of hydrogenases possess carbonyl and cyanide ligands bound to iron. The presence of these ligands in hydrogenases came as a surprise and to-date these ligands have not been observed to be associated with any other enzymatic metallocenter. The elucidation of the structures of these unique metalloenzymes and their associated metal clusters created opportunity for a number of different lines of research. For synthetic chemists, the structures of hydrogenase active sites have provided attractive targets for syntheses that advance our understanding of the electronic structure and reactivity of these unique enzyme active sites. These efforts contribute to the synthesis of first row transition metal catalysts for hydrogen oxidation and hydrogen production that could have significant impacts on alternative and renewable energy solutions. Although effective synthetic approaches have been identified to generate models with a high degree of similarity to these active sites, the details of how these metal clusters are synthesized biochemically have not been resolved. Since hydrogen metabolism is presumed to be an early feature in the energetics of life and hydrogen metabolizing organisms can be traced very early in molecular phylogeny, the metal clusters at hydrogenase active sites are presumed to be among the earliest of known co-factors. Comparison of mineral based precursors and synthetic cluster analog chemistry to what is observed in contemporary biological systems may shed light on how proto-metabolically relevant catalysts first arose prebiotically by the processes of adoption of pre-existing functionality and ligand assisted catalysis.
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Affiliation(s)
- Shawn E McGlynn
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715, USA
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McGlynn SE, Shepard EM, Winslow MA, Naumov AV, Duschene KS, Posewitz MC, Broderick WE, Broderick JB, Peters JW. HydF as a scaffold protein in [FeFe] hydrogenase H-cluster biosynthesis. FEBS Lett 2008; 582:2183-7. [PMID: 18501709 DOI: 10.1016/j.febslet.2008.04.063] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Accepted: 04/24/2008] [Indexed: 10/22/2022]
Abstract
In an effort to determine the specific protein component(s) responsible for in vitro activation of the [FeFe] hydrogenase (HydA), the individual maturation proteins HydE, HydF, and HydG from Clostridium acetobutylicum were purified from heterologous expressions in Escherichia coli. Our results demonstrate that HydF isolated from a strain expressing all three maturation proteins is sufficient to confer hydrogenase activity to purified inactive heterologously expressed HydA (expressed in the absence of HydE, HydF, and HydG). These results represent the first in vitro maturation of [FeFe] hydrogenase with purified proteins, and suggest that HydF functions as a scaffold upon which an H-cluster intermediate is synthesized.
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Affiliation(s)
- Shawn E McGlynn
- Department of Chemistry and Biochemistry, The Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, MT 59717, USA
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McGlynn SE, Ruebush SS, Naumov A, Nagy LE, Dubini A, King PW, Broderick JB, Posewitz MC, Peters JW. In vitro activation of [FeFe] hydrogenase: new insights into hydrogenase maturation. J Biol Inorg Chem 2007; 12:443-7. [PMID: 17372774 DOI: 10.1007/s00775-007-0224-z] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2006] [Accepted: 02/22/2007] [Indexed: 10/23/2022]
Abstract
The in vitro activation of the [FeFe] hydrogenase is accomplished by combining Escherichia coli cell extracts containing the heterologously expressed inactive HydA with extracts in which hydrogenase-specific maturation proteins HydE, HydF, and HydG are expressed in concert. Interestingly, the process of HydA activation occurs rapidly and in the absence of potential substrates, which suggests that the hydrogenase accessory proteins synthesize an H-cluster precursor that can be quickly transferred to the hydrogenase enzyme to affect activation. HydA activity is observed to be dependent on the protein fraction containing all three accessory proteins expressed in concert and cannot be accomplished with addition of heat-treated extract or extract filtrate, suggesting that the activation of the hydrogenase structural protein is mediated by interaction with the accessory assembly protein(s). These results represent the first important step in understanding the process of H-cluster assembly and provide significant insights into hydrogenase maturation.
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Affiliation(s)
- Shawn E McGlynn
- Department of Chemistry and Biochemistry, Montana State University Bozeman, Bozeman, MT 59717, USA
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