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Rodriguez LE, Altair T, Hermis NY, Jia TZ, Roche TP, Steller LH, Weber JM. Chapter 4: A Geological and Chemical Context for the Origins of Life on Early Earth. ASTROBIOLOGY 2024; 24:S76-S106. [PMID: 38498817 DOI: 10.1089/ast.2021.0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Within the first billion years of Earth's history, the planet transformed from a hot, barren, and inhospitable landscape to an environment conducive to the emergence and persistence of life. This chapter will review the state of knowledge concerning early Earth's (Hadean/Eoarchean) geochemical environment, including the origin and composition of the planet's moon, crust, oceans, atmosphere, and organic content. It will also discuss abiotic geochemical cycling of the CHONPS elements and how these species could have been converted to biologically relevant building blocks, polymers, and chemical networks. Proposed environments for abiogenesis events are also described and evaluated. An understanding of the geochemical processes under which life may have emerged can better inform our assessment of the habitability of other worlds, the potential complexity that abiotic chemistry can achieve (which has implications for putative biosignatures), and the possibility for biochemistries that are vastly different from those on Earth.
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Affiliation(s)
- Laura E Rodriguez
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA. (Current)
| | - Thiago Altair
- Institute of Chemistry of São Carlos, Universidade de São Paulo, São Carlos, Brazil
- Department of Chemistry, College of the Atlantic, Bar Harbor, Maine, USA. (Current)
| | - Ninos Y Hermis
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Department of Physics and Space Sciences, University of Granada, Granada Spain. (Current)
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Luke H Steller
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Australia
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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2
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Mahendrarajah TA, Moody ERR, Schrempf D, Szánthó LL, Dombrowski N, Davín AA, Pisani D, Donoghue PCJ, Szöllősi GJ, Williams TA, Spang A. ATP synthase evolution on a cross-braced dated tree of life. Nat Commun 2023; 14:7456. [PMID: 37978174 PMCID: PMC10656485 DOI: 10.1038/s41467-023-42924-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023] Open
Abstract
The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.
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Affiliation(s)
- Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Edmund R R Moody
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Dominik Schrempf
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
| | - Lénárd L Szánthó
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Karolina ut 29, H-1113, Budapest, Hungary
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Adrián A Davín
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Gergely J Szöllősi
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK.
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands.
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
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Ravin NV, Muntyan MS, Smolyakov DD, Rudenko TS, Beletsky AV, Mardanov AV, Grabovich MY. Metagenomics Revealed a New Genus ' Candidatus Thiocaldithrix dubininis' gen. nov., sp. nov. and a New Species ' Candidatus Thiothrix putei' sp. nov. in the Family Thiotrichaceae, Some Members of Which Have Traits of Both Na +- and H +-Motive Energetics. Int J Mol Sci 2023; 24:14199. [PMID: 37762502 PMCID: PMC10532065 DOI: 10.3390/ijms241814199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Two metagenome-assembled genomes (MAGs), GKL-01 and GKL-02, related to the family Thiotrichaceae have been assembled from the metagenome of bacterial mat obtained from a sulfide-rich thermal spring in the North Caucasus. Based on average amino acid identity (AAI) values and genome-based phylogeny, MAG GKL-01 represented a new genus within the Thiotrichaceae family. The GC content of the GKL-01 DNA (44%) differed significantly from that of other known members of the genus Thiothrix (50.1-55.6%). We proposed to assign GKL-01 to a new species and genus 'Candidatus Thiocaldithrix dubininis' gen. nov., sp. nov. GKL-01. The phylogenetic analysis and estimated distances between MAG GKL-02 and the genomes of the previously described species of the genus Thiothrix allowed assigning GKL-02 to a new species with the proposed name 'Candidatus Thiothrix putei' sp. nov. GKL-02 within the genus Thiothrix. Genome data first revealed the presence of both Na+-ATPases and H+-ATPases in several Thiothrix species. According to genomic analysis, bacteria GKL-01 and GKL-02 are metabolically versatile facultative aerobes capable of growing either chemolithoautotrophically or chemolithoheterotrophically in the presence of hydrogen sulfide and/or thiosulfate or chemoorganoheterotrophically.
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Affiliation(s)
- Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospect, 33-2, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Maria S. Muntyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
| | - Dmitry D. Smolyakov
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (T.S.R.)
| | - Tatyana S. Rudenko
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (T.S.R.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospect, 33-2, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospect, 33-2, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Margarita Yu. Grabovich
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (D.D.S.); (T.S.R.)
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Booker AE, D'Angelo T, Adams-Beyea A, Brown JM, Nigro O, Rappé MS, Stepanauskas R, Orcutt BN. Life strategies for Aminicenantia in subseafloor oceanic crust. THE ISME JOURNAL 2023; 17:1406-1415. [PMID: 37328571 PMCID: PMC10432499 DOI: 10.1038/s41396-023-01454-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 04/11/2023] [Accepted: 04/17/2023] [Indexed: 06/18/2023]
Abstract
After decades studying the microbial "deep biosphere" in subseafloor oceanic crust, the growth and life strategies in this anoxic, low energy habitat remain poorly described. Using both single cell genomics and metagenomics, we reveal the life strategies of two distinct lineages of uncultivated Aminicenantia bacteria from the basaltic subseafloor oceanic crust of the eastern flank of the Juan de Fuca Ridge. Both lineages appear adapted to scavenge organic carbon, as each have genetic potential to catabolize amino acids and fatty acids, aligning with previous Aminicenantia reports. Given the organic carbon limitation in this habitat, seawater recharge and necromass may be important carbon sources for heterotrophic microorganisms inhabiting the ocean crust. Both lineages generate ATP via several mechanisms including substrate-level phosphorylation, anaerobic respiration, and electron bifurcation driving an Rnf ion translocation membrane complex. Genomic comparisons suggest these Aminicenantia transfer electrons extracellularly, perhaps to iron or sulfur oxides consistent with mineralogy of this site. One lineage, called JdFR-78, has small genomes that are basal to the Aminicenantia class and potentially use "primordial" siroheme biosynthetic intermediates for heme synthesis, suggesting this lineage retain characteristics of early evolved life. Lineage JdFR-78 contains CRISPR-Cas defenses to evade viruses, while other lineages contain prophage that may help prevent super-infection or no detectable viral defenses. Overall, genomic evidence points to Aminicenantia being well adapted to oceanic crust environments by taking advantage of simple organic molecules and extracellular electron transport.
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Affiliation(s)
- Anne E Booker
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | - Annabelle Adams-Beyea
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
- Eugene Lang College of Liberal Arts at The New School, New York City, NY, USA
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Olivia Nigro
- Department of Natural Science, Hawai'i Pacific University, Honolulu, HI, USA
| | - Michael S Rappé
- Hawai'i Institute of Marine Biology, SOEST, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | | | - Beth N Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
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5
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Nicholls JWF, Chin JP, Williams TA, Lenton TM, O’Flaherty V, McGrath JW. On the potential roles of phosphorus in the early evolution of energy metabolism. Front Microbiol 2023; 14:1239189. [PMID: 37601379 PMCID: PMC10433651 DOI: 10.3389/fmicb.2023.1239189] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
Energy metabolism in extant life is centered around phosphate and the energy-dense phosphoanhydride bonds of adenosine triphosphate (ATP), a deeply conserved and ancient bioenergetic system. Yet, ATP synthesis relies on numerous complex enzymes and has an autocatalytic requirement for ATP itself. This implies the existence of evolutionarily simpler bioenergetic pathways and potentially primordial alternatives to ATP. The centrality of phosphate in modern bioenergetics, coupled with the energetic properties of phosphorylated compounds, may suggest that primordial precursors to ATP also utilized phosphate in compounds such as pyrophosphate, acetyl phosphate and polyphosphate. However, bioavailable phosphate may have been notably scarce on the early Earth, raising doubts about the roles that phosphorylated molecules might have played in the early evolution of life. A largely overlooked phosphorus redox cycle on the ancient Earth might have provided phosphorus and energy, with reduced phosphorus compounds potentially playing a key role in the early evolution of energy metabolism. Here, we speculate on the biological phosphorus compounds that may have acted as primordial energy currencies, sources of environmental energy, or sources of phosphorus for the synthesis of phosphorylated energy currencies. This review encompasses discussions on the evolutionary history of modern bioenergetics, and specifically those pathways with primordial relevance, and the geochemistry of bioavailable phosphorus on the ancient Earth. We highlight the importance of phosphorus, not only in the form of phosphate, to early biology and suggest future directions of study that may improve our understanding of the early evolution of bioenergetics.
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Affiliation(s)
- Jack W. F. Nicholls
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
| | - Jason P. Chin
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
| | - Tom A. Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Timothy M. Lenton
- Global Systems Institute, University of Exeter, Exeter, United Kingdom
| | | | - John W. McGrath
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
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6
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Barrera-Rojas J, Gurubel-Tun KJ, Ríos-Castro E, López-Méndez MC, Sulbarán-Rangel B. An Initial Proteomic Analysis of Biogas-Related Metabolism of Euryarchaeota Consortia in Sediments from the Santiago River, México. Microorganisms 2023; 11:1640. [PMID: 37512813 PMCID: PMC10384328 DOI: 10.3390/microorganisms11071640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
In this paper, sediments from the Santiago River were characterized to look for an alternative source of inoculum for biogas production. A proteomic analysis of methane-processing archaea present in these sediments was carried out. The Euryarchaeota superkingdom of archaea is responsible for methane production and methane assimilation in the environment. The Santiago River is a major river in México with great pollution and exceeded recovery capacity. Its sediments could contain nutrients and the anaerobic conditions for optimal growth of Euryarchaeota consortia. Batch bioreactor experiments were performed, and a proteomic analysis was conducted with current database information. The maximum biogas production was 266 NmL·L-1·g VS-1, with 33.34% of methane, and for proteomics, 3206 proteins were detected from 303 species of 69 genera. Most of them are metabolically versatile members of the genera Methanosarcina and Methanosarcinales, both with 934 and 260 proteins, respectively. These results showed a diverse euryarcheotic species with high potential to methane production. Although related proteins were found and could be feeding this metabolism through the methanol and acetyl-CoA pathways, the quality obtained from the biogas suggests that this metabolism is not the main one in carbon use, possibly the sum of several conditions including growth conditions and the pollution present in these sediments.
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Affiliation(s)
- Jesús Barrera-Rojas
- Department of Water and Energy, Campus Tonalá, University of Guadalajara, Tonalá 45425, Mexico
| | - Kelly Joel Gurubel-Tun
- Department of Water and Energy, Campus Tonalá, University of Guadalajara, Tonalá 45425, Mexico
| | - Emmanuel Ríos-Castro
- Laboratorios Nacionales de Servicios Experimentales, Centro de Investigación y Estudios Avanzados del IPN, Ciudad de México 07000, Mexico
| | - María Cristina López-Méndez
- Wetlands and Environmental Sustainability Laboratory, Division of Graduate Studies and Research, Tecnológico Nacional de México/ITS de Misantla, Veracruz 93850, Mexico
| | - Belkis Sulbarán-Rangel
- Department of Water and Energy, Campus Tonalá, University of Guadalajara, Tonalá 45425, Mexico
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Trutschel LR, Kruger BR, Sackett JD, Chadwick GL, Rowe AR. Determining resident microbial community members and their correlations with geochemistry in a serpentinizing spring. Front Microbiol 2023; 14:1182497. [PMID: 37396382 PMCID: PMC10308030 DOI: 10.3389/fmicb.2023.1182497] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/24/2023] [Indexed: 07/04/2023] Open
Abstract
Terrestrial serpentinizing systems allow us insight into the realm of alkaliphilic microbial communities driven by geology in a way that is frequently more accessible than their deep subsurface or marine counterparts. However, these systems are also marked by geochemical and microbial community variation due to the interactions of serpentinized fluids with host geology and the surface environment. To separate the transient from the endemic microbes in a hyperalkaline environment, we assessed the Ney Springs terrestrial serpentinizing system microbial community and geochemistry at six time points over the span of a year. Using 16S rRNA gene surveys we observed 93 amplicon sequence variants (ASVs) that were found at every sampling event. This is compared to ~17,000 transient ASVs that were detected only once across the six sampling events. Of the resident community members, 16 of these ASVs were regularly greater than 1% of the community during every sampling period. Additionally, many of these core taxa experienced statistically significant changes in relative abundance with time. Variation in the abundance of some core populations correlated with geochemical variation. For example, members of the Tindallia group, showed a positive correlation with variation in levels of ammonia at the spring. Investigating the metagenome assembled genomes of these microbes revealed evidence of the potential for ammonia generation via Stickland reactions within Tindallia. This observation offers new insight into the origin of high ammonia concentrations (>70 mg/L) seen at this site. Similarly, the abundance of putative sulfur-oxidizing microbes like Thiomicrospira, Halomonas, and a Rhodobacteraceae species could be linked to changes observed in sulfur-oxidation intermediates like tetrathionate and thiosulfate. While these data supports the influence of core microbial community members on a hyperalkaline spring's geochemistry, there is also evidence that subsurface processes affect geochemistry and may impact community dynamics as well. Though the physiology and ecology of these astrobiologically relevant ecosystems are still being uncovered, this work helps identify a stable microbial community that impacts spring geochemistry in ways not previously observed in serpentinizing ecosystems.
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Affiliation(s)
- Leah R. Trutschel
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Brittany R. Kruger
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, Las Vegas, NV, United States
| | - Joshua D. Sackett
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Grayson L. Chadwick
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Annette R. Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
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Khomyakova MA, Merkel AY, Segliuk VS, Slobodkin AI. Desulfatitalea alkaliphila sp. nov., an alkalipilic sulfate- and arsenate- reducing bacterium isolated from a terrestrial mud volcano. Extremophiles 2023; 27:12. [PMID: 37178152 DOI: 10.1007/s00792-023-01297-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
A novel alkaliphilic sulfate-reducing bacterium, strain M08butT, was isolated from a salsa lake of terrestrial mud volcano (Taman Peninsula, Russia). Cells were rod-shaped, motile and Gram-stain-negative. The temperature range for growth was 15-42 °C (optimum at 30 °C). The pH range for growth was 7.0-11.0, with an optimum at pH 8.5-9.0 Strain M08butT used sulfate, thiosulfate, sulfite, dimethyl sulfoxide and arsenate as electron acceptors. Acetate, formate, butyrate, fumarate, succinate, glycerol and pyruvate were utilized as electron donors with sulfate. Fermentative growth was observed with fumarate, pyruvate, crotonate. Strain M08butT grew chemolithoautotrophically with H2 and CO2. The G + C content of the genomic DNA was 60.1%. The fatty acid profile of strain M08butT was characterized by the presence of anteiso-C15:0 as the major component (68.8%). The closest phylogenetic relative of strain M08butT was Desulfatitalea tepidiphila (the order Desulfobacterales) with 96.3% 16S rRNA gene sequence similarity. Based on the phenotypic, genotypic and phylogenetic characteristics of the isolate, strain M08butT is considered to represent a novel species of the genus Desulfatitalea, with proposed name Desulfatitalea alkaliphila sp. nov. The type strain of Desulfatitalea alkaliphila is M08butT (= KCTC 25382T = VKM B-3560T = DSM 113909T = JCM 39202T = UQM 41473T).
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Affiliation(s)
- M A Khomyakova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, Bld. 2, 119071, Moscow, Russia.
| | - A Yu Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, Bld. 2, 119071, Moscow, Russia
| | - V S Segliuk
- Gubkin University, Leninskiy Prospect, 65/1, 119991, Moscow, Russia
| | - A I Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, Bld. 2, 119071, Moscow, Russia
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9
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Glass JB, Elbon CE, Williams LD. Something old, something new, something borrowed, something blue: the anaerobic microbial ancestry of aerobic respiration. Trends Microbiol 2023; 31:135-141. [PMID: 36058785 DOI: 10.1016/j.tim.2022.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 01/27/2023]
Abstract
Aerobic respiration evolved by bricolage, with modules cobbled together as microbial biochemistry coevolved with Earth's geochemistry. The mitochondrial electron transport chain represents a patchwork of respiratory modules inherited from microbial methanogenesis, iron oxidation, anoxygenic photosynthesis, and denitrification pathways, and preserves a biochemical record of Earth's redox environment over its four-billion-year history. Imprints of the anoxic early Earth are recognizable in Complex I's numerous iron-sulfur cofactors and vestigial binding sites for ferredoxin, nickel-iron, and molybdopterin, whereas the more recent advent of oxygen as a terminal electron acceptor necessitated use of heme and copper cofactors by Complex IV. Bricolage of respiratory complexes resulted in supercomplexes for improved electron transfer efficiency in some bacteria and archaea, and in many eukaryotes. Accessory subunits evolved to wrap mitochondrial supercomplexes for improved assembly and stability. Environmental microbes with 'fossil' proteins that are similar to ancestral forms of the respiratory complexes deserve further scrutiny and may reveal new insights on the evolution of aerobic respiration.
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Affiliation(s)
- Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Claire E Elbon
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
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10
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Ridone P, Ishida T, Lin A, Humphreys DT, Giannoulatou E, Sowa Y, Baker MAB. The rapid evolution of flagellar ion selectivity in experimental populations of E. coli. SCIENCE ADVANCES 2022; 8:eabq2492. [PMID: 36417540 PMCID: PMC9683732 DOI: 10.1126/sciadv.abq2492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Determining which cellular processes facilitate adaptation requires a tractable experimental model where an environmental cue can generate variants that rescue function. The bacterial flagellar motor (BFM) is an excellent candidate-an ancient and highly conserved molecular complex for bacterial propulsion toward favorable environments. Motor rotation is often powered by H+ or Na+ ion transit through the torque-generating stator subunit of the motor complex, and ion selectivity has adapted over evolutionary time scales. Here, we used CRISPR engineering to replace the native Escherichia coli H+-powered stator with Na+-powered stator genes and report the spontaneous reversion of our edit in a low-sodium environment. We followed the evolution of the stators during their reversion to H+-powered motility and used both whole-genome and RNA sequencing to identify genes involved in the cell's adaptation. Our transplant of an unfit protein and the cells' rapid response to this edit demonstrate the adaptability of the stator subunit and highlight the hierarchical modularity of the flagellar motor.
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Affiliation(s)
- Pietro Ridone
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Tsubasa Ishida
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
- Research Center for Micro-Nano Technology, Hosei University, Tokyo, Japan
| | - Angela Lin
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - David T. Humphreys
- Victor Chang Cardiac Research Institute, Sydney, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Australia
| | | | - Yoshiyuki Sowa
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
- Research Center for Micro-Nano Technology, Hosei University, Tokyo, Japan
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, Australia
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Abstract
Little is known of acetogens in contemporary serpentinizing systems, despite widely supported theories that serpentinite-hosted environments supported the first life on Earth via acetogenesis. To address this knowledge gap, genome-resolved metagenomics was applied to subsurface fracture water communities from an area of active serpentinization in the Samail Ophiolite, Sultanate of Oman. Two deeply branching putative bacterial acetogen types were identified in the communities belonging to the Acetothermia (hereafter, types I and II) that exhibited distinct distributions among waters with lower and higher water-rock reaction (i.e., serpentinization influence), respectively. Metabolic reconstructions revealed contrasting core metabolic pathways of type I and II Acetothermia, including in acetogenic pathway components (e.g., bacterial- vs. archaeal-like carbon monoxide dehydrogenases [CODH], respectively), hydrogen use to drive acetogenesis, and chemiosmotic potential generation via respiratory (type I) or canonical acetogen ferredoxin-based complexes (type II). Notably, type II Acetothermia metabolic pathways allow for use of serpentinization-derived substrates and implicate them as key primary producers in contemporary hyperalkaline serpentinite environments. Phylogenomic analyses indicate that 1) archaeal-like CODH of the type II genomes and those of other serpentinite-associated Bacteria derive from a deeply rooted horizontal transfer or origin among archaeal methanogens and 2) Acetothermia are among the earliest evolving bacterial lineages. The discovery of dominant and early-branching acetogens in subsurface waters of the largest near-surface serpentinite formation provides insight into the physiological traits that likely facilitated rock-supported life to flourish on a primitive Earth and possibly on other rocky planets undergoing serpentinization.
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12
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Occurrence of Capnophilic Lactic Fermentation in the Hyperthermophilic Anaerobic Bacterium Thermotoga sp. Strain RQ7. Int J Mol Sci 2022; 23:ijms231912049. [PMID: 36233345 PMCID: PMC9570489 DOI: 10.3390/ijms231912049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 11/17/2022] Open
Abstract
Capnophilic lactic fermentation (CLF) is an anaplerotic pathway exclusively identified in the anaerobic hyperthermophilic bacterium Thermotoga neapolitana, a member of the order Thermotogales. The CO2-activated pathway enables non-competitive synthesis of hydrogen and L-lactic acid at high yields, making it an economically attractive process for bioenergy production. In this work, we discovered and characterized CLF in Thermotoga sp. strain RQ7, a naturally competent strain, opening a new avenue for molecular investigation of the pathway. Evaluation of the fermentation products and expression analyses of key CLF-genes by RT-PCR revealed similar CLF-phenotypes between T. neapolitana and T. sp. strain RQ7, which were absent in the non-CLF-performing strain T. maritima. Key CLF enzymes, such as PFOR, HYD, LDH, RNF, and NFN, are up-regulated in the two CLF strains. Another important finding is the up-regulation of V-ATPase, which couples ATP hydrolysis to proton transport across the membranes, in the two CLF-performing strains. The fact that V-ATPase is absent in T. maritima suggested that this enzyme plays a key role in maintaining the necessary proton gradient to support high demand of reducing equivalents for simultaneous hydrogen and lactic acid synthesis in CLF.
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13
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Trutschel LR, Chadwick GL, Kruger B, Blank JG, Brazelton WJ, Dart ER, Rowe AR. Investigation of microbial metabolisms in an extremely high pH marine-like terrestrial serpentinizing system: Ney Springs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 836:155492. [PMID: 35476949 DOI: 10.1016/j.scitotenv.2022.155492] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/06/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Ney Springs, a continental serpentinizing spring in northern California, has an exceptionally high reported pH (12.4) for a naturally occurring water source. With high conductivity fluids, it is geochemically more akin to marine serpentinizing systems than other terrestrial locations. Our geochemical analyses also revealed high sulfide concentrations (544 mg/L) and methane emissions (83% volume gas content) relative to other serpentinizing systems. Thermodynamic calculations were used to investigate the potential for substrates resulting from serpentinization to fuel microbial life, and were found to support the energetic feasibility of sulfate reduction, anaerobic methane oxidation, denitrification, and anaerobic sulfide oxidation within this system. Assessment of the microbial community via 16S rRNA taxonomic gene surveys and metagenome sequencing revealed a community composition dominated by poorly characterized members of the Izemoplasmatales and Clostridiales. The genomes of these dominant taxa point to a fermentative lifestyle, though other highly complete (>90%) metagenome assembled genomes support the potential for organisms to perform sulfate reduction, sulfur disproportionation and/or sulfur oxidation (aerobic and anaerobic). Two chemolithoheterotrophs identified in the metagenome, a Halomonas sp. and a Rhodobacteraceae sp., were isolated and shown to oxidize thiosulfate and were capable of growth in conditions up to pH 12.4. Despite being characteristic products of serpentinization reactions, little evidence was seen for hydrogen and methane utilization in the Ney Springs microbial community. Hydrogen is not highly abundant and could be consumed prior to reaching the spring community. Other metabolic strategies may be outcompeted by more energetically favorable heterotrophic or fermentation reactions, or even inhibited by other compounds in the spring such as ammonia. The unique geochemistry of Ney Springs provides an opportunity to study how local geology interacts with serpentinized fluids, while its microbial community can better inform us of the metabolic strategies employed in hyperalkaline environments.
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Affiliation(s)
- Leah R Trutschel
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Grayson L Chadwick
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Jennifer G Blank
- Blue Marble Space Institute of Science, Livermore, CA, USA; NASA Ames Research Center in Silicon Valley, Moffett Field, CA, USA
| | | | - Emily R Dart
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Annette R Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA.
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14
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White N, Sadeeshkumar H, Sun A, Sudarsan N, Breaker RR. Na + riboswitches regulate genes for diverse physiological processes in bacteria. Nat Chem Biol 2022; 18:878-885. [PMID: 35879547 PMCID: PMC9337991 DOI: 10.1038/s41589-022-01086-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 06/10/2022] [Indexed: 01/31/2023]
Abstract
Organisms presumably have mechanisms to monitor and physiologically adapt to changes in cellular Na+ concentrations. Only a single bacterial protein has previously been demonstrated to selectively sense Na+ and regulate gene expression. Here we report a riboswitch class, previously called the ‘DUF1646 motif’, whose members selectively sense Na+ and regulate the expression of genes relevant to sodium biology. Many proteins encoded by Na+-riboswitch-regulated genes are annotated as metal ion transporters, whereas others are involved in mitigating osmotic stress or harnessing Na+ gradients for ATP production. Na+ riboswitches exhibit dissociation constants in the low mM range, and strongly reject all other alkali and alkaline earth ions. Likewise, only Na+ triggers riboswitch-mediated transcription and gene expression changes. These findings reveal that some bacteria use Na+ riboswitches to monitor, adjust and exploit Na+ concentrations and gradients, and in some instances collaborate with c-di-AMP riboswitches to coordinate gene expression during osmotic stress. ![]()
Only one protein factor is known that senses Na+ and controls gene expression. The Breaker Laboratory describes a bacterial riboswitch class selective for Na+ that regulates genes important for Na+ homeostasis, pH maintenance, osmotic stress response and ATP synthesis.
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Affiliation(s)
- Neil White
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
| | - Harini Sadeeshkumar
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Anna Sun
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA. .,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA. .,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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15
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Marshansky V. Discovery and Study of Transmembrane Rotary Ion-Translocating Nano-Motors: F-ATPase/Synthase of Mitochondria/Bacteria and V-ATPase of Eukaryotic Cells. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:702-719. [PMID: 36171652 DOI: 10.1134/s000629792208003x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 06/16/2023]
Abstract
This review discusses the history of discovery and study of the operation of the two rotary ion-translocating ATPase nano-motors: (i) F-ATPase/synthase (holocomplex F1FO) of mitochondria/bacteria and (ii) eukaryotic V-ATPase (holocomplex V1VO). Vacuolar adenosine triphosphatase (V-ATPase) is a transmembrane multisubunit complex found in all eukaryotes from yeast to humans. It is structurally and functionally similar to the F-ATPase/synthase of mitochondria/bacteria and the A-ATPase/synthase of archaebacteria, which indicates a common evolutionary origin of the rotary ion-translocating nano-motors built into cell membranes and invented by Nature billions of years ago. Previously we have published several reviews on this topic with appropriate citations of our original research. This review is focused on the historical analysis of the discovery and study of transmembrane rotary ion-translocating ATPase nano-motors functioning in bacteria, eukaryotic cells and mitochondria of animals.
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16
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Buessecker S, Palmer M, Lai D, Dimapilis J, Mayali X, Mosier D, Jiao JY, Colman DR, Keller LM, St John E, Miranda M, Gonzalez C, Gonzalez L, Sam C, Villa C, Zhuo M, Bodman N, Robles F, Boyd ES, Cox AD, St Clair B, Hua ZS, Li WJ, Reysenbach AL, Stott MB, Weber PK, Pett-Ridge J, Dekas AE, Hedlund BP, Dodsworth JA. An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea. Nat Commun 2022; 13:3773. [PMID: 35773279 PMCID: PMC9246946 DOI: 10.1038/s41467-022-31452-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 06/17/2022] [Indexed: 11/19/2022] Open
Abstract
Trace metals have been an important ingredient for life throughout Earth's history. Here, we describe the genome-guided cultivation of a member of the elusive archaeal lineage Caldarchaeales (syn. Aigarchaeota), Wolframiiraptor gerlachensis, and its growth dependence on tungsten. A metagenome-assembled genome (MAG) of W. gerlachensis encodes putative tungsten membrane transport systems, as well as pathways for anaerobic oxidation of sugars probably mediated by tungsten-dependent ferredoxin oxidoreductases that are expressed during growth. Catalyzed reporter deposition-fluorescence in-situ hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (nanoSIMS) show that W. gerlachensis preferentially assimilates xylose. Phylogenetic analyses of 78 high-quality Wolframiiraptoraceae MAGs from terrestrial and marine hydrothermal systems suggest that tungsten-associated enzymes were present in the last common ancestor of extant Wolframiiraptoraceae. Our observations imply a crucial role for tungsten-dependent metabolism in the origin and evolution of this lineage, and hint at a relic metabolic dependence on this trace metal in early anaerobic thermophiles.
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Affiliation(s)
- Steffen Buessecker
- Department of Earth System Science, Stanford University, Stanford, CA, USA.
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA.
| | - Dengxun Lai
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Joshua Dimapilis
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Damon Mosier
- Department of Biology, California State University, San Bernardino, CA, USA
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Lisa M Keller
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Emily St John
- Department of Biology, Portland State University, Portland, OR, USA
| | - Michelle Miranda
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Cristina Gonzalez
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Lizett Gonzalez
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Christian Sam
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Christopher Villa
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Madeline Zhuo
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Nicholas Bodman
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Fernando Robles
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Alysia D Cox
- Department of Chemistry and Geochemistry, Montana Technological University, Butte, MT, USA
| | - Brian St Clair
- Department of Chemistry and Geochemistry, Montana Technological University, Butte, MT, USA
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
- College of Fisheries, Henan Normal University, Xinxiang, PR China
| | | | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of Merced, Merced, CA, USA
| | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, USA.
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17
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Namirimu T, Yang JA, Yang SH, Yu J, Kim YJ, Kwon KK. Proteiniclasticum aestuarii sp. nov., isolated from tidal flat sediment, and emended descriptions of the genus Proteiniclasticum and Proteiniclasticum ruminis. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005275] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium, designated SCR006T, was isolated from tidal flat sediment from Suncheon Bay, Republic of Korea. Cells of strain SCR006T were strictly anaerobic, motile cocci, Gram-reaction-negative, and catalase- and oxidase-negative. Growth was observed at 4–41 °C (optimum, 34–37 °C), at pH 6.5–10.0 (optimum, pH 7.0–7.5) and in presence of 0–8 % NaCl (optimum, 0–2 %). Fermentation products of peptone–yeast–glucose medium were acetate and ethanol. Results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SCR006T had high sequence similarity to
Proteiniclasticum ruminis
D3RC-2T (97.9 %), followed by
Youngiibacter multivorans
DSM 6139T (95.9 %) and
Youngiibacter fragilis
232.1T (95.0 %). The average nucleotide identity value between strain SCR006T and
P. ruminis
DSM 24773T was 72.7 %, which strongly supported that strain SCR006T reresents a novel species within the genus
Proteiniclasticum
. The major cellular fatty acids are iso-C15 : 0 (27.2 %) and anteiso-C15 : 0 (16.9 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unidentified phospholipids, an unidentified aminolipid and five unidentified lipids. The genomic size was 3.2 Mb with genomic DNA G+C content of 45.6 mol%. The results of 16S rRNA-based and genome-based phylogenetic tree analyses indicated that SCR006T should be assigned to the genus
Proteiniclasticum
. Strain SCR006T could be distinguished from
P. ruminis
D3RC-2T by its growth conditions, cell morphology and genomic characteristics. Based on the phenotypic, phylogenetic, genomic and chemotaxonomic features, strain SCR006T represents a novel species, for which the name Proteiniclasticum aestuarii sp. nov. is proposed, with the type strain SCR006T (=KCTC 25245T= JCM 34531T)
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Affiliation(s)
- Teddy Namirimu
- Major of Applied Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Jhung-Ahn Yang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Sung-Hyun Yang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Jihyun Yu
- Major of Applied Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Yun Jae Kim
- Major of Applied Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
- Major of Applied Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
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18
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Wang Y, Li W, Baker BJ, Zhou Y, He L, Danchin A, Li Q, Gao Z. Carbon metabolism and adaptation of hyperalkaliphilic microbes in serpentinizing spring of Manleluag, the Philippines. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:308-319. [PMID: 35199456 DOI: 10.1111/1758-2229.13052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Reduced substrates produced by the serpentinization reaction under hydration of olivine may have fuelled biological processes on early Earth. To understand the adaptive strategies and carbon metabolism of the microbes in the serpentinizing ecosystems, we reconstructed 18 draft genomes representing dominant species of Omnitrophicaeota, Gammaproteobacteria and Methanobacteria from the Manleluag serpentinizing spring in Zambales, Philippines (hyperalkaline and rich in methane and hydrogen). Phylogenomics revealed that two genomes were affiliated with a candidate phylum NPL-UPA2 and the references of all our genomes were derived from ground waters, hot springs and the deep biosphere. C1 metabolism appears to be widespread as most of the genomes code for methanogenesis, CO oxidation and CO2 fixation. However, likely due to the low CO2 concentration and election acceptors, the biomass in the spring was extremely low (<103 cell/ml). Various Na+ and K+ transporters and Na+ -driving ATPases appear to be encoded by these genomes, suggesting that nutrient acquisition, bioenergetics and normal cytoplasmic pH were dependent on Na+ and K+ pumps. Our results advance our understanding of the metabolic potentials and bioenergetics of serpentinizing springs and provide a framework of the ecology of early Earth.
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Affiliation(s)
- Yong Wang
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, P. R. China
| | - Wenli Li
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, P. R. China
| | - Brett J Baker
- Department of Integrative Biology and Marine Science, University of Texas Austin, Austin, TX, 78373, USA
| | - Yingli Zhou
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Lisheng He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, P. R. China
| | - Antoine Danchin
- Kodikos Labs, Institut Cochin, 24 rue du Faubourg Saint Jacques, Paris, 75014, France
| | - Qingmei Li
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Zhaoming Gao
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, P. R. China
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19
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'Whole Organism', Systems Biology, and Top-Down Criteria for Evaluating Scenarios for the Origin of Life. Life (Basel) 2021; 11:life11070690. [PMID: 34357062 PMCID: PMC8306273 DOI: 10.3390/life11070690] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022] Open
Abstract
While most advances in the study of the origin of life on Earth (OoLoE) are piecemeal, tested against the laws of chemistry and physics, ultimately the goal is to develop an overall scenario for life's origin(s). However, the dimensionality of non-equilibrium chemical systems, from the range of possible boundary conditions and chemical interactions, renders the application of chemical and physical laws difficult. Here we outline a set of simple criteria for evaluating OoLoE scenarios. These include the need for containment, steady energy and material flows, and structured spatial heterogeneity from the outset. The Principle of Continuity, the fact that all life today was derived from first life, suggests favoring scenarios with fewer non-analog (not seen in life today) to analog (seen in life today) transitions in the inferred first biochemical pathways. Top-down data also indicate that a complex metabolism predated ribozymes and enzymes, and that full cellular autonomy and motility occurred post-LUCA. Using these criteria, we find the alkaline hydrothermal vent microchamber complex scenario with a late evolving exploitation of the natural occurring pH (or Na+ gradient) by ATP synthase the most compelling. However, there are as yet so many unknowns, we also advocate for the continued development of as many plausible scenarios as possible.
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20
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Coskun D, Deshmukh R, Shivaraj SM, Isenring P, Bélanger RR. Lsi2: A black box in plant silicon transport. PLANT AND SOIL 2021; 466:1-20. [PMID: 34720209 PMCID: PMC8550040 DOI: 10.1007/s11104-021-05061-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/22/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Silicon (Si) is widely considered a non-essential but beneficial element for higher plants, providing broad protection against various environmental stresses (both biotic and abiotic), particularly in species that can readily absorb the element. Two plasma-membrane proteins are known to coordinate the radial transport of Si (in the form of Si(OH)4) from soil to xylem within roots: the influx channel Lsi1 and the efflux transporter Lsi2. From a structural and mechanistic perspective, much more is known about Lsi1 (a member of the NIP-III subgroup of the Major Intrinsic Proteins) compared to Lsi2 (a putative Si(OH)4/H+ antiporter, with some homology to bacterial anion transporters). SCOPE Here, we critically review the current state of understanding regarding the physiological role and molecular characteristics of Lsi2. We demonstrate that the structure-function relationship of Lsi2 is largely uncharted and that the standing transport model requires much better supportive evidence. We also provide (to our knowledge) the most current and extensive phylogenetic analysis of Lsi2 from all fully sequenced higher-plant genomes. We end by suggesting research directions and hypotheses to elucidate the properties of Lsi2. CONCLUSIONS Given that Lsi2 is proposed to mediate xylem Si loading and thus root-to-shoot translocation and biosilicification, it is imperative that the field of Si transport focus its efforts on a better understanding of this important topic. With this review, we aim to stimulate and advance research in the field of Si transport and thus better exploit Si to improve crop resilience and agricultural output. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11104-021-05061-1.
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Affiliation(s)
- Devrim Coskun
- Département de Phytologie, Faculté Des Sciences de L’Agriculture Et de L’Alimentation (FSAA), Université Laval, Québec, Québec Canada
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - S. M. Shivaraj
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
- CSIR-National Chemical Laboratory, Pune, India
| | - Paul Isenring
- Département de Médecine, Faculté de Médecine, Université Laval, Québec, Québec Canada
| | - Richard R. Bélanger
- Département de Phytologie, Faculté Des Sciences de L’Agriculture Et de L’Alimentation (FSAA), Université Laval, Québec, Québec Canada
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21
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Britto DT, Coskun D, Kronzucker HJ. Potassium physiology from Archean to Holocene: A higher-plant perspective. JOURNAL OF PLANT PHYSIOLOGY 2021; 262:153432. [PMID: 34034042 DOI: 10.1016/j.jplph.2021.153432] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/22/2021] [Accepted: 04/22/2021] [Indexed: 05/27/2023]
Abstract
In this paper, we discuss biological potassium acquisition and utilization processes over an evolutionary timescale, with emphasis on modern vascular plants. The quintessential osmotic and electrical functions of the K+ ion are shown to be intimately tied to K+-transport systems and membrane energization. Several prominent themes in plant K+-transport physiology are explored in greater detail, including: (1) channel mediated K+ acquisition by roots at low external [K+]; (2) K+ loading of root xylem elements by active transport; (3) variations on the theme of K+ efflux from root cells to the extracellular environment; (4) the veracity and utility of the "affinity" concept in relation to transport systems. We close with a discussion of the importance of plant-potassium relations to our human world, and current trends in potassium nutrition from farm to table.
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Affiliation(s)
- Dev T Britto
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Devrim Coskun
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation (FSAA), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Herbert J Kronzucker
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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22
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Zubareva VM, Lapashina AS, Shugaeva TE, Litvin AV, Feniouk BA. Rotary Ion-Translocating ATPases/ATP Synthases: Diversity, Similarities, and Differences. BIOCHEMISTRY (MOSCOW) 2021; 85:1613-1630. [PMID: 33705299 DOI: 10.1134/s0006297920120135] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Ion-translocating ATPases and ATP synthases (F-, V-, A-type ATPases, and several P-type ATPases and ABC-transporters) catalyze ATP hydrolysis or ATP synthesis coupled with the ion transport across the membrane. F-, V-, and A-ATPases are protein nanomachines that combine transmembrane transport of protons or sodium ions with ATP synthesis/hydrolysis by means of a rotary mechanism. These enzymes are composed of two multisubunit subcomplexes that rotate relative to each other during catalysis. Rotary ATPases phosphorylate/dephosphorylate nucleotides directly, without the generation of phosphorylated protein intermediates. F-type ATPases are found in chloroplasts, mitochondria, most eubacteria, and in few archaea. V-type ATPases are eukaryotic enzymes present in a variety of cellular membranes, including the plasma membrane, vacuoles, late endosomes, and trans-Golgi cisternae. A-type ATPases are found in archaea and some eubacteria. F- and A-ATPases have two main functions: ATP synthesis powered by the proton motive force (pmf) or, in some prokaryotes, sodium-motive force (smf) and generation of the pmf or smf at the expense of ATP hydrolysis. In prokaryotes, both functions may be vitally important, depending on the environment and the presence of other enzymes capable of pmf or smf generation. In eukaryotes, the primary and the most crucial function of F-ATPases is ATP synthesis. Eukaryotic V-ATPases function exclusively as ATP-dependent proton pumps that generate pmf necessary for the transmembrane transport of ions and metabolites and are vitally important for pH regulation. This review describes the diversity of rotary ion-translocating ATPases from different organisms and compares the structural, functional, and regulatory features of these enzymes.
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Affiliation(s)
- V M Zubareva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - A S Lapashina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - T E Shugaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - A V Litvin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - B A Feniouk
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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23
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Kozlova MI, Bushmakin IM, Belyaeva JD, Shalaeva DN, Dibrova DV, Cherepanov DA, Mulkidjanian AY. Expansion of the "Sodium World" through Evolutionary Time and Taxonomic Space. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:1518-1542. [PMID: 33705291 DOI: 10.1134/s0006297920120056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In 1986, Vladimir Skulachev and his colleagues coined the term "Sodium World" for the group of diverse organisms with sodium (Na)-based bioenergetics. Albeit only few such organisms had been discovered by that time, the authors insightfully noted that "the great taxonomic variety of organisms employing the Na-cycle points to the ubiquitous distribution of this novel type of membrane-linked energy transductions". Here we used tools of bioinformatics to follow expansion of the Sodium World through the evolutionary time and taxonomic space. We searched for those membrane protein families in prokaryotic genomes that correlate with the use of the Na-potential for ATP synthesis by different organisms. In addition to the known Na-translocators, we found a plethora of uncharacterized protein families; most of them show no homology with studied proteins. In addition, we traced the presence of Na-based energetics in many novel archaeal and bacterial clades, which were recently identified by metagenomic techniques. The data obtained support the view that the Na-based energetics preceded the proton-dependent energetics in evolution and prevailed during the first two billion years of the Earth history before the oxygenation of atmosphere. Hence, the full capacity of Na-based energetics in prokaryotes remains largely unexplored. The Sodium World expanded owing to the acquisition of new functions by Na-translocating systems. Specifically, most classes of G-protein-coupled receptors (GPCRs), which are targeted by almost half of the known drugs, appear to evolve from the Na-translocating microbial rhodopsins. Thereby the GPCRs of class A, with 700 representatives in human genome, retained the Na-binding site in the center of the transmembrane heptahelical bundle together with the capacity of Na-translocation. Mathematical modeling showed that the class A GPCRs could use the energy of transmembrane Na-potential for increasing both their sensitivity and selectivity. Thus, GPCRs, the largest protein family coded by human genome, stem from the Sodium World, which encourages exploration of other Na-dependent enzymes of eukaryotes.
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Affiliation(s)
- M I Kozlova
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - I M Bushmakin
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - J D Belyaeva
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - D N Shalaeva
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany.
| | - D V Dibrova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - D A Cherepanov
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - A Y Mulkidjanian
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia
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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] [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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25
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Zhong H, Lehtovirta-Morley L, Liu J, Zheng Y, Lin H, Song D, Todd JD, Tian J, Zhang XH. Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms. MICROBIOME 2020; 8:78. [PMID: 32482169 PMCID: PMC7265257 DOI: 10.1186/s40168-020-00849-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/27/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans-the hadal zone (depth > 6000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the "shallower" deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water. RESULTS In this study, metagenomic data were obtained from 0-10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1000-4000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics, we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+ and Na+ respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. We also found that hadal MGI have the genetic potential to import a far higher range of organic compounds than their shallower water counterparts. Despite this trait, hadal MDI ammonia oxidation and carbon fixation genes are highly transcribed providing evidence they are likely autotrophic, contributing to the primary production in the aphotic deep sea. CONCLUSIONS Our study reveals potentially novel adaptation mechanisms of deep-sea thaumarchaeotal clades and suggests key functions of deep-sea Thaumarchaeota in carbon and nitrogen cycling. Video Abstract.
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Affiliation(s)
- Haohui Zhong
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Laura Lehtovirta-Morley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Jiwen Liu
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yanfen Zheng
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Heyu Lin
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Delei Song
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100, China.
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26
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Mencía M. The archaeal-bacterial lipid divide, could a distinct lateral proton route hold the answer? Biol Direct 2020; 15:7. [PMID: 32317017 PMCID: PMC7171761 DOI: 10.1186/s13062-020-00262-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/03/2020] [Indexed: 11/17/2022] Open
Abstract
The archaea-bacteria lipid divide is one of the big evolutionary enigmas concerning these two domains of life. In short, bacterial membranes are made of fatty-acid esters whereas archaeal ones contain isoprenoid ethers, though at present we do not have a good understanding on why they evolved differently. The lateral proton transfer mode of energy transduction in membranes posits that protons utilize the solvation layer of the membrane interface as the main route between proton pumps and ATPases, avoiding dissipation of energy to the bulk phase. In this article I present the hypothesis on a proton-transport route through the ester groups of bacterial phospholipids as an explanation for the evolutionary divergence seen between bacteria and archaea. REVIEWERS: This article was reviewed by Uri Gophna (Editorial Board member) and Víctor Sojo.
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Affiliation(s)
- Mario Mencía
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid - Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain.
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27
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Galperin MY, Kristensen DM, Makarova KS, Wolf YI, Koonin EV. Microbial genome analysis: the COG approach. Brief Bioinform 2020; 20:1063-1070. [PMID: 28968633 DOI: 10.1093/bib/bbx117] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/01/2017] [Indexed: 11/15/2022] Open
Abstract
For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis.
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28
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Abstract
The bacterial flagellar motor is driven by an ion flux that is converted to torque by motor-attendant complexes known as stators. The dynamics of stator assembly around the motor in response to external stimuli have been the subject of much recent research, but less is known about the evolutionary origins of stator complexes and how they select for specific ions. Here, we review the latest structural and biochemical data for the stator complexes and compare these with other ion transporters and microbial motors to examine possible evolutionary origins of the stator complex.
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29
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Yichie Y, Hasan MT, Tobias PA, Pascovici D, Goold HD, Van Sluyter SC, Roberts TH, Atwell BJ. Salt-Treated Roots of Oryza australiensis Seedlings are Enriched with Proteins Involved in Energetics and Transport. Proteomics 2019; 19:e1900175. [PMID: 31475433 DOI: 10.1002/pmic.201900175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/05/2019] [Indexed: 11/08/2022]
Abstract
Salinity is a major constraint on rice productivity worldwide. However, mechanisms of salt tolerance in wild rice relatives are unknown. Root microsomal proteins are extracted from two Oryza australiensis accessions contrasting in salt tolerance. Whole roots of 2-week-old seedlings are treated with 80 mM NaCl for 30 days to induce salt stress. Proteins are quantified by tandem mass tags (TMT) and triple-stage Mass Spectrometry. More than 200 differentially expressed proteins between the salt-treated and control samples in the two accessions (p-value <0.05) are found. Gene Ontology (GO) analysis shows that proteins categorized as "metabolic process," "transport," and "transmembrane transporter" are highly responsive to salt treatment. In particular, mitochondrial ATPases and SNARE proteins are more abundant in roots of the salt-tolerant accession and responded strongly when roots are exposed to salinity. mRNA quantification validated the elevated protein abundances of a monosaccharide transporter and an antiporter observed in the salt-tolerant genotype. The importance of the upregulated monosaccharide transporter and a VAMP-like protein by measuring salinity responses of two yeast knockout mutants for genes homologous to those encoding these proteins in rice are confirmed. Potential new mechanisms of salt tolerance in rice, with implications for breeding of elite cultivars are also discussed.
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Affiliation(s)
- Yoav Yichie
- Sydney Institute of Agriculture, University of Sydney, Sydney, Australia
| | - Mafruha T Hasan
- Sydney Institute of Agriculture, University of Sydney, Sydney, Australia
| | - Peri A Tobias
- Sydney Institute of Agriculture, University of Sydney, Sydney, Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility, Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Hugh D Goold
- NSW Department of Primary Industries, Macquarie University, Sydney, Australia.,Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | | | - Thomas H Roberts
- Sydney Institute of Agriculture, University of Sydney, Sydney, Australia
| | - Brian J Atwell
- Department of Biological Sciences, Macquarie University, Sydney, Australia
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30
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Shalaeva DN, Cherepanov DA, Galperin MY, Vriend G, Mulkidjanian AY. G protein-coupled receptors of class A harness the energy of membrane potential to increase their sensitivity and selectivity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183051. [PMID: 31449800 DOI: 10.1016/j.bbamem.2019.183051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/28/2019] [Accepted: 08/21/2019] [Indexed: 12/31/2022]
Abstract
The human genome contains about 700 genes of G protein-coupled receptors (GPCRs) of class A; these seven-helical membrane proteins are the targets of almost half of all known drugs. In the middle of the helix bundle, crystal structures reveal a highly conserved sodium-binding site, which is connected with the extracellular side by a water-filled tunnel. This binding site contains a sodium ion in those GPCRs that are crystallized in their inactive conformations but does not in those GPCRs that are trapped in agonist-bound active conformations. The escape route of the sodium ion upon the inactive-to-active transition and its very direction have until now remained obscure. Here, by modeling the available experimental data, we show that the sodium gradient over the cell membrane increases the sensitivity of GPCRs if their activation is thermodynamically coupled to the sodium ion translocation into the cytoplasm but decreases it if the sodium ion retreats into the extracellular space upon receptor activation. The model quantitatively describes the available data on both activation and suppression of distinct GPCRs by membrane voltage. The model also predicts selective amplification of the signal from (endogenous) agonists if only they, but not their (partial) analogs, induce sodium translocation. Comparative structure and sequence analyses of sodium-binding GPCRs indicate a key role for the conserved leucine residue in the second transmembrane helix (Leu2.46) in coupling sodium translocation to receptor activation. Hence, class A GPCRs appear to harness the energy of the transmembrane sodium potential to increase their sensitivity and selectivity.
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Affiliation(s)
- Daria N Shalaeva
- School of Physics, Osnabrueck University, 49069 Osnabrück, Germany; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Dmitry A Cherepanov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; N.N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, 117977 Moscow, Russia.
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, 6525 HP Nijmegen, the Netherlands.
| | - Armen Y Mulkidjanian
- School of Physics, Osnabrueck University, 49069 Osnabrück, Germany; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia.
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31
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Sun D, Wan X, Liu W, Xia X, Huang F, Wang A, Smith JA, Dang Y, Holmes DE. Characterization of the genome from Geobacter anodireducens, a strain with enhanced current production in bioelectrochemical systems. RSC Adv 2019; 9:25890-25899. [PMID: 35530078 PMCID: PMC9070056 DOI: 10.1039/c9ra02343g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/20/2019] [Indexed: 11/21/2022] Open
Abstract
Geobacter anodireducens is unique in that it can generate high current densities in bioelectrochemical systems (BES) operating under high salt conditions. This ability is important for the development of BES treating high salt wastewater and microbial desalination cells. Therefore, the genome of G. anodireducens was characterized to identify proteins that might allow this strain to survive in high salt BES. Comparison to other Geobacter species revealed that 81 of its 87 c-type cytochromes had homologs in G. soli and G. sulfurreducens. Genes coding for many extracellular electron transfer proteins were also detected, including the outer membrane c-type cytochromes OmcS and OmcZ and the soluble c-type cytochrome PgcA. G. anodireducens also appears to have numerous membrane complexes involved in the translocation of protons and sodium ions and channels that provide protection against osmotic shock. In addition, it has more DNA repair genes than most Geobacter species, suggesting that it might be able to more rapidly repair DNA damage caused in high salt and low pH anode environments. Although this genomic analysis provides invaluable insight into mechanisms used by G. anodireducens to survive in high salt BES, genetic, transcriptomic, and proteomic studies will need to be done to validate their roles.
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Affiliation(s)
- Dan Sun
- Ocean College, Zhejiang University Zhoushan 316021 P. R. China
| | - Xinyuan Wan
- Ocean College, Zhejiang University Zhoushan 316021 P. R. China
| | - Wenzong Liu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, China Academy of Sciences Beijing 100084 P. R. China
| | - Xue Xia
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, China Academy of Sciences Beijing 100084 P. R. China
| | - Fangliang Huang
- College of Life Sciences, Zhejiang University Hangzhou 310058 P. R. China
| | - Aijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, China Academy of Sciences Beijing 100084 P. R. China
| | - Jessica A Smith
- Department of Biomolecular Sciences, Central Connecticut State University 1615 Stanley Street New Britain CT 06050 USA
| | - Yan Dang
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science & Engineering, Beijing Forestry University 35 Tsinghua East Road Beijing 100083 China
| | - Dawn E Holmes
- Department of Physical and Biological Sciences, Western New England University 1215 Wilbraham Rd Springfield MA 01190 USA
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32
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Tsallagov SI, Sorokin DY, Tikhonova TV, Popov VO, Muyzer G. Comparative Genomics of Thiohalobacter thiocyanaticus HRh1 T and Guyparkeria sp. SCN-R1, Halophilic Chemolithoautotrophic Sulfur-Oxidizing Gammaproteobacteria Capable of Using Thiocyanate as Energy Source. Front Microbiol 2019; 10:898. [PMID: 31118923 PMCID: PMC6504805 DOI: 10.3389/fmicb.2019.00898] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/09/2019] [Indexed: 12/01/2022] Open
Abstract
The genomes of Thiohalobacter thiocyanaticus and Guyparkeria (formerly known as Halothiobacillus) sp. SCN-R1, two gammaproteobacterial halophilic sulfur-oxidizing bacteria (SOB) capable of thiocyanate oxidation via the "cyanate pathway", have been analyzed with a particular focus on their thiocyanate-oxidizing potential and sulfur oxidation pathways. Both genomes encode homologs of the enzyme thiocyanate dehydrogenase (TcDH) that oxidizes thiocyanate via the "cyanate pathway" in members of the haloalkaliphilic SOB of the genus Thioalkalivibrio. However, despite the presence of conservative motives indicative of TcDH, the putative TcDH of the halophilic SOB have a low overall amino acid similarity to the Thioalkalivibrio enzyme, and also the surrounding genes in the TcDH locus were different. In particular, an alternative copper transport system Cus is present instead of Cop and a putative zero-valent sulfur acceptor protein gene appears just before TcDH. Moreover, in contrast to the thiocyanate-oxidizing Thioalkalivibrio species, both genomes of the halophilic SOB contained a gene encoding the enzyme cyanate hydratase. The sulfur-oxidizing pathway in the genome of Thiohalobacter includes a Fcc type of sulfide dehydrogenase, a rDsr complex/AprAB/Sat for oxidation of zero-valent sulfur to sulfate, and an incomplete Sox pathway, lacking SoxCD. The sulfur oxidation pathway reconstructed from the genome of Guyparkeria sp. SCN-R1 was more similar to that of members of the Thiomicrospira-Hydrogenovibrio group, including a Fcc type of sulfide dehydrogenase and a complete Sox complex. One of the outstanding properties of Thiohalobacter is the presence of a Na+-dependent ATP synthase, which is rarely found in aerobic Prokaryotes.Overall, the results showed that, despite an obvious difference in the general sulfur-oxidation pathways, halophilic and haloalkaliphilic SOB belonging to different genera within the Gammaproteobacteria developed a similar unique thiocyanate-degrading mechanism based on the direct oxidative attack on the sulfane atom of thiocyanate.
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Affiliation(s)
- Stanislav I. Tsallagov
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Tamara V. Tikhonova
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir O. Popov
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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Shanbhag AP. FabG: from a core to circumstantial catalyst. Biotechnol Lett 2019; 41:675-688. [PMID: 31037463 DOI: 10.1007/s10529-019-02678-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/22/2019] [Indexed: 12/30/2022]
Abstract
Core biochemical pathways such as Fatty-acid synthesis II (FAS II) is ascribed to the synthesis of fatty-acids, biotin and lipoic acid in prokaryotes. It has two dehydrogenases namely, FabG and FabI which interact with the fatty-acid chain bound to Acyl-carrier protein (ACP), a well-studied enzyme which binds to substrates of varying lengths. This protein-protein interaction 'broadens' the active site of these dehydrogenases thus, contributing to their flexible nature. This property is exploited for catalysing numerous chiral synthons, alkanes, long-chain alcohols and secondary metabolites in industries especially with FabG. FASI relegates FASII in eukaryotes making it a 'relic gene pool' and an antibacterial drug target with diverse inhibitor and substrate markush. FabG often substitutes other dehydrogenases for producing secondary metabolites in nature. This redundancy is probably due to gene duplication or addition events possibly making FabG, a progenitor to some of the complex short-chain dehydrogenases used in organisms and industries today.
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Affiliation(s)
- Anirudh P Shanbhag
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, India. .,Bugworks Research India Pvt. Ltd, C-CAMP, NCBS Campus, UAS-GKVK, Bellary Road, Bangalore, 560065, India.
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34
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Proton leakage across lipid bilayers: Oxygen atoms of phospholipid ester linkers align water molecules into transmembrane water wires. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:439-451. [PMID: 30904457 DOI: 10.1016/j.bbabio.2019.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/20/2019] [Accepted: 03/10/2019] [Indexed: 12/31/2022]
Abstract
Up to half of the cellular energy gets lost owing to membrane proton leakage. The permeability of lipid bilayers to protons is by several orders of magnitude higher than to other cations, which implies efficient proton-specific passages. The nature of these passages remains obscure. By combining experimental measurements of proton flow across phosphatidylcholine vesicles, steered molecular dynamics (MD) simulations of phosphatidylcholine bilayers and kinetic modelling, we have analyzed whether protons could pass between opposite phospholipid molecules when they sporadically converge. The MD simulations showed that each time, when the phosphorus atoms of the two phosphatidylcholine molecules got closer than 1.6 nm, the eight oxygen atoms of their ester linkages could form a transmembrane 'oxygen passage' along which several water molecules aligned into a water wire. Proton permeability along such water wires would be limited by rearrangement of oxygen atoms, which could explain the experimentally shown independence of the proton permeability of pH, H2O/D2O substitution, and membrane dipole potential. We suggest that protons can cross lipid bilayers by moving along short, self-sustaining water wires supported by oxygen atoms of lipid ester linkages.
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35
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Graf S, Brzezinski P, von Ballmoos C. The proton pumping bo oxidase from Vitreoscilla. Sci Rep 2019; 9:4766. [PMID: 30886219 PMCID: PMC6423279 DOI: 10.1038/s41598-019-40723-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/18/2019] [Indexed: 01/31/2023] Open
Abstract
The cytochrome bo3 quinol oxidase from Vitreoscilla (vbo3) catalyses oxidation of ubiquinol and reduction of O2 to H2O. Data from earlier studies suggested that the free energy released in this reaction is used to pump sodium ions instead of protons across a membrane. Here, we have studied the functional properties of heterologously expressed vbo3 with a variety of methods. (i) Following oxygen consumption with a Clark-type electrode, we did not observe a measurable effect of Na+ on the oxidase activity of purified vbo3 solubilized in detergent or reconstituted in liposomes. (ii) Using fluorescent dyes, we find that vbo3 does not pump Na+ ions, but H+ across the membrane, and that H+-pumping is not influenced by the presence of Na+. (iii) Using an oxygen pulse method, it was found that 2 H+/e- are ejected from proteoliposomes, in agreement with the values found for the H+-pumping bo3 oxidase of Escherichia coli (ecbo3). This coincides with the interpretation that 1 H+/e- is pumped across the membrane and 1 H+/e- is released during quinol oxidation. (iv) When the electron transfer kinetics of vbo3 upon reaction with oxygen were followed in single turnover experiments, a similar sequence of reaction steps was observed as reported for the E. coli enzyme and none of these reactions was notably affected by the presence of Na+. Overall the data show that vbo3 is a proton pumping terminal oxidase, behaving similarly to the Escherichia coli bo3 quinol oxidase.
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Affiliation(s)
- Simone Graf
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Christoph von Ballmoos
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland.
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36
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Nesbø CL, Charchuk R, Pollo SMJ, Budwill K, Kublanov IV, Haverkamp THA, Foght J. Genomic analysis of the mesophilic Thermotogae genusMesotogareveals phylogeographic structure and genomic determinants of its distinct metabolism. Environ Microbiol 2018; 21:456-470. [DOI: 10.1111/1462-2920.14477] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/15/2018] [Accepted: 11/06/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Camilla L. Nesbø
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
- BioZone, Department of Chemical Engineering and Applied Chemistry; Wallberg Building, University of Toronto; Toronto ON Canada
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences; University of Oslo; Blindern, Oslo Norway
| | - Rhianna Charchuk
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
| | - Stephen M. J. Pollo
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
| | | | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology; Russian Academy of Sciences; Moscow Russia
| | - Thomas H. A. Haverkamp
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences; University of Oslo; Blindern, Oslo Norway
- Norwegian Veterinary Institute; Oslo Norway
| | - Julia Foght
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
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37
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Suzuki S, Nealson KH, Ishii S. Genomic and in-situ Transcriptomic Characterization of the Candidate Phylum NPL-UPL2 From Highly Alkaline Highly Reducing Serpentinized Groundwater. Front Microbiol 2018; 9:3141. [PMID: 30619209 PMCID: PMC6305446 DOI: 10.3389/fmicb.2018.03141] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/04/2018] [Indexed: 12/05/2022] Open
Abstract
Serpentinization is a process whereby water interacts with reduced mantle rock called peridotite to produce a new suite of minerals (e.g., serpentine), a highly alkaline fluid, and hydrogen. In previous reports, we identified abundance of microbes of the candidate phylum NPL-UPA2 in a serpentinization site called The Cedars. Here, we report the first metagenome assembled genome (MAG) of the candidate phylum as well as the in-situ gene expression. The MAG of the phylum NPL-UPA2, named Unc8, is only about 1 Mbp and its biosynthetic properties suggest it should be capable of independent growth. In keeping with the highly reducing niche of Unc8, its genome encodes none of the known oxidative stress response genes including superoxide dismutases. With regard to energy metabolism, the MAG of Unc8 encodes all enzymes for Wood-Ljungdahl acetogenesis pathway, a ferredoxin:NAD+ oxidoreductase (Rnf) and electron carriers for flavin-based electron bifurcation (Etf, Hdr). Furthermore, the transcriptome of Unc8 in the waters of The Cedars showed enhanced levels of gene expression in the key enzymes of the Wood-Ljungdahl pathway [e.g., Carbon monoxide dehydrogenase /Acetyl-CoA synthase complex (CODH/ACS), Rnf, Acetyl-CoA synthetase (Acd)], which indicated that the Unc8 is an acetogen. However, the MAG of Unc8 encoded no well-known hydrogenase genes, suggesting that the energy metabolism of Unc8 might be focused on CO as the carbon and energy sources for the acetate formation. Given that CO could be supplied via abiotic reaction associated with deep subsurface serpentinization, while available CO2 would be at extremely low concentrations in this high pH environment, CO-associated metabolism could provide advantageous approach. The CODH/ACS in Unc8 is a Bacteria/Archaea hybrid type of six-subunit complex and the electron carriers, Etf and Hdr, showed the highest similarity to those in Archaea, suggesting that archaeal methanogenic energy metabolism was incorporated into the bacterial acetogenesis in NPL-UPA2. Given that serpentinization systems are viewed as potential habitats for early life, and that acetogenesis via the Wood-Ljungdahl pathway is proposed as an energy metabolism of Last Universal Common Ancestor, a phylogenetically distinct acetogen from an early earth analog site may provide important insights in primordial lithotrophs and their habitat.
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Affiliation(s)
- Shino Suzuki
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Nankoku, Japan.,Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, United States.,Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Shun'ichi Ishii
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, United States.,R&D Center for Submarine Resources, JAMSTEC, Nankoku, Japan
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38
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Tsunoda J, Song C, Imai FL, Takagi J, Ueno H, Murata T, Iino R, Murata K. Off-axis rotor in Enterococcus hirae V-ATPase visualized by Zernike phase plate single-particle cryo-electron microscopy. Sci Rep 2018; 8:15632. [PMID: 30353110 PMCID: PMC6199243 DOI: 10.1038/s41598-018-33977-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/09/2018] [Indexed: 12/25/2022] Open
Abstract
EhV-ATPase is an ATP-driven Na+ pump in the eubacteria Enterococcus hirae (Eh). Here, we present the first entire structure of detergent-solubilized EhV-ATPase by single-particle cryo-electron microscopy (cryo-EM) using Zernike phase plate. The cryo-EM map dominantly showed one of three catalytic conformations in this rotary enzyme. To further stabilize the originally heterogeneous structure caused by the ATP hydrolysis states of the V1-ATPases, a peptide epitope tag system was adopted, in which the inserted peptide epitope sequence interfered with rotation of the central rotor by binding the Fab. As a result, the map unexpectedly showed another catalytic conformation of EhV-ATPase. Interestingly, these two conformations identified with and without Fab conversely coincided with those of the minor state 2 and the major state 1 of Thermus thermophilus V/A-ATPase, respectively. The most prominent feature in EhV-ATPase was the off-axis rotor, where the cytoplasmic V1 domain was connected to the transmembrane Vo domain through the off-axis central rotor. Furthermore, compared to the structure of ATP synthases, the larger size of the interface between the transmembrane a-subunit and c-ring of EhV-ATPase would be more advantageous for active ion pumping.
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Affiliation(s)
- Jun Tsunoda
- The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan.,National Institute for Physiological Sciences, Okazaki, Aichi, 444-8585, Japan
| | - Chihong Song
- National Institute for Physiological Sciences, Okazaki, Aichi, 444-8585, Japan
| | - Fabiana Lica Imai
- Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba, 263-8522, Japan
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, 3-2 Suita, Osaka, 565-0871, Japan
| | - Hiroshi Ueno
- Department of Applied Chemistry, University of Tokyo, Tokyo, 113-8656, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba, 263-8522, Japan.,JST, PRESTO, Inage, Chiba, 263-8522, Japan
| | - Ryota Iino
- The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan.,Institute for Molecular Science, Okazaki, Aichi, 444-8787, Japan
| | - Kazuyoshi Murata
- The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan. .,National Institute for Physiological Sciences, Okazaki, Aichi, 444-8585, Japan.
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39
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Broadly conserved Na +-binding site in the N-lobe of prokaryotic multidrug MATE transporters. Proc Natl Acad Sci U S A 2018; 115:E6172-E6181. [PMID: 29915058 DOI: 10.1073/pnas.1802080115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Multidrug and toxic-compound extrusion (MATE) proteins comprise an important but largely uncharacterized family of secondary-active transporters. In both eukaryotes and prokaryotes, these transporters protect the cell by catalyzing the efflux of a broad range of cytotoxic compounds, including human-made antibiotics and anticancer drugs. MATEs are thus potential pharmacological targets against drug-resistant pathogenic bacteria and tumor cells. The activity of MATEs is powered by transmembrane electrochemical ion gradients, but their molecular mechanism and ion specificity are not understood, in part because high-quality structural information is limited. Here, we use computational methods to study PfMATE, from Pyrococcus furiosus, whose structure is the best resolved to date. Analysis of available crystallographic data and additional molecular dynamics simulations unequivocally reveal an occupied Na+-binding site in the N-lobe of this transporter, which had not been previously recognized. We find this site to be selective against K+ and broadly conserved among prokaryotic MATEs, including homologs known to be Na+-dependent such as NorM-VC, VmrA, and ClbM, for which the location of the Na+ site had been debated. We note, however, that the chemical makeup of the proposed Na+ site indicates it is weakly specific against H+, explaining why MATEs featuring this Na+-binding motif may be solely driven by H+ in laboratory conditions. We further posit that the concurrent coupling to H+ and Na+ gradients observed for some Na+-driven MATEs owes to a second H+-binding site, within the C-lobe. In summary, our study provides insights into the structural basis for the complex ion dependency of MATE transporters.
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40
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Figueroa IA, Barnum TP, Somasekhar PY, Carlström CI, Engelbrektson AL, Coates JD. Metagenomics-guided analysis of microbial chemolithoautotrophic phosphite oxidation yields evidence of a seventh natural CO 2 fixation pathway. Proc Natl Acad Sci U S A 2018; 115:E92-E101. [PMID: 29183985 PMCID: PMC5776814 DOI: 10.1073/pnas.1715549114] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dissimilatory phosphite oxidation (DPO), a microbial metabolism by which phosphite (HPO32-) is oxidized to phosphate (PO43-), is the most energetically favorable chemotrophic electron-donating process known. Only one DPO organism has been described to date, and little is known about the environmental relevance of this metabolism. In this study, we used 16S rRNA gene community analysis and genome-resolved metagenomics to characterize anaerobic wastewater treatment sludge enrichments performing DPO coupled to CO2 reduction. We identified an uncultivated DPO bacterium, Candidatus Phosphitivorax (Ca. P.) anaerolimi strain Phox-21, that belongs to candidate order GW-28 within the Deltaproteobacteria, which has no known cultured isolates. Genes for phosphite oxidation and for CO2 reduction to formate were found in the genome of Ca. P. anaerolimi, but it appears to lack any of the known natural carbon fixation pathways. These observations led us to propose a metabolic model for autotrophic growth by Ca. P. anaerolimi whereby DPO drives CO2 reduction to formate, which is then assimilated into biomass via the reductive glycine pathway.
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Affiliation(s)
- Israel A Figueroa
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Tyler P Barnum
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Pranav Y Somasekhar
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Charlotte I Carlström
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Anna L Engelbrektson
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - John D Coates
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
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41
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Dibrov P, Dibrov E, Pierce GN. Na+-NQR (Na+-translocating NADH:ubiquinone oxidoreductase) as a novel target for antibiotics. FEMS Microbiol Rev 2017; 41:653-671. [PMID: 28961953 DOI: 10.1093/femsre/fux032] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/17/2017] [Indexed: 01/08/2023] Open
Abstract
The recent breakthrough in structural studies on Na+-translocating NADH:ubiquinone oxidoreductase (Na+-NQR) from the human pathogen Vibrio cholerae creates a perspective for the systematic design of inhibitors for this unique enzyme, which is the major Na+ pump in aerobic pathogens. Widespread distribution of Na+-NQR among pathogenic species, its key role in energy metabolism, its relation to virulence in different species as well as its absence in eukaryotic cells makes this enzyme especially attractive as a target for prospective antibiotics. In this review, the major biochemical, physiological and, especially, the pharmacological aspects of Na+-NQR are discussed to assess its 'target potential' for drug development. A comparison to other primary bacterial Na+ pumps supports the contention that NQR is a first rate prospective target for a new generation of antimicrobials. A new, narrowly targeted furanone inhibitor of NQR designed in our group is presented as a molecular platform for the development of anti-NQR remedies.
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Affiliation(s)
- Pavel Dibrov
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Elena Dibrov
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St. Boniface Hospital, Winnipeg, Canada.,Department of Physiology and Pathophysiology, Colleges of Medicine and Pharmacy, Faculty of Health Sciences, Winnipeg, Canada
| | - Grant N Pierce
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St. Boniface Hospital, Winnipeg, Canada.,Department of Physiology and Pathophysiology, Colleges of Medicine and Pharmacy, Faculty of Health Sciences, Winnipeg, Canada
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42
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Melton ED, Sorokin DY, Overmars L, Lapidus AL, Pillay M, Ivanova N, Del Rio TG, Kyrpides NC, Woyke T, Muyzer G. Draft genome sequence of Dethiobacter alkaliphilus strain AHT1 T, a gram-positive sulfidogenic polyextremophile. Stand Genomic Sci 2017; 12:57. [PMID: 28943998 PMCID: PMC5609068 DOI: 10.1186/s40793-017-0268-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 09/08/2017] [Indexed: 12/01/2022] Open
Abstract
Dethiobacter alkaliphilus strain AHT1T is an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is a Gram-positive bacterium with low GC content, within the phylum Firmicutes. Here we report its draft genome sequence, which consists of 34 contigs with a total sequence length of 3.12 Mbp. D. alkaliphilus strain AHT1T was sequenced by the Joint Genome Institute (JGI) as part of the Community Science Program due to its relevance to bioremediation and biotechnological applications.
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Affiliation(s)
- Emily Denise Melton
- Department of Freshwater and Marine Ecology, Microbial Systems Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, RAS, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Lex Overmars
- Department of Freshwater and Marine Ecology, Microbial Systems Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Alla L Lapidus
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State, University, St. Petersburg, Russia
| | - Manoj Pillay
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | | | - Nikos C Kyrpides
- Joint Genome Institute, Walnut Creek, CA USA.,Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA.,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Tanja Woyke
- Joint Genome Institute, Walnut Creek, CA USA
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Microbial Systems Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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43
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Ryzhkova EP. Alternative enzymes as a special strategy for the adaptation of procaryotic organisms (Review). APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683817050131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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44
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Golyshina OV, Toshchakov SV, Makarova KS, Gavrilov SN, Korzhenkov AA, La Cono V, Arcadi E, Nechitaylo TY, Ferrer M, Kublanov IV, Wolf YI, Yakimov MM, Golyshin PN. 'ARMAN' archaea depend on association with euryarchaeal host in culture and in situ. Nat Commun 2017; 8:60. [PMID: 28680072 PMCID: PMC5498576 DOI: 10.1038/s41467-017-00104-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/31/2017] [Indexed: 11/09/2022] Open
Abstract
Intriguing, yet uncultured ‘ARMAN’-like archaea are metabolically dependent on other members of the microbial community. It remains uncertain though which hosts they rely upon, and, because of the lack of complete genomes, to what extent. Here, we report the co-culturing of ARMAN-2-related organism, Mia14, with Cuniculiplasma divulgatum PM4 during the isolation of this strain from acidic streamer in Parys Mountain (Isle of Anglesey, UK). Mia14 is highly enriched in the binary culture (ca. 10% genomic reads) and its ungapped 0.95 Mbp genome points at severe voids in central metabolic pathways, indicating dependence on the host, C. divulgatum PM4. Analysis of C. divulgatum isolates from different sites and shotgun sequence data of Parys Mountain samples suggests an extensive genetic exchange between Mia14 and hosts in situ. Within the subset of organisms with high-quality genomic assemblies representing the ‘DPANN’ superphylum, the Mia14 lineage has had the largest gene flux, with dozens of genes gained that are implicated in the host interaction. In the absence of complete genomes, the metabolic capabilities of uncultured ARMAN-like archaea have been uncertain. Here, Golyshina et al. apply an enrichment culture technique and find that the ungapped genome of the ARMAN-like archaeon Mia14 has lost key metabolic pathways, suggesting dependence on the host archaeon Cuniculiplasma divulgatum.
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Affiliation(s)
- Olga V Golyshina
- School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK.
| | | | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine-National Institutes of Health, Bethesda, MD, 20894, USA
| | - Sergey N Gavrilov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/2, Moscow, 117312, Russia
| | | | - Violetta La Cono
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Erika Arcadi
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Taras Y Nechitaylo
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, Jena, 07745, Germany
| | - Manuel Ferrer
- Institute of Catalysis CSIC, Campus Cantoblanco, 28049, Madrid, Spain
| | - Ilya V Kublanov
- Immanuel Kant Baltic Federal University, Kaliningrad, 236040, Russia.,Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/2, Moscow, 117312, Russia
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine-National Institutes of Health, Bethesda, MD, 20894, USA
| | - Michail M Yakimov
- Immanuel Kant Baltic Federal University, Kaliningrad, 236040, Russia.,Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
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45
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Novakovsky GE, Dibrova DV, Mulkidjanian AY. Phylogenomic Analysis of Type 1 NADH:Quinone Oxidoreductase. BIOCHEMISTRY (MOSCOW) 2017; 81:770-84. [PMID: 27449624 DOI: 10.1134/s0006297916070142] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We performed phylogenomic analysis of the catalytic core of NADH:quinone oxidoreductases of type 1 (NDH-1). Analysis of phylogenetic trees, as constructed for the core subunits of NDH-1, revealed fundamental differences in their topologies. In the case of four putatively homologous ion-carrying membrane subunits, the trees for the NuoH and NuoN subunits contained separate archaeal clades, whereas subunits NuoL and NuoM were characterized by multiple archaeal clades spread among bacterial branches. Large, separate clades, which united sequences belonging to different archaeal subdomains, were also found for cytoplasmic subunits NuoD and NuoB, homologous to the large and small subunits of nickel-iron hydrogenases. A smaller such clade was also shown for subunit NuoC. Based on these data, we suggest that the ancestral NDH-1 complex could be present already at the stage of the Last Universal Cellular Ancestor (LUCA). Ancestral forms of membrane subunits NuoN and NuoH and cytoplasmic subunits NuoD, NuoB, and, perhaps NuoC, may have formed a membrane complex that operated as an ion-translocating membrane hydrogenase. After the complex attained the ability to reduce membrane quinones, gene duplications could yield the subunits NuoL and NuoM, which enabled translocation of additional ions.
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Affiliation(s)
- G E Novakovsky
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
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46
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Two independent evolutionary routes to Na+/H+ cotransport function in membrane pyrophosphatases. Biochem J 2016; 473:3099-111. [DOI: 10.1042/bcj20160529] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 08/03/2016] [Indexed: 11/17/2022]
Abstract
Membrane-bound pyrophosphatases (mPPases) hydrolyze pyrophosphate (PPi) to transport H+, Na+ or both and help organisms to cope with stress conditions, such as high salinity or limiting nutrients. Recent elucidation of mPPase structure and identification of subfamilies that have fully or partially switched from Na+ to H+ pumping have established mPPases as versatile models for studying the principles governing the mechanism, specificity and evolution of cation transporters. In the present study, we constructed an accurate phylogenetic map of the interface of Na+-transporting PPases (Na+-PPases) and Na+- and H+-transporting PPases (Na+,H+-PPases), which guided our experimental exploration of the variations in PPi hydrolysis and ion transport activities during evolution. Surprisingly, we identified two mPPase lineages that independently acquired physiologically significant Na+ and H+ cotransport function. Na+,H+-PPases of the first lineage transport H+ over an extended [Na+] range, but progressively lose H+ transport efficiency at high [Na+]. In contrast, H+-transport by Na+,H+-PPases of the second lineage is not inhibited by up to 100 mM Na+. With the identification of Na+,H+-PPase subtypes, the mPPases protein superfamily appears as a continuum, ranging from monospecific Na+ transporters to transporters with tunable levels of Na+ and H+ cotransport and further to monospecific H+ transporters. Our results lend credence to the concept that Na+ and H+ are transported by similar mechanisms, allowing the relative efficiencies of Na+ and H+ transport to be modulated by minor changes in protein structure during the course of adaptation to a changing environment.
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Jackson JB. Natural pH Gradients in Hydrothermal Alkali Vents Were Unlikely to Have Played a Role in the Origin of Life. J Mol Evol 2016; 83:1-11. [PMID: 27534947 PMCID: PMC4999464 DOI: 10.1007/s00239-016-9756-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/09/2016] [Indexed: 12/01/2022]
Abstract
The hypothesis that a natural pH gradient across inorganic membranes lying between the ocean and fluid issuing from hydrothermal alkali vents provided energy to drive chemical reactions during the origin of life has an attractive parallel with chemiosmotic ATP synthesis in present-day organisms. However, arguments raised in this review suggest that such natural pH gradients are unlikely to have played a part in life’s origin. There is as yet no evidence for thin inorganic membranes holding sharp pH gradients in modern hydrothermal alkali vents at Lost City near the Mid-Atlantic Ridge. Proposed models of non-protein forms of the H+-pyrophosphate synthase that could have functioned as a molecular machine utilizing the energy of a natural pH gradient are unsatisfactory. Some hypothetical designs of non-protein motors utilizing a natural pH gradient to drive redox reactions are plausible but complex, and such motors are deemed unlikely to have assembled by chance in prebiotic times. Small molecular motors comprising a few hundred atoms would have been unable to function in the relatively thick (>1 μm) inorganic membranes that have hitherto been used as descriptive models for the natural pH gradient hypothesis. Alternative hypotheses for the evolution of chemiosmotic systems following the emergence of error-prone gene replication and translation are more likely to be correct.
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Affiliation(s)
- J Baz Jackson
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
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48
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The physiology and habitat of the last universal common ancestor. Nat Microbiol 2016; 1:16116. [DOI: 10.1038/nmicrobiol.2016.116] [Citation(s) in RCA: 545] [Impact Index Per Article: 68.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/21/2016] [Indexed: 02/03/2023]
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Mazhab-Jafari MT, Rubinstein JL. Cryo-EM studies of the structure and dynamics of vacuolar-type ATPases. SCIENCE ADVANCES 2016; 2:e1600725. [PMID: 27532044 PMCID: PMC4985227 DOI: 10.1126/sciadv.1600725] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/15/2016] [Indexed: 06/06/2023]
Abstract
Electron cryomicroscopy (cryo-EM) has significantly advanced our understanding of molecular structure in biology. Recent innovations in both hardware and software have made cryo-EM a viable alternative for targets that are not amenable to x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Cryo-EM has even become the method of choice in some situations where x-ray crystallography and NMR spectroscopy are possible but where cryo-EM can determine structures at higher resolution or with less time or effort. Rotary adenosine triphosphatases (ATPases) are crucial to the maintenance of cellular homeostasis. These enzymes couple the synthesis or hydrolysis of adenosine triphosphate to the use or production of a transmembrane electrochemical ion gradient, respectively. However, the membrane-embedded nature and conformational heterogeneity of intact rotary ATPases have prevented their high-resolution structural analysis to date. Recent application of cryo-EM methods to the different types of rotary ATPase has led to sudden advances in understanding the structure and function of these enzymes, revealing significant conformational heterogeneity and characteristic transmembrane α helices that are highly tilted with respect to the membrane. In this Review, we will discuss what has been learned recently about rotary ATPase structure and function, with a particular focus on the vacuolar-type ATPases.
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Affiliation(s)
- Mohammad T. Mazhab-Jafari
- Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
| | - John L. Rubinstein
- Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, The University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada
- Department of Medical Biophysics, The University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
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Spring S, Bunk B, Spröer C, Schumann P, Rohde M, Tindall BJ, Klenk HP. Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum. ISME JOURNAL 2016; 10:2801-2816. [PMID: 27300277 PMCID: PMC5148204 DOI: 10.1038/ismej.2016.84] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 04/15/2016] [Accepted: 04/21/2016] [Indexed: 12/29/2022]
Abstract
The recently isolated strain L21-Fru-ABT represents moderately halophilic, obligately anaerobic and saccharolytic bacteria that thrive in the suboxic transition zones of hypersaline microbial mats. Phylogenetic analyses based on 16S rRNA genes, RpoB proteins and gene content indicated that strain L21-Fru-ABT represents a novel species and genus affiliated with a distinct phylum-level lineage originally designated Verrucomicrobia subdivision 5. A survey of environmental 16S rRNA gene sequences revealed that members of this newly recognized phylum are wide-spread and ecologically important in various anoxic environments ranging from hypersaline sediments to wastewater and the intestine of animals. Characteristic phenotypic traits of the novel strain included the formation of extracellular polymeric substances, a Gram-negative cell wall containing peptidoglycan and the absence of odd-numbered cellular fatty acids. Unusual metabolic features deduced from analysis of the genome sequence were the production of sucrose as osmoprotectant, an atypical glycolytic pathway lacking pyruvate kinase and the synthesis of isoprenoids via mevalonate. On the basis of the analyses of phenotypic, genomic and environmental data, it is proposed that strain L21-Fru-ABT and related bacteria are specifically adapted to the utilization of sulfated glycopolymers produced in microbial mats or biofilms.
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Affiliation(s)
- Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Department Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Department Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Peter Schumann
- Department Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz-Centre of Infection Research, Braunschweig, Germany
| | - Brian J Tindall
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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