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Murray L, Fullerton H, Moyer CL. Microbial metabolic potential of hydrothermal vent chimneys along the submarine ring of fire. Front Microbiol 2024; 15:1399422. [PMID: 39165569 PMCID: PMC11333457 DOI: 10.3389/fmicb.2024.1399422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 07/22/2024] [Indexed: 08/22/2024] Open
Abstract
Hydrothermal vents host a diverse community of microorganisms that utilize chemical gradients from the venting fluid for their metabolisms. The venting fluid can solidify to form chimney structures that these microbes adhere to and colonize. These chimney structures are found throughout many different locations in the world's oceans. In this study, comparative metagenomic analyses of microbial communities on five chimney structures from around the Pacific Ocean were elucidated focusing on the core taxa and genes that are characteristic of each of these hydrothermal vent chimneys. The differences among the taxa and genes found at each chimney due to parameters such as physical characteristics, chemistry, and activity of the vents were highlighted. DNA from the chimneys was sequenced, assembled into contigs, and annotated for gene function. Genes used for carbon, oxygen, sulfur, nitrogen, iron, and arsenic metabolisms were found at varying abundances at each of the chimneys, largely from either Gammaproteobacteria or Campylobacteria. Many taxa shared an overlap of these functional metabolic genes, indicating that functional redundancy is critical for life at these hydrothermal vents. A high relative abundance of oxygen metabolism genes coupled with a low abundance of carbon fixation genes could be used as a unique identifier for inactive chimneys. Genes used for DNA repair, chemotaxis, and transposases were found at high abundances at each of these hydrothermal chimneys allowing for enhanced adaptations to the ever-changing chemical and physical conditions encountered.
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Affiliation(s)
- Laura Murray
- Department of Biology, Western Washington University, Bellingham, WA, United States
| | - Heather Fullerton
- Department of Biology, College of Charleston, Charleston, SC, United States
| | - Craig L. Moyer
- Department of Biology, Western Washington University, Bellingham, WA, United States
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2
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de Pins B, Greenspoon L, Bar-On YM, Shamshoum M, Ben-Nissan R, Milshtein E, Davidi D, Sharon I, Mueller-Cajar O, Noor E, Milo R. A systematic exploration of bacterial form I rubisco maximal carboxylation rates. EMBO J 2024; 43:3072-3083. [PMID: 38806660 PMCID: PMC11251275 DOI: 10.1038/s44318-024-00119-z] [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: 02/01/2024] [Revised: 03/26/2024] [Accepted: 04/22/2024] [Indexed: 05/30/2024] Open
Abstract
Autotrophy is the basis for complex life on Earth. Central to this process is rubisco-the enzyme that catalyzes almost all carbon fixation on the planet. Yet, with only a small fraction of rubisco diversity kinetically characterized so far, the underlying biological factors driving the evolution of fast rubiscos in nature remain unclear. We conducted a high-throughput kinetic characterization of over 100 bacterial form I rubiscos, the most ubiquitous group of rubisco sequences in nature, to uncover the determinants of rubisco's carboxylation velocity. We show that the presence of a carboxysome CO2 concentrating mechanism correlates with faster rubiscos with a median fivefold higher rate. In contrast to prior studies, we find that rubiscos originating from α-cyanobacteria exhibit the highest carboxylation rates among form I enzymes (≈10 s-1 median versus <7 s-1 in other groups). Our study systematically reveals biological and environmental properties associated with kinetic variation across rubiscos from nature.
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Affiliation(s)
- Benoit de Pins
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Lior Greenspoon
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yinon M Bar-On
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Melina Shamshoum
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Roee Ben-Nissan
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Eliya Milshtein
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Dan Davidi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
- Aleph, Tel Aviv-Yafo, 6688210, Israel
| | - Itai Sharon
- Migal Galilee Research Institute, Kiryat Shmona, 11016, Israel
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel.
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3
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Bouvier JW, Emms DM, Kelly S. Rubisco is evolving for improved catalytic efficiency and CO 2 assimilation in plants. Proc Natl Acad Sci U S A 2024; 121:e2321050121. [PMID: 38442173 PMCID: PMC10945770 DOI: 10.1073/pnas.2321050121] [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: 11/30/2023] [Accepted: 01/25/2024] [Indexed: 03/07/2024] Open
Abstract
Rubisco is the primary entry point for carbon into the biosphere. However, rubisco is widely regarded as inefficient leading many to question whether the enzyme can adapt to become a better catalyst. Through a phylogenetic investigation of the molecular and kinetic evolution of Form I rubisco we uncover the evolutionary trajectory of rubisco kinetic evolution in angiosperms. We show that rbcL is among the 1% of slowest-evolving genes and enzymes on Earth, accumulating one nucleotide substitution every 0.9 My and one amino acid mutation every 7.2 My. Despite this, rubisco catalysis has been continually evolving toward improved CO2/O2 specificity, carboxylase turnover, and carboxylation efficiency. Consistent with this kinetic adaptation, increased rubisco evolution has led to a concomitant improvement in leaf-level CO2 assimilation. Thus, rubisco has been slowly but continually evolving toward improved catalytic efficiency and CO2 assimilation in plants.
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Affiliation(s)
- Jacques W Bouvier
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - David M Emms
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Steven Kelly
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
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4
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Tsuji JM, Shaw NA, Nagashima S, Venkiteswaran JJ, Schiff SL, Watanabe T, Fukui M, Hanada S, Tank M, Neufeld JD. Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre. Nature 2024; 627:915-922. [PMID: 38480893 PMCID: PMC10972752 DOI: 10.1038/s41586-024-07180-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 02/08/2024] [Indexed: 04/01/2024]
Abstract
Scientific exploration of phototrophic bacteria over nearly 200 years has revealed large phylogenetic gaps between known phototrophic groups that limit understanding of how phototrophy evolved and diversified1,2. Here, through Boreal Shield lake water incubations, we cultivated an anoxygenic phototrophic bacterium from a previously unknown order within the Chloroflexota phylum that represents a highly novel transition form in the evolution of photosynthesis. Unlike all other known phototrophs, this bacterium uses a type I reaction centre (RCI) for light energy conversion yet belongs to the same bacterial phylum as organisms that use a type II reaction centre (RCII) for phototrophy. Using physiological, phylogenomic and environmental metatranscriptomic data, we demonstrate active RCI-utilizing metabolism by the strain alongside usage of chlorosomes3 and bacteriochlorophylls4 related to those of RCII-utilizing Chloroflexota members. Despite using different reaction centres, our phylogenomic data provide strong evidence that RCI-utilizing and RCII-utilizing Chloroflexia members inherited phototrophy from a most recent common phototrophic ancestor. The Chloroflexota phylum preserves an evolutionary record of the use of contrasting phototrophic modes among genetically related bacteria, giving new context for exploring the diversification of phototrophy on Earth.
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Affiliation(s)
- J M Tsuji
- University of Waterloo, Waterloo, Ontario, Canada.
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan.
| | - N A Shaw
- University of Waterloo, Waterloo, Ontario, Canada
| | - S Nagashima
- Tokyo Metropolitan University, Tokyo, Japan
- Kanagawa University, Yokohama, Japan
| | - J J Venkiteswaran
- University of Waterloo, Waterloo, Ontario, Canada
- Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - S L Schiff
- University of Waterloo, Waterloo, Ontario, Canada
| | - T Watanabe
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - M Fukui
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - S Hanada
- Tokyo Metropolitan University, Tokyo, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - M Tank
- Tokyo Metropolitan University, Tokyo, Japan
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - J D Neufeld
- University of Waterloo, Waterloo, Ontario, Canada.
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5
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Cohen AB, Christensen LN, Weber F, Yagudaeva M, Lo E, Henkes GA, McCormick ML, Taylor GT. Preserved particulate organic carbon is likely derived from the subsurface sulfidic photic zone of the Proterozoic Ocean: evidence from a modern, oxygen-deficient lake. GEOBIOLOGY 2024; 22:e12593. [PMID: 38476006 DOI: 10.1111/gbi.12593] [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: 08/14/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024]
Abstract
Biological processes in the Proterozoic Ocean are often inferred from modern oxygen-deficient environments (MODEs) or from stable isotopes in preserved sediment. To date, few MODE studies have simultaneously quantified carbon fixation genes and attendant stable isotopic signatures. Consequently, how carbon isotope patterns reflect these pathways has not been thoroughly vetted. Addressing this, we profiled planktonic productivity and quantified carbon fixation pathway genes and associated organic carbon isotope values (δ13 CPOC ) of size-fractionated (0.2-2.7 and >2.7 μm) particulate matter from meromictic Fayetteville Green Lake, NY, USA. The high-O2 Calvin-Benson-Bassham (CBB) gene (cbbL) was most abundant in the <2.7 μm size fraction in shallow oxic and deep hypoxic waters, corresponding with cyanobacterial and eukaryote algal populations. The low-O2 CBB gene (cbbM) was most abundant near the lower oxycline boundary in the larger size fraction, coincident with purple sulfur bacteria populations. The reverse citric acid cycle gene (aclB) was equally abundant in both size fractions in the deepest photic zone, coinciding with green sulfur bacteria populations. Methane coenzyme reductase A (mcrA), of anaerobic methane cyclers, was most abundant at the lower oxycline boundary in both size fractions, coinciding with Methanoregula populations. δ13 CPOC values overlapped with the high-O2 CBB fixation range except for two negative excursions near the lower oxycline boundary, likely reflecting assimilation of isotopically-depleted groundwater-derived carbon by autotrophs and sulfate-reducers. Throughout aphotic waters, δ13 CPOC values of the large size fraction became 13 C-enriched, likely reflecting abundant purple sulfur bacterial aggregates. Eukaryote algae- or cyanobacteria-like isotopic signatures corresponded with increases in cbbL, cbbM, and aclB, and enrichment of exopolymer-rich prokaryotic photoautotrophs aggregates. Results suggest that δ13 CPOC values of preserved sediments from areas of the Proterozoic Ocean with sulfidic photic zones may reflect a mixture of alternate carbon-fixing populations exported from the deep photic zone, challenging the paradigm that sedimentary stable carbon isotope values predominantly reflect oxygenic photosynthesis from surface waters.
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Affiliation(s)
- Ashley B Cohen
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
| | | | - Felix Weber
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Milana Yagudaeva
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Evan Lo
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Gregory A Henkes
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
- Department of Geosciences, Stony Brook University, Stony Brook, New York, USA
| | | | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
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Mujakić I, Cabello-Yeves PJ, Villena-Alemany C, Piwosz K, Rodriguez-Valera F, Picazo A, Camacho A, Koblížek M. Multi-environment ecogenomics analysis of the cosmopolitan phylum Gemmatimonadota. Microbiol Spectr 2023; 11:e0111223. [PMID: 37732776 PMCID: PMC10581226 DOI: 10.1128/spectrum.01112-23] [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: 03/14/2023] [Accepted: 08/02/2023] [Indexed: 09/22/2023] Open
Abstract
Gemmatimonadota is a diverse bacterial phylum commonly found in environments such as soils, rhizospheres, fresh waters, and sediments. So far, the phylum contains just six cultured species (five of them sequenced), which limits our understanding of their diversity and metabolism. Therefore, we analyzed over 400 metagenome-assembled genomes (MAGs) and 5 culture-derived genomes representing Gemmatimonadota from various aquatic environments, hydrothermal vents, sediments, soils, and host-associated (with marine sponges and coral) species. The principal coordinate analysis based on the presence/absence of genes in Gemmatimonadota genomes and phylogenomic analysis documented that marine and host-associated Gemmatimonadota were the most distant from freshwater and wastewater species. A smaller genome size and coding sequences (CDS) number reduction were observed in marine MAGs, pointing to an oligotrophic environmental adaptation. Several metabolic pathways are restricted to specific environments. For example, genes for anoxygenic phototrophy were found only in freshwater, wastewater, and soda lake sediment genomes. There were several genomes from soda lake sediments and wastewater containing type IC/ID ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Various genomes from wastewater harbored bacterial type II RuBisCO, whereas RuBisCO-like protein was found in genomes from fresh waters, soil, host-associated, and marine sediments. Gemmatimonadota does not contain nitrogen fixation genes; however, the nosZ gene, involved in the reduction of N2O, was present in genomes from most environments, missing only in marine water and host-associated Gemmatimonadota. The presented data suggest that Gemmatimonadota evolved as an organotrophic species relying on aerobic respiration and then remodeled its genome inventory when adapting to particular environments. IMPORTANCE Gemmatimonadota is a rarely studied bacterial phylum consisting of a handful of cultured species. Recent culture-independent studies documented that these organisms are distributed in many environments, including soil, marine, fresh, and waste waters. However, due to the lack of cultured species, information about their metabolic potential and environmental role is scarce. Therefore, we collected Gemmatimonadota metagenome-assembled genomes (MAGs) from different habitats and performed a systematic analysis of their genomic characteristics and metabolic potential. Our results show how Gemmatimonadota have adapted their genomes to different environments.
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Affiliation(s)
- Izabela Mujakić
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Pedro J. Cabello-Yeves
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Valencia, Spain
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Cristian Villena-Alemany
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Kasia Piwosz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Gdynia, Poland
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Valencia, Spain
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Valencia, Spain
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
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7
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Bouvier JW, Kelly S. Response to Tcherkez and Farquhar: Rubisco adaptation is more limited by phylogenetic constraint than by catalytic trade-off. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:154021. [PMID: 37392528 DOI: 10.1016/j.jplph.2023.154021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 07/03/2023]
Abstract
Rubisco is the primary entry point for carbon into the biosphere. It has been widely proposed that rubisco is highly constrained by catalytic trade-offs due to correlations between the enzyme's kinetic traits across species. In previous work, we have shown that the strength of these correlations, and thus the strength of catalytic trade-offs, have been overestimated due to the presence of phylogenetic signal in the kinetic trait data (Bouvier et al., 2021). We demonstrated that only the trade-offs between the Michaelis constant for CO2 and carboxylase turnover, and between the Michaelis constants for CO2 and O2 were robust to phylogenetic effects. We further demonstrated that phylogenetic constraints have limited rubisco adaptation to a greater extent than the combined action of catalytic trade-offs. Recently, however, our claims have been contested by Tcherkez and Farquhar (2021), who have argued that the phylogenetic signal we detect in rubisco kinetic traits is an artefact of species sampling, the use of rbcL-based trees for phylogenetic inference, laboratory-to-laboratory variability in kinetic measurements, and homoplasy of the C4 trait. In the present article, we respond to these criticisms on a point-by-point basis and conclusively show that all are unfounded. As such, we stand by our original conclusions. Namely, although rubisco kinetic evolution has been limited by biochemical trade-offs, these are not absolute and have been previously overestimated due to phylogenetic biases. Instead, rubisco adaptation has in fact been more limited by phylogenetic constraint.
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Affiliation(s)
- Jacques W Bouvier
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, United Kingdom
| | - Steven Kelly
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, United Kingdom.
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8
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Oh ZG, Askey B, Gunn LH. Red Rubiscos and opportunities for engineering green plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:520-542. [PMID: 36055563 PMCID: PMC9833100 DOI: 10.1093/jxb/erac349] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Nature's vital, but notoriously inefficient, CO2-fixing enzyme Rubisco often limits the growth of photosynthetic organisms including crop species. Form I Rubiscos comprise eight catalytic large subunits and eight auxiliary small subunits and can be classified into two distinct lineages-'red' and 'green'. While red-type Rubiscos (Form IC and ID) are found in rhodophytes, their secondary symbionts, and certain proteobacteria, green-type Rubiscos (Form IA and IB) exist in terrestrial plants, chlorophytes, cyanobacteria, and other proteobacteria. Eukaryotic red-type Rubiscos exhibit desirable kinetic properties, namely high specificity and high catalytic efficiency, with certain isoforms outperforming green-type Rubiscos. However, it is not yet possible to functionally express a high-performing red-type Rubisco in chloroplasts to boost photosynthetic carbon assimilation in green plants. Understanding the molecular and evolutionary basis for divergence between red- and green-type Rubiscos could help us to harness the superior CO2-fixing power of red-type Rubiscos. Here we review our current understanding about red-type Rubisco distribution, biogenesis, and sequence-structure, and present opportunities and challenges for utilizing red-type Rubisco kinetics towards crop improvements.
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Affiliation(s)
- Zhen Guo Oh
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Bryce Askey
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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Chimeric inheritance and crown-group acquisitions of carbon fixation genes within Chlorobiales: Origins of autotrophy in Chlorobiales and implication for geological biomarkers. PLoS One 2022; 17:e0275539. [PMID: 36227849 PMCID: PMC9560492 DOI: 10.1371/journal.pone.0275539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/16/2022] [Indexed: 11/21/2022] Open
Abstract
The geological record of microbial metabolisms and ecologies primarily consists of stable isotope fractionations and the diagenetic products of biogenic lipids. Carotenoid lipid biomarkers are particularly useful proxies for reconstructing this record, providing information on microbial phototroph primary productivity, redox couples, and oxygenation. The biomarkers okenane, chlorobactane, and isorenieratene are generally considered to be evidence of anoxygenic phototrophs, and provide a record that extends to 1.64 Ga. The utility of the carotenoid biomarker record may be enhanced by examining the carbon isotopic ratios in these products, which are diagnostic for specific pathways of biological carbon fixation found today within different microbial groups. However, this joint inference assumes that microbes have conserved these pathways across the duration of the preserved biomarker record. Testing this hypothesis, we performed phylogenetic analyses of the enzymes constituting the reductive tricarboxylic acid (rTCA) cycle in Chlorobiales, the group of anoxygenic phototrophic bacteria usually implicated in the deposition of chlorobactane and isorenieretane. We find phylogenetically incongruent patterns of inheritance across all enzymes, indicative of horizontal gene transfers to both stem and crown Chlorobiales from multiple potential donor lineages. This indicates that a complete rTCA cycle was independently acquired at least twice within Chlorobiales and was not present in the last common ancestor. When combined with recent molecular clock analyses, these results predict that the Mesoproterzoic lipid biomarker record diagnostic for Chlorobiales should not preserve isotopic fractionations indicative of a full rTCA cycle. Furthermore, we conclude that coupling isotopic and biomarker records is insufficient for reliably reconstructing microbial paleoecologies in the absence of a complementary and consistent phylogenomic narrative.
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10
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Sutter M, Kerfeld CA, Scott KM. Atypical Carboxysome Loci: JEEPs or Junk? Front Microbiol 2022; 13:872708. [PMID: 35668770 PMCID: PMC9164163 DOI: 10.3389/fmicb.2022.872708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/10/2022] [Indexed: 11/13/2022] Open
Abstract
Carboxysomes, responsible for a substantial fraction of CO2 fixation on Earth, are proteinaceous microcompartments found in many autotrophic members of domain Bacteria, primarily from the phyla Proteobacteria and Cyanobacteria. Carboxysomes facilitate CO2 fixation by the Calvin-Benson-Bassham (CBB) cycle, particularly under conditions where the CO2 concentration is variable or low, or O2 is abundant. These microcompartments are composed of an icosahedral shell containing the enzymes ribulose 1,5-carboxylase/oxygenase (RubisCO) and carbonic anhydrase. They function as part of a CO2 concentrating mechanism, in which cells accumulate HCO3 - in the cytoplasm via active transport, HCO3 - enters the carboxysomes through pores in the carboxysomal shell proteins, and carboxysomal carbonic anhydrase facilitates the conversion of HCO3 - to CO2, which RubisCO fixes. Two forms of carboxysomes have been described: α-carboxysomes and β-carboxysomes, which arose independently from ancestral microcompartments. The α-carboxysomes present in Proteobacteria and some Cyanobacteria have shells comprised of four types of proteins [CsoS1 hexamers, CsoS4 pentamers, CsoS2 assembly proteins, and α-carboxysomal carbonic anhydrase (CsoSCA)], and contain form IA RubisCO (CbbL and CbbS). In the majority of cases, these components are encoded in the genome near each other in a gene locus, and transcribed together as an operon. Interestingly, genome sequencing has revealed some α-carboxysome loci that are missing genes encoding one or more of these components. Some loci lack the genes encoding RubisCO, others lack a gene encoding carbonic anhydrase, some loci are missing shell protein genes, and in some organisms, genes homologous to those encoding the carboxysome-associated carbonic anhydrase are the only carboxysome-related genes present in the genome. Given that RubisCO, assembly factors, carbonic anhydrase, and shell proteins are all essential for carboxysome function, these absences are quite intriguing. In this review, we provide an overview of the most recent studies of the structural components of carboxysomes, describe the genomic context and taxonomic distribution of atypical carboxysome loci, and propose functions for these variants. We suggest that these atypical loci are JEEPs, which have modified functions based on the presence of Just Enough Essential Parts.
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Affiliation(s)
| | | | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kathleen M. Scott
- Integrative Biology Department, University of South Florida, Tampa, FL, United States
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11
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Hu J, Tang H, Wang YZ, Yang C, Gao MT, Tsang YF, Li J. Effect of dissolved solids released from biochar on soil microbial metabolism. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:598-608. [PMID: 35332912 DOI: 10.1039/d2em00036a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Dissolved solids released from biochar (DSRB), including organic and inorganic compounds, may affect the role of biochar as a soil amendment. In this study, the effects of DSRB on soil microbe metabolism, especially CO2 fixation, were evaluated in liquid soil extract. DSRB were found to be released in large amounts (289.05 mg L-1 at 1 hour) from biochar over a short period of time before their rate of release slowed to a gradual pace. They increased the microbial biomass and provided energy and reducing power to microbes, while reducing their metabolic output of extracellular proteins and polysaccharides. DSRB inputs led to the redistribution of metabolic flux in soil microorganisms and an increased organic carbon content in the short term. This content gradually decreased as it was utilized. DSRB did not improve microbial CO2 fixation but, rather, enhanced its release, while promoting specific soil microorganism genera, including Cupriavidus, Flavisolibacter, and Pseudoxanthomonas. These heterotrophic genera may compete with autotrophic microorganisms for nutrients but have positive synergistic relationships with autotrophs during CO2 fixation. These results demonstrated that reducing the DSRB in biochar can improve its role as a soil amendment by enhancing soil carbon storage and CO2 fixation capabilities.
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Affiliation(s)
- Jiajun Hu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Han Tang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Ya Zhu Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Chen Yang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Min-Tian Gao
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Yiu Fai Tsang
- Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong, China
| | - Jixiang Li
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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12
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Pierella Karlusich JJ, Pelletier E, Zinger L, Lombard F, Zingone A, Colin S, Gasol JM, Dorrell RG, Henry N, Scalco E, Acinas SG, Wincker P, de Vargas C, Bowler C. A robust approach to estimate relative phytoplankton cell abundances from metagenomes. Mol Ecol Resour 2022; 23:16-40. [PMID: 35108459 PMCID: PMC10078663 DOI: 10.1111/1755-0998.13592] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 01/09/2022] [Accepted: 01/25/2022] [Indexed: 11/28/2022]
Abstract
Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size-fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.
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Affiliation(s)
- Juan José Pierella Karlusich
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Eric Pelletier
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Fabien Lombard
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Océanographie de Villefranche (LOV), 06230, Villefranche-sur-Mer, France.,Institut Universitaire de France (IUF), Paris, France
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Sébastien Colin
- European Molecular Biology Laboratory, Heidelberg, Germany.,Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP, 29680, Roscoff, France.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Richard G Dorrell
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France
| | - Nicolas Henry
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Eleonora Scalco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Patrick Wincker
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Colomban de Vargas
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP, 29680, Roscoff, France
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
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13
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Pavan M, Reinmets K, Garg S, Mueller AP, Marcellin E, Köpke M, Valgepea K. Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy. Metab Eng 2022; 71:117-141. [DOI: 10.1016/j.ymben.2022.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/16/2022]
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14
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An Insight of RuBisCO Evolution through a Multilevel Approach. Biomolecules 2021; 11:biom11121761. [PMID: 34944405 PMCID: PMC8698309 DOI: 10.3390/biom11121761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/15/2021] [Accepted: 10/23/2021] [Indexed: 12/28/2022] Open
Abstract
RuBisCO is the most abundant enzyme on earth; it regulates the organic carbon cycle in the biosphere. Studying its structural evolution will help to develop new strategies of genetic improvement in order to increase food production and mitigate CO2 emissions. In the present work, we evaluate how the evolution of sequence and structure among isoforms I, II and III of RuBisCO defines their intrinsic flexibility and residue-residue interactions. To do this, we used a multilevel approach based on phylogenetic inferences, multiple sequence alignment, normal mode analysis, and molecular dynamics. Our results show that the three isoforms exhibit greater fluctuation in the loop between αB and βC, and also present a positive correlation with loop 6, an important region for enzymatic activity because it regulates RuBisCO conformational states. Likewise, an increase in the flexibility of the loop structure between αB and βC, as well as Lys330 (form II) and Lys322 (form III) of loop 6, is important to increase photosynthetic efficiency. Thus, the cross-correlation dynamics analysis showed changes in the direction of movement of the secondary structures in the three isoforms. Finally, key amino acid residues related to the flexibility of the RuBisCO structure were indicated, providing important information for its enzymatic engineering.
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15
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Dang Z, Jia Y, Tian Y, Li J, Zhang Y, Huang L, Liang C, Lockhart PJ, Matthew C, Li FY. Transcriptome-Wide Gene Expression Plasticity in Stipa grandis in Response to Grazing Intensity Differences. Int J Mol Sci 2021; 22:ijms222111882. [PMID: 34769324 PMCID: PMC8611654 DOI: 10.3390/ijms222111882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 01/15/2023] Open
Abstract
Organisms have evolved effective and distinct adaptive strategies to survive. Stipa grandis is a representative species for studying the grazing effect on typical steppe plants in the Inner Mongolia Plateau. Although phenotypic (morphological and physiological) variations in S. grandis in response to long-term grazing have been identified, the molecular mechanisms underlying adaptations and plastic responses remain largely unknown. Here, we performed a transcriptomic analysis to investigate changes in gene expression of S. grandis under four different grazing intensities. As a result, a total of 2357 differentially expressed genes (DEGs) were identified among the tested grazing intensities, suggesting long-term grazing resulted in gene expression plasticity that affected diverse biological processes and metabolic pathways in S. grandis. DEGs were identified in RNA-Seq and qRT-PCR analyses that indicated the modulation of the Calvin–Benson cycle and photorespiration metabolic pathways. The key gene expression profiles encoding various proteins (e.g., ribulose-1,5-bisphosphate carboxylase/oxygenase, fructose-1,6-bisphosphate aldolase, glycolate oxidase, etc.) involved in these pathways suggest that they may synergistically respond to grazing to increase the resilience and stress tolerance of S. grandis. Our findings provide scientific clues for improving grassland use and protection and identifying important questions to address in future transcriptome studies.
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Affiliation(s)
- Zhenhua Dang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Y.J.); (J.L.); (Y.Z.); (L.H.); (C.L.); (F.Y.L.)
- Correspondence: ; Tel.: +86-1514-802-6396
| | - Yuanyuan Jia
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Y.J.); (J.L.); (Y.Z.); (L.H.); (C.L.); (F.Y.L.)
| | - Yunyun Tian
- Ministry of Education Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China;
| | - Jiabin Li
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Y.J.); (J.L.); (Y.Z.); (L.H.); (C.L.); (F.Y.L.)
| | - Yanan Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Y.J.); (J.L.); (Y.Z.); (L.H.); (C.L.); (F.Y.L.)
| | - Lei Huang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Y.J.); (J.L.); (Y.Z.); (L.H.); (C.L.); (F.Y.L.)
| | - Cunzhu Liang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Y.J.); (J.L.); (Y.Z.); (L.H.); (C.L.); (F.Y.L.)
| | - Peter J. Lockhart
- School of Fundamental Sciences, College of Sciences, Massey University, Palmerston North 4442, New Zealand;
| | - Cory Matthew
- School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand;
| | - Frank Yonghong Li
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Y.J.); (J.L.); (Y.Z.); (L.H.); (C.L.); (F.Y.L.)
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16
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Fan SH, Matsuo M, Huang L, Tribelli PM, Götz F. The MpsAB Bicarbonate Transporter Is Superior to Carbonic Anhydrase in Biofilm-Forming Bacteria with Limited CO 2 Diffusion. Microbiol Spectr 2021; 9:e0030521. [PMID: 34287032 PMCID: PMC8552792 DOI: 10.1128/spectrum.00305-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 06/30/2021] [Indexed: 11/20/2022] Open
Abstract
CO2 and bicarbonate are required for carboxylation reactions, which are essential in most bacteria. To provide the cells with sufficient CO2, there exist two dissolved inorganic carbon supply (DICS) systems: the membrane potential-generating system (MpsAB) and the carbonic anhydrase (CA). Recently, it has been shown that MpsAB is a bicarbonate transporter that is present not only in photo- and autotrophic bacteria, but also in a diverse range of nonautotrophic microorganisms. Since the two systems rarely coexist in a species but are interchangeable, we investigated what advantages the one system might have over the other. Using the genus Staphylococcus as a model, we deleted the CA gene can in Staphylococcus carnosus and mpsABC genes in Staphylococcus aureus. Deletion of the respective gene in one or the other species led to growth inhibition that could only be reversed by CO2 supplementation. While the S. carnosus Δcan mutant could be fully complemented with mpsABC, the S. aureus ΔmpsABC mutant was only partially complemented by can, suggesting that MpsAB outperforms CA. Interestingly, we provide evidence that mucus biofilm formation such as that involving polysaccharide intercellular adhesin (PIA) impedes the diffusion of CO2 into cells, making MpsAB more advantageous in biofilm-producing strains or species. Coexpression of MpsAB and CA does not confer any growth benefits, even under stress conditions. In conclusion, the distribution of MpsAB or CA in bacteria does not appear to be random as expression of bicarbonate transporters provides an advantage where diffusion of CO2 is impeded. IMPORTANCE CO2 and bicarbonate are required for carboxylation reactions in central metabolism and biosynthesis of small molecules in all bacteria. This is achieved by two different systems for dissolved inorganic carbon supply (DICS): these are the membrane potential-generating system (MpsAB) and the carbonic anhydrase (CA), but both rarely coexist in a given species. Here, we compared both systems and demonstrate that the distribution of MpsAB and/or CA within the phylum Firmicutes is apparently not random. The bicarbonate transporter MpsAB has an advantage in species where CO2 diffusion is hampered-for instance, in mucus- and biofilm-forming bacteria. However, coexpression of MpsAB and CA does not confer any growth benefits, even under stress conditions. Given the clinical relevance of Staphylococcus in the medical environment, such findings contribute to the understanding of bacterial metabolism and thus are crucial for exploration of potential targets for antimicrobials. The knowledge gained here as exemplified by staphylococcal species could be extended to other pathogenic bacteria.
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Affiliation(s)
- Sook-Ha Fan
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Germany
| | - Miki Matsuo
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Germany
| | - Li Huang
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Germany
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Paula M. Tribelli
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Germany
- Departamento de Química Biológica, FCEyN-UBA, Buenos Aires, Argentina
| | - Friedrich Götz
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Germany
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17
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Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations. THE ISME JOURNAL 2021; 15:2692-2707. [PMID: 33753881 PMCID: PMC8397712 DOI: 10.1038/s41396-021-00944-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 02/01/2023]
Abstract
Candidatus phylum Eremiobacterota (formerly WPS-2) is an as-yet-uncultured bacterial clade that takes its name from Ca. Eremiobacter, an Antarctic soil aerobe proposed to be capable of a novel form of chemolithoautotrophy termed atmospheric chemosynthesis, that uses the energy derived from atmospheric H2-oxidation to fix CO2 through the Calvin-Benson-Bassham (CBB) cycle via type 1E RuBisCO. To elucidate the phylogenetic affiliation and metabolic capacities of Ca. Eremiobacterota, we analysed 63 public metagenome-assembled genomes (MAGs) and nine new MAGs generated from Antarctic soil metagenomes. These MAGs represent both recognized classes within Ca. Eremiobacterota, namely Ca. Eremiobacteria and UBP9. Ca. Eremiobacteria are inferred to be facultatively acidophilic with a preference for peptides and amino acids as nutrient sources. Epifluorescence microscopy revealed Ca. Eremiobacteria cells from Antarctica desert soil to be coccoid in shape. Two orders are recognized within class Ca. Eremiobacteria: Ca. Eremiobacterales and Ca. Baltobacterales. The latter are metabolically versatile, with individual members having genes required for trace gas driven autotrophy, anoxygenic photosynthesis, CO oxidation, and anaerobic respiration. UBP9, here renamed Ca. Xenobia class. nov., are inferred to be obligate heterotrophs with acidophilic adaptations, but individual members having highly divergent metabolic capacities compared to Ca. Eremiobacteria, especially with regard to respiration and central carbon metabolism. We conclude Ca. Eremiobacterota to be an ecologically versatile phylum with the potential to thrive under an array of "extreme" environmental conditions.
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18
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Rillema R, Hoang Y, MacCready JS, Vecchiarelli AG. Carboxysome Mispositioning Alters Growth, Morphology, and Rubisco Level of the Cyanobacterium Synechococcus elongatus PCC 7942. mBio 2021; 12:e0269620. [PMID: 34340540 PMCID: PMC8406218 DOI: 10.1128/mbio.02696-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/01/2021] [Indexed: 12/23/2022] Open
Abstract
Cyanobacteria are the prokaryotic group of phytoplankton responsible for a significant fraction of global CO2 fixation. Like plants, cyanobacteria use the enzyme ribulose 1,5-bisphosphate carboxylase/oxidase (Rubisco) to fix CO2 into organic carbon molecules via the Calvin-Benson-Bassham cycle. Unlike plants, cyanobacteria evolved a carbon-concentrating organelle called the carboxysome-a proteinaceous compartment that encapsulates and concentrates Rubisco along with its CO2 substrate. In the rod-shaped cyanobacterium Synechococcus elongatus PCC 7942, we recently identified the McdAB system responsible for uniformly distributing carboxysomes along the cell length. It remains unknown what role carboxysome positioning plays with respect to cellular physiology. Here, we show that a failure to distribute carboxysomes leads to slower cell growth, cell elongation, asymmetric cell division, and elevated levels of cellular Rubisco. Unexpectedly, we also report that even wild-type S. elongatus undergoes cell elongation and asymmetric cell division when grown at the cool, but environmentally relevant, growth temperature of 20°C or when switched from a high- to ambient-CO2 environment. The findings suggest that carboxysome positioning by the McdAB system functions to maintain the carbon fixation efficiency of Rubisco by preventing carboxysome aggregation, which is particularly important under growth conditions where rod-shaped cyanobacteria adopt a filamentous morphology. IMPORTANCE Photosynthetic cyanobacteria are responsible for almost half of global CO2 fixation. Due to eutrophication, rising temperatures, and increasing atmospheric CO2 concentrations, cyanobacteria have gained notoriety for their ability to form massive blooms in both freshwater and marine ecosystems across the globe. Like plants, cyanobacteria use the most abundant enzyme on Earth, Rubisco, to provide the sole source of organic carbon required for its photosynthetic growth. Unlike plants, cyanobacteria have evolved a carbon-concentrating organelle called the carboxysome that encapsulates and concentrates Rubisco with its CO2 substrate to significantly increase carbon fixation efficiency and cell growth. We recently identified the positioning system that distributes carboxysomes in cyanobacteria. However, the physiological consequence of carboxysome mispositioning in the absence of this distribution system remains unknown. Here, we find that carboxysome mispositioning triggers changes in cell growth and morphology as well as elevated levels of cellular Rubisco.
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Affiliation(s)
- Rees Rillema
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Y Hoang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Joshua S. MacCready
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Anthony G. Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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19
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Garcia AK, Cavanaugh CM, Kacar B. The curious consistency of carbon biosignatures over billions of years of Earth-life coevolution. THE ISME JOURNAL 2021; 15:2183-2194. [PMID: 33846565 PMCID: PMC8319343 DOI: 10.1038/s41396-021-00971-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/12/2021] [Accepted: 03/25/2021] [Indexed: 11/09/2022]
Abstract
The oldest and most wide-ranging signal of biological activity (biosignature) on our planet is the carbon isotope composition of organic materials preserved in rocks. These biosignatures preserve the long-term evolution of the microorganism-hosted metabolic machinery responsible for producing deviations in the isotopic compositions of inorganic and organic carbon. Despite billions of years of ecosystem turnover, evolutionary innovation, organismic complexification, and geological events, the organic carbon that is a residuum of the global marine biosphere in the rock record tells an essentially static story. The ~25‰ mean deviation between inorganic and organic 13C/12C values has remained remarkably unchanged over >3.5 billion years. The bulk of this record is conventionally attributed to early-evolved, RuBisCO-mediated CO2 fixation that, in extant oxygenic phototrophs, produces comparable isotopic effects and dominates modern primary production. However, billions of years of environmental transition, for example, in the progressive oxygenation of the Earth's atmosphere, would be expected to have accompanied shifts in the predominant RuBisCO forms as well as enzyme-level adaptive responses in RuBisCO CO2-specificity. These factors would also be expected to result in preserved isotopic signatures deviating from those produced by extant RuBisCO in oxygenic phototrophs. Why does the bulk carbon isotope record not reflect these expected environmental transitions and evolutionary innovations? Here, we discuss this apparent discrepancy and highlight the need for greater quantitative understanding of carbon isotope fractionation behavior in extant metabolic pathways. We propose novel, laboratory-based approaches to reconstructing ancestral states of carbon metabolisms and associated enzymes that can constrain isotopic biosignature production in ancient biological systems. Together, these strategies are crucial for integrating the complementary toolsets of biological and geological sciences and for interpretation of the oldest record of life on Earth.
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Affiliation(s)
- Amanda K Garcia
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Colleen M Cavanaugh
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Betul Kacar
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA.
- Lunar and Planetary Laboratory and Steward Observatory, University of Arizona, Tucson, AZ, USA.
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20
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Abstract
Tremendous chemical diversity is the hallmark of plants and is supported by highly complex biochemical machinery. Plant metabolic enzymes originated and were transferred from eukaryotic and prokaryotic ancestors and further diversified by the unprecedented rates of gene duplication and functionalization experienced in land plants. Unlike microbes, which have frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced very few, if any, gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner and on existing networks under various evolutionary constraints. This review aims to take a broader view of plant metabolic evolution and lay a framework to further explore evolutionary mechanisms of the complex metabolic network. Understanding the underlying metabolic and genetic constraints is also an empirical prerequisite for rational engineering and redesigning of plant metabolic pathways.
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Affiliation(s)
- Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany;
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21
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Photorespiration: The Futile Cycle? PLANTS 2021; 10:plants10050908. [PMID: 34062784 PMCID: PMC8147352 DOI: 10.3390/plants10050908] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 04/29/2021] [Accepted: 04/29/2021] [Indexed: 12/03/2022]
Abstract
Photorespiration, or C2 photosynthesis, is generally considered a futile cycle that potentially decreases photosynthetic carbon fixation by more than 25%. Nonetheless, many essential processes, such as nitrogen assimilation, C1 metabolism, and sulfur assimilation, depend on photorespiration. Most studies of photosynthetic and photorespiratory reactions are conducted with magnesium as the sole metal cofactor despite many of the enzymes involved in these reactions readily associating with manganese. Indeed, when manganese is present, the energy efficiency of these reactions may improve. This review summarizes some commonly used methods to quantify photorespiration, outlines the influence of metal cofactors on photorespiratory enzymes, and discusses why photorespiration may not be as wasteful as previously believed.
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22
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Coutinho FH, von Meijenfeldt FAB, Walter JM, Haro-Moreno JM, Lopéz-Pérez M, van Verk MC, Thompson CC, Cosenza CAN, Appolinario L, Paranhos R, Cabral A, Dutilh BE, Thompson FL. Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:142758. [PMID: 33183813 DOI: 10.1016/j.scitotenv.2020.142758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 05/18/2023]
Abstract
The unique combination of depth, salinity, and water masses make the South Atlantic Ocean an ecosystem of special relevance within the global ocean. Yet, the microbiome of this ecosystem has received less attention than other regions of the global Ocean. This has hampered our understanding of the diversity and metabolic potential of the microorganisms that dwell in this habitat. To fill this knowledge gap, we analyzed a collection of 31 metagenomes from the Atlantic Ocean that spanned the epipelagic, mesopelagic and bathypelagic zones (surface to 4000 m). Read-centric and gene-centric analysis revealed the unique taxonomic and functional composition of metagenomes from each depth zone, which was driven by differences in physical and chemical parameters. In parallel, a total of 40 metagenome-assembled genomes were obtained, which recovered one third of the total community. Phylogenomic reconstruction revealed that many of these genomes are derived from poorly characterized taxa of Bacteria and Archaea. Genomes derived from heterotrophic bacteria of the aphotic zone displayed a large apparatus of genes suited for the utilization of recalcitrant organic compounds such as cellulose, chitin and alkanes. In addition, we found genomic evidence suggesting that mixotrophic bacteria from the bathypelagic zone could perform carbon fixation through the Calvin-Benson-Bassham cycle, fueled by sulfur oxidation. Finally, we found that the viral communities shifted throughout the water column regarding their targeted hosts and virus-to-microbe ratio, in response to shifts in the composition and functioning their microbial counterparts. Our findings shed light on the microbial and viral drivers of important biogeochemical processes that take place in the South Atlantic Ocean.
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Affiliation(s)
- F H Coutinho
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre/Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands; Theoretical Biology and Bioinformatics, Science for Life, Utrecht University (UU), Utrecht, the Netherlands; Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - F A B von Meijenfeldt
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University (UU), Utrecht, the Netherlands
| | - J M Walter
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - J M Haro-Moreno
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - M Lopéz-Pérez
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - M C van Verk
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University (UU), Utrecht, the Netherlands
| | - C C Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - C A N Cosenza
- COPPE/SAGE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - L Appolinario
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - R Paranhos
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - A Cabral
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - B E Dutilh
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre/Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands; Theoretical Biology and Bioinformatics, Science for Life, Utrecht University (UU), Utrecht, the Netherlands
| | - F L Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; COPPE/SAGE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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23
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Mujakić I, Andrei AŞ, Shabarova T, Fecskeová LK, Salcher MM, Piwosz K, Ghai R, Koblížek M. Common Presence of Phototrophic Gemmatimonadota in Temperate Freshwater Lakes. mSystems 2021; 6:e01241-20. [PMID: 33727400 PMCID: PMC8547001 DOI: 10.1128/msystems.01241-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/21/2021] [Indexed: 12/11/2022] Open
Abstract
Members of the bacterial phylum Gemmatimonadota are ubiquitous in most natural environments and represent one of the top 10 most abundant bacterial phyla in soil. Sequences affiliated with Gemmatimonadota were also reported from diverse aquatic habitats; however, it remains unknown whether they are native organisms or represent bacteria passively transported from sediment or soil. To address this question, we analyzed metagenomes constructed from five freshwater lakes in central Europe. Based on the 16S rRNA gene frequency, Gemmatimonadota represented from 0.02 to 0.6% of all bacteria in the epilimnion and between 0.1 and 1% in the hypolimnion. These proportions were independently confirmed using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Some cells in the epilimnion were attached to diatoms (Fragilaria sp.) or cyanobacteria (Microcystis sp.), which suggests a close association with phytoplankton. In addition, we reconstructed 45 metagenome-assembled genomes (MAGs) related to Gemmatimonadota They represent several novel lineages, which persist in the studied lakes during the seasons. Three lineages contained photosynthesis gene clusters. One of these lineages was related to Gemmatimonas phototrophica and represented the majority of Gemmatimonadota retrieved from the lakes' epilimnion. The other two lineages came from hypolimnion and probably represented novel photoheterotrophic genera. None of these phototrophic MAGs contained genes for carbon fixation. Since most of the identified MAGs were present during the whole year and cells associated with phytoplankton were observed, we conclude that they represent truly limnic Gemmatimonadota distinct from the previously described species isolated from soils or sediments.IMPORTANCE Photoheterotrophic bacterial phyla such as Gemmatimonadota are key components of many natural environments. Its first photoheterotrophic cultured member, Gemmatimonas phototrophica, was isolated in 2014 from a shallow lake in the Gobi Desert. It contains a unique type of photosynthetic complex encoded by a set of genes which were likely received via horizontal transfer from Proteobacteria We were intrigued to discover how widespread this group is in the natural environment. In the presented study, we analyzed 45 metagenome-assembled genomes (MAGs) that were obtained from five freshwater lakes in Switzerland and Czechia. Interestingly, it was found that phototrophic Gemmatimonadota are relatively common in euphotic zones of the studied lakes, whereas heterotrophic Gemmatimonadota prevail in deeper waters. Moreover, our analysis of the MAGs documented that these freshwater species contain almost the same set of photosynthesis genes identified before in Gemmatimonas phototrophica originating from the Gobi Desert.
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Affiliation(s)
- Izabela Mujakić
- Laboratory of Anoxygenic Phototrophs, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Tanja Shabarova
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Lívia Kolesár Fecskeová
- Laboratory of Anoxygenic Phototrophs, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Kasia Piwosz
- Laboratory of Anoxygenic Phototrophs, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
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24
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Asplund-Samuelsson J, Hudson EP. Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes. PLoS Comput Biol 2021; 17:e1008742. [PMID: 33556078 PMCID: PMC7895386 DOI: 10.1371/journal.pcbi.1008742] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/19/2021] [Accepted: 01/25/2021] [Indexed: 11/21/2022] Open
Abstract
Knowledge of the genetic basis for autotrophic metabolism is valuable since it relates to both the emergence of life and to the metabolic engineering challenge of incorporating CO2 as a potential substrate for biorefining. The most common CO2 fixation pathway is the Calvin cycle, which utilizes Rubisco and phosphoribulokinase enzymes. We searched thousands of microbial genomes and found that 6.0% contained the Calvin cycle. We then contrasted the genomes of Calvin cycle-positive, non-cyanobacterial microbes and their closest relatives by enrichment analysis, ancestral character estimation, and random forest machine learning, to explore genetic adaptations associated with acquisition of the Calvin cycle. The Calvin cycle overlaps with the pentose phosphate pathway and glycolysis, and we could confirm positive associations with fructose-1,6-bisphosphatase, aldolase, and transketolase, constituting a conserved operon, as well as ribulose-phosphate 3-epimerase, ribose-5-phosphate isomerase, and phosphoglycerate kinase. Additionally, carbohydrate storage enzymes, carboxysome proteins (that raise CO2 concentration around Rubisco), and Rubisco activases CbbQ and CbbX accompanied the Calvin cycle. Photorespiration did not appear to be adapted specifically for the Calvin cycle in the non-cyanobacterial microbes under study. Our results suggest that chemoautotrophy in Calvin cycle-positive organisms was commonly enabled by hydrogenase, and less commonly ammonia monooxygenase (nitrification). The enrichment of specific DNA-binding domains indicated Calvin-cycle associated genetic regulation. Metabolic regulatory adaptations were illustrated by negative correlation to AraC and the enzyme arabinose-5-phosphate isomerase, which suggests a downregulation of the metabolite arabinose-5-phosphate, which may interfere with the Calvin cycle through enzyme inhibition and substrate competition. Certain domains of unknown function that were found to be important in the analysis may indicate yet unknown regulatory mechanisms in Calvin cycle-utilizing microbes. Our gene ranking provides targets for experiments seeking to improve CO2 fixation, or engineer novel CO2-fixing organisms.
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Affiliation(s)
- Johannes Asplund-Samuelsson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Elton P. Hudson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
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25
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Fuchsman CA, Carlson MCG, Garcia Prieto D, Hays MD, Rocap G. Cyanophage host-derived genes reflect contrasting selective pressures with depth in the oxic and anoxic water column of the Eastern Tropical North Pacific. Environ Microbiol 2020; 23:2782-2800. [PMID: 32869473 DOI: 10.1111/1462-2920.15219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 08/14/2020] [Accepted: 08/27/2020] [Indexed: 01/19/2023]
Abstract
Cyanophages encode host-derived genes that may increase their fitness. We examined the relative abundance of 18 host-derived cyanophages genes in metagenomes and viromes along depth profiles from the Eastern Tropical North Pacific Oxygen Deficient Zone (ETNP ODZ) where Prochlorococcus dominates a secondary chlorophyll maximum within the ODZ. Cyanophages at the oxic primary chlorophyll maximum encoded genes related to light and phosphate stress (psbA, psbD and pstS in T4-like and psbA in T7-like), but the proportion of cyanophage with these genes decreased with depth. The proportion of cyanophage with purine biosynthesis genes increased with depth in T4-like, but not T7-like cyanophages. No additional host-derived genes were found in deep T7-like cyanophages, suggesting that T4-like and T7-like cyanophages have different host-derived gene acquisition strategies, possibly linked to their different genome packaging mechanisms. In contrast to the ETNP, in the oxic North Atlantic T4-like cyanophages encoded psbA and pstS throughout the euphotic zone. Differences in pstS between the ETNP and the North Atlantic stations were consistent with differences in phosphate concentrations in those regimes. We suggest that the low proportion of cyanophage with psbA within the ODZ reflects the stably stratified low-light conditions occupied by their hosts, a Prochlorococcus ecotype endemic to ODZs.
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Affiliation(s)
- Clara A Fuchsman
- School of Oceanography, University of Washington, Seattle, WA, USA.,Horn Point Laboratory, University of Maryland Center of Environmental Science, Cambridge, MD, 21613, USA
| | - Michael C G Carlson
- School of Oceanography, University of Washington, Seattle, WA, USA.,Technion-Israel Institute of Technology, Haifa, Israel
| | - David Garcia Prieto
- School of Oceanography, University of Washington, Seattle, WA, USA.,Horn Point Laboratory, University of Maryland Center of Environmental Science, Cambridge, MD, 21613, USA
| | - Matthew D Hays
- Horn Point Laboratory, University of Maryland Center of Environmental Science, Cambridge, MD, 21613, USA
| | - Gabrielle Rocap
- School of Oceanography, University of Washington, Seattle, WA, USA
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26
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Perry MJ. A 50-Year Journey from Phosphate to Autonomous Underwater Vehicles. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:1-22. [PMID: 31525127 DOI: 10.1146/annurev-marine-010419-010945] [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: 06/10/2023]
Abstract
This narrative is a personal account of my evolution as a student of phytoplankton and the ocean. Initially I focused on phytoplankton nutrient physiology and uptake, later switching to photosynthetic physiology. Better models of photosynthesis naturally require a better understanding of spectral underwater light fields and absorption coefficients, which precipitated my involvement in the nascent field of bio-optical oceanography. Establishment of the now 34-year-old summer graduate course in ocean optics, which continues to attract students from around the globe, is a legacy of my jumping into optics. The importance of social interactions in advancing science cannot be underestimated; a prime example is how a TGIF gathering led to my immersion in the world of autonomous underwater vehicles for the past two decades of my career. Working with people who you like and respect is also critical; I believe collegial friendship played a major role in the great success of the 2008 North Atlantic Bloom Experiment.
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Affiliation(s)
- Mary Jane Perry
- School of Marine Sciences, University of Maine, Orono, Maine 04469, USA;
- School of Oceanography, University of Washington, Seattle, Washington 98195, USA
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27
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Chi XQ, Wang L, Guo R, Zhao D, Li J, Zhang Y, Jiao N. RuBisCO large subunit gene primers for assessing the CO2-assimilating planktonic community structure in Jiaozhou Bay, China. FEMS Microbiol Lett 2019; 365:5040227. [PMID: 29931181 DOI: 10.1093/femsle/fny140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 06/02/2018] [Indexed: 11/13/2022] Open
Abstract
The protein coding genes (rbcL/cbbL/cbbM) for RuBisCO large subunit, the most abundant protein on earth that drives biological CO2 fixation, were considered as useful marker genes in characterizing CO2-assimilating plankton. However, their community specificity has hindered comprehensive screening of genetic diversity. In this study, six different rbcL/cbbL/cbbM primers were employed to screen clone libraries to identify CO2-assimilating plankton in Jiaozhou Bay. The following community compositions were observed: the community components in Form I A/B rbcL/cbbL clone library mainly comprised Chlorophyta and Proteobacteria, Form ID2 and ID3 libraries consisted of Bacillariophyta, Form II cbbM library consisted of Proteobacteria and Alveolata, and both Form I green and red libraries included Proteobacteria, respectively. At the genus taxonomic level, no overlaps among these clone libraries were observed, except for ID2 and ID3. Overall, the phytoplankton in Jiaozhou Bay mainly consists of Bacillariophyta, Chlorophyta, Cryptophyta, Haptophyceae and Alveolata. The CO2-assimilating prokaryotes mainly consist of Proteobacteria. Considering the high-sequence specificities of these marker genes, we propose that the joint use of multiple primers may be utilized in unveiling the diversity of CO2-assimilating organisms. In addition, designing novel RuBisCO gene primers that generate longer amplicons and have broader phylogenetic coverage may be necessary in the future.
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Affiliation(s)
- Xiang-Qun Chi
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Road, Qingdao 266101, Shandong, China.,BGI-Qingdao, Qingdao 266555, China
| | - Long Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Road, Qingdao 266101, Shandong, China
| | - Ruoyu Guo
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Road, Qingdao 266101, Shandong, China
| | - Dexi Zhao
- Tianjin Branch of China National Offshore Oil Corporation Ltd. Tianjin 300450, China
| | - Jia Li
- Tianjin Branch of China National Offshore Oil Corporation Ltd. Tianjin 300450, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Road, Qingdao 266101, Shandong, China
| | - Nianzhi Jiao
- Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
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28
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Satagopan S, North JA, Arbing MA, Varaljay VA, Haines SN, Wildenthal JA, Byerly KM, Shin A, Tabita FR. Structural Perturbations of Rhodopseudomonas palustris Form II RuBisCO Mutant Enzymes That Affect CO2 Fixation. Biochemistry 2019; 58:3880-3892. [DOI: 10.1021/acs.biochem.9b00617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sriram Satagopan
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Justin A. North
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark A. Arbing
- UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Vanessa A. Varaljay
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sidney N. Haines
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - John A. Wildenthal
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kathryn M. Byerly
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Annie Shin
- UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - F. Robert Tabita
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
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29
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MpsAB is important for Staphylococcus aureus virulence and growth at atmospheric CO 2 levels. Nat Commun 2019; 10:3627. [PMID: 31399577 PMCID: PMC6689103 DOI: 10.1038/s41467-019-11547-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 07/16/2019] [Indexed: 01/06/2023] Open
Abstract
The mechanisms behind carbon dioxide (CO2) dependency in non-autotrophic bacterial isolates are unclear. Here we show that the Staphylococcus aureus mpsAB operon, known to play a role in membrane potential generation, is crucial for growth at atmospheric CO2 levels. The genes mpsAB can complement an Escherichia coli carbonic anhydrase (CA) mutant, and CA from E. coli can complement the S. aureus delta-mpsABC mutant. In comparison with the wild type, S. aureus mps mutants produce less hemolytic toxin and are less virulent in animal models of infection. Homologs of mpsA and mpsB are widespread among bacteria and are often found adjacent to each other on the genome. We propose that MpsAB represents a dissolved inorganic carbon transporter, or bicarbonate concentrating system, possibly acting as a sodium bicarbonate cotransporter.
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30
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Tveit AT, Hestnes AG, Robinson SL, Schintlmeister A, Dedysh SN, Jehmlich N, von Bergen M, Herbold C, Wagner M, Richter A, Svenning MM. Widespread soil bacterium that oxidizes atmospheric methane. Proc Natl Acad Sci U S A 2019; 116:8515-8524. [PMID: 30962365 PMCID: PMC6486757 DOI: 10.1073/pnas.1817812116] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The global atmospheric level of methane (CH4), the second most important greenhouse gas, is currently increasing by ∼10 million tons per year. Microbial oxidation in unsaturated soils is the only known biological process that removes CH4 from the atmosphere, but so far, bacteria that can grow on atmospheric CH4 have eluded all cultivation efforts. In this study, we have isolated a pure culture of a bacterium, strain MG08 that grows on air at atmospheric concentrations of CH4 [1.86 parts per million volume (p.p.m.v.)]. This organism, named Methylocapsa gorgona, is globally distributed in soils and closely related to uncultured members of the upland soil cluster α. CH4 oxidation experiments and 13C-single cell isotope analyses demonstrated that it oxidizes atmospheric CH4 aerobically and assimilates carbon from both CH4 and CO2 Its estimated specific affinity for CH4 (a0s) is the highest for any cultivated methanotroph. However, growth on ambient air was also confirmed for Methylocapsa acidiphila and Methylocapsa aurea, close relatives with a lower specific affinity for CH4, suggesting that the ability to utilize atmospheric CH4 for growth is more widespread than previously believed. The closed genome of M. gorgona MG08 encodes a single particulate methane monooxygenase, the serine cycle for assimilation of carbon from CH4 and CO2, and CO2 fixation via the recently postulated reductive glycine pathway. It also fixes dinitrogen and expresses the genes for a high-affinity hydrogenase and carbon monoxide dehydrogenase, suggesting that atmospheric CH4 oxidizers harvest additional energy from oxidation of the atmospheric trace gases carbon monoxide (0.2 p.p.m.v.) and hydrogen (0.5 p.p.m.v.).
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Affiliation(s)
- Alexander T Tveit
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, 9037 Tromsoe, Norway
| | - Anne Grethe Hestnes
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, 9037 Tromsoe, Norway
| | - Serina L Robinson
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, 9037 Tromsoe, Norway
| | - Arno Schintlmeister
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of Russian Academy of Sciences, 117312 Moscow, Russia
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, 04109 Leipzig, Germany
| | - Craig Herbold
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Michael Wagner
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Andreas Richter
- Center of Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1090 Vienna, Austria
| | - Mette M Svenning
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, 9037 Tromsoe, Norway;
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31
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The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism. Microbiol Mol Biol Rev 2018; 83:83/1/e00040-18. [PMID: 30567937 DOI: 10.1128/mmbr.00040-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ribosyl 1,5-bisphosphate (PRibP) was discovered 65 years ago and was believed to be an important intermediate in ribonucleotide metabolism, a role immediately taken over by its "big brother" phosphoribosyldiphosphate. Only recently has PRibP come back into focus as an important player in the metabolism of ribonucleotides with the discovery of the pentose bisphosphate pathway that comprises, among others, the intermediates PRibP and ribulose 1,5-bisphosphate (cf. ribose 5-phosphate and ribulose 5-phosphate of the pentose phosphate pathway). Enzymes of several pathways produce and utilize PRibP not only in ribonucleotide metabolism but also in the catabolism of phosphonates, i.e., compounds containing a carbon-phosphorus bond. Pathways for PRibP metabolism are found in all three domains of life, most prominently among organisms of the archaeal domain, where they have been identified either experimentally or by bioinformatic analysis within all of the four main taxonomic groups, Euryarchaeota, TACK, DPANN, and Asgard. Advances in molecular genetics of archaea have greatly improved the understanding of the physiology of PRibP metabolism, and reconciliation of molecular enzymology and three-dimensional structure analysis of enzymes producing or utilizing PRibP emphasize the versatility of the compound. Finally, PRibP is also an effector of several metabolic activities in many organisms, including higher organisms such as mammals. In the present review, we describe all aspects of PRibP metabolism, with emphasis on the biochemical, genetic, and physiological aspects of the enzymes that produce or utilize PRibP. The inclusion of high-resolution structures of relevant enzymes that bind PRibP provides evidence for the flexibility and importance of the compound in metabolism.
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32
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Thomas PJ, Boller AJ, Satagopan S, Tabita FR, Cavanaugh CM, Scott KM. Isotope discrimination by form IC RubisCO from
Ralstonia eutropha
and
Rhodobacter sphaeroides
, metabolically versatile members of ‘
Proteobacteria
’ from aquatic and soil habitats. Environ Microbiol 2018; 21:72-80. [DOI: 10.1111/1462-2920.14423] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 09/18/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Phaedra J. Thomas
- Department of Integrative Biology University of South Florida Tampa FL USA
| | - Amanda J. Boller
- Department of Integrative Biology University of South Florida Tampa FL USA
| | - Sriram Satagopan
- Department of Microbiology The Ohio State University Columbus OH USA
| | - F. Robert Tabita
- Department of Microbiology The Ohio State University Columbus OH USA
| | - Colleen M. Cavanaugh
- Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| | - Kathleen M. Scott
- Department of Integrative Biology University of South Florida Tampa FL USA
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33
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Hsieh CJ, Zhan SH, Liao CP, Tang SL, Wang LC, Watanabe T, Geraldino PJL, Liu SL. The effects of contemporary selection and dispersal limitation on the community assembly of acidophilic microalgae. JOURNAL OF PHYCOLOGY 2018; 54:720-733. [PMID: 30055054 DOI: 10.1111/jpy.12771] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 06/07/2018] [Indexed: 06/08/2023]
Abstract
Extremophilic microalgae are primary producers in acidic habitats, such as volcanic sites and acid mine drainages, and play a central role in biogeochemical cycles. Yet, basic knowledge about their species composition and community assembly is lacking. Here, we begin to fill this knowledge gap by performing the first large-scale survey of microalgal diversity in acidic geothermal sites across the West Pacific Island Chain. We collected 72 environmental samples in 12 geothermal sites, measured temperature and pH, and performed rbcL amplicon-based 454 pyrosequencing. Using these data, we estimated the diversity of microalgal species, and then examined the relative contribution of contemporary selection (i.e., local environmental variables) and dispersal limitation on the assembly of these communities. A species delimitation analysis uncovered seven major microalgae (four red, two green, and one diatom) and higher species diversity than previously appreciated. A distance-based redundancy analysis with variation partitioning revealed that dispersal limitation has a greater influence on the community assembly of microalgae than contemporary selection. Consistent with this finding, community similarity among the sampled sites decayed more quickly over geographical distance than differences in environmental factors. Our work paves the way for future studies to understand the ecology and biogeography of microalgae in extreme habitats.
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Affiliation(s)
- Chia-Jung Hsieh
- Department of Life Science, Tunghai University, Taichung, 40704, Taiwan
| | - Shing Hei Zhan
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Chen-Pan Liao
- Department of Life Science, Tunghai University, Taichung, 40704, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Liang-Chi Wang
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, 621, Taiwan
| | - Tsuyoshi Watanabe
- Tohoku National Fisheries Research Institute, Fisheries Research Agency, Miyagi, 985-0001, Japan
| | | | - Shao-Lun Liu
- Department of Life Science, Tunghai University, Taichung, 40704, Taiwan
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Phoma S, Vikram S, Jansson JK, Ansorge IJ, Cowan DA, Van de Peer Y, Makhalanyane TP. Agulhas Current properties shape microbial community diversity and potential functionality. Sci Rep 2018; 8:10542. [PMID: 30002454 PMCID: PMC6043601 DOI: 10.1038/s41598-018-28939-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 06/28/2018] [Indexed: 11/21/2022] Open
Abstract
Understanding the impact of oceanographic features on marine microbial ecosystems remains a major ecological endeavour. Here we assess microbial diversity, community structure and functional capacity along the Agulhas Current system and the Subtropical Front in the South Indian Ocean (SIO). Samples collected from the epipelagic, oxygen minimum and bathypelagic zones were analysed by 16S rRNA gene amplicon and metagenomic sequencing. In contrast to previous studies, we found high taxonomic richness in surface and deep water samples, but generally low richness for OMZ communities. Beta-diversity analysis revealed significant dissimilarity between the three water depths. Most microbial communities were dominated by marine Gammaproteobacteria, with strikingly low levels of picocyanobacteria. Community composition was strongly influenced by specific environmental factors including depth, salinity, and the availability of both oxygen and light. Carbon, nitrogen and sulfur cycling capacity in the SIO was linked to several autotrophic and copiotrophic Alphaproteobacteria and Gammaproteobacteria. Taken together, our data suggest that the environmental conditions in the Agulhas Current system, particularly depth-related parameters, substantially influence microbial community structure. In addition, the capacity for biogeochemical cycling of nitrogen and sulfur is linked primarily to the dominant Gammaproteobacteria taxa, whereas ecologically rare taxa drive carbon cycling.
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Affiliation(s)
- Sandra Phoma
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratories, P.O. Box 999, Richland, WA, USA
| | - Isabelle J Ansorge
- Department of Oceanography and Marine Research Institute (Ma-Re), University of Cape Town, Rondebosch, 7701, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa
| | - Yves Van de Peer
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa
- VIB Centre for Plant Systems Biology, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa.
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Carter MS, Zhang X, Huang H, Bouvier JT, Francisco BS, Vetting MW, Al-Obaidi N, Bonanno JB, Ghosh A, Zallot RG, Andersen HM, Almo SC, Gerlt JA. Functional assignment of multiple catabolic pathways for D-apiose. Nat Chem Biol 2018; 14:696-705. [PMID: 29867142 DOI: 10.1038/s41589-018-0067-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 03/29/2018] [Indexed: 11/09/2022]
Abstract
Colocation of the genes encoding ABC, TRAP, and TCT transport systems and catabolic pathways for the transported ligand provides a strategy for discovering novel microbial enzymes and pathways. We screened solute-binding proteins (SBPs) for ABC transport systems and identified three that bind D-apiose, a branched pentose in the cell walls of higher plants. Guided by sequence similarity networks (SSNs) and genome neighborhood networks (GNNs), the identities of the SBPs enabled the discovery of four catabolic pathways for D-apiose with eleven previously unknown reactions. The new enzymes include D-apionate oxidoisomerase, which catalyzes hydroxymethyl group migration, as well as 3-oxo-isoapionate-4-phosphate decarboxylase and 3-oxo-isoapionate-4-phosphate transcarboxylase/hydrolase, which are RuBisCO-like proteins (RLPs). The web tools for generating SSNs and GNNs are publicly accessible ( http://efi.igb.illinois.edu/efi-est/ ), so similar 'genomic enzymology' strategies for discovering novel pathways can be used by the community.
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Affiliation(s)
- Michael S Carter
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xinshuai Zhang
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hua Huang
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jason T Bouvier
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Brian San Francisco
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nawar Al-Obaidi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jeffrey B Bonanno
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Agnidipta Ghosh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi G Zallot
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Harvey M Andersen
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - John A Gerlt
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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36
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Boden R, Scott KM. Evaluation of the genus Thiothrix Winogradsky 1888 (Approved Lists 1980) emend. Aruga et al. 2002: reclassification of Thiothrix disciformis to Thiolinea disciformis gen. nov., comb. nov., and of Thiothrix flexilis to Thiofilum flexile gen. nov., comb nov., with emended description of Thiothrix. Int J Syst Evol Microbiol 2018; 68:2226-2239. [PMID: 29851374 DOI: 10.1099/ijsem.0.002816] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thiothrix is the type genus of the Thiotrichaceae in the Thiotrichales of the Gammaproteobacteria, comprising nine species of sulfur-oxidising filamentous bacteria, which are variously autotrophic, heterotrophic or have mixed metabolic modes. Within the genus, four species show 16S rRNA gene identities lower the Yarza threshold for the rank of genus (94.5 %) - Thiothrix disciformis, Thiothrix flexilis, Thiothrix defluvii and Thiothrix eikelboomii - as they show no affiliation to extant genera, a polyphasic study was undertaken including biochemical, physiological and genomic properties and phylogeny based on the 16S rRNA gene (rrs), recombination protein A (RecA), polynucleotide nucleotidyltransferase (Pnp), translation initiation factor IF-2 (InfB), glyceraldehyde-3-phosphate dehydrogenase (GapA), glutaminyl-tRNA synthetase (GlnS), elongation factor EF-G (FusA) and concatamers of 53 ribosomal proteins encoded by rps, rpl and rpm operons, all of which support the reclassification of these species. We thus propose Thiolinea gen. nov. and Thiofilum gen. nov. for which the type species are Thiolinea disciformis gen. nov., comb. nov. and Thiofilum flexile gen. nov., comb. nov. We also propose that these genera are each circumscribed into novel families Thiolinaceae fam. nov. and Thiofilaceae fam. nov., and that Leucothrix and Cocleimonas are circumscribed into Leucotrichaceaefam. nov. and provide emended descriptions of Thiothrix and Thiotrichaceae.
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Affiliation(s)
- Rich Boden
- Sustainable Earth Institute, University of Plymouth, Plymouth, UK.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - Kathleen M Scott
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
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37
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Scott KM, Williams J, Porter CMB, Russel S, Harmer TL, Paul JH, Antonen KM, Bridges MK, Camper GJ, Campla CK, Casella LG, Chase E, Conrad JW, Cruz MC, Dunlap DS, Duran L, Fahsbender EM, Goldsmith DB, Keeley RF, Kondoff MR, Kussy BI, Lane MK, Lawler S, Leigh BA, Lewis C, Lostal LM, Marking D, Mancera PA, McClenthan EC, McIntyre EA, Mine JA, Modi S, Moore BD, Morgan WA, Nelson KM, Nguyen KN, Ogburn N, Parrino DG, Pedapudi AD, Pelham RP, Preece AM, Rampersad EA, Richardson JC, Rodgers CM, Schaffer BL, Sheridan NE, Solone MR, Staley ZR, Tabuchi M, Waide RJ, Wanjugi PW, Young S, Clum A, Daum C, Huntemann M, Ivanova N, Kyrpides N, Mikhailova N, Palaniappan K, Pillay M, Reddy TBK, Shapiro N, Stamatis D, Varghese N, Woyke T, Boden R, Freyermuth SK, Kerfeld CA. Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments. Environ Microbiol 2018. [PMID: 29521452 DOI: 10.1111/1462-2920.14090] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemolithoautotrophic bacteria from the genera Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira are common, sometimes dominant, isolates from sulfidic habitats including hydrothermal vents, soda and salt lakes and marine sediments. Their genome sequences confirm their membership in a deeply branching clade of the Gammaproteobacteria. Several adaptations to heterogeneous habitats are apparent. Their genomes include large numbers of genes for sensing and responding to their environment (EAL- and GGDEF-domain proteins and methyl-accepting chemotaxis proteins) despite their small sizes (2.1-3.1 Mbp). An array of sulfur-oxidizing complexes are encoded, likely to facilitate these organisms' use of multiple forms of reduced sulfur as electron donors. Hydrogenase genes are present in some taxa, including group 1d and 2b hydrogenases in Hydrogenovibrio marinus and H. thermophilus MA2-6, acquired via horizontal gene transfer. In addition to high-affinity cbb3 cytochrome c oxidase, some also encode cytochrome bd-type quinol oxidase or ba3 -type cytochrome c oxidase, which could facilitate growth under different oxygen tensions, or maintain redox balance. Carboxysome operons are present in most, with genes downstream encoding transporters from four evolutionarily distinct families, which may act with the carboxysomes to form CO2 concentrating mechanisms. These adaptations to habitat variability likely contribute to the cosmopolitan distribution of these organisms.
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Affiliation(s)
- Kathleen M Scott
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - John Williams
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Cody M B Porter
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Sydney Russel
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Tara L Harmer
- Biology Program, Stockton University, Galloway, NJ, USA
| | - John H Paul
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Kirsten M Antonen
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Megan K Bridges
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Gary J Camper
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Christie K Campla
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Leila G Casella
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Eva Chase
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - James W Conrad
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Mercedez C Cruz
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Darren S Dunlap
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Laura Duran
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Elizabeth M Fahsbender
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Dawn B Goldsmith
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Ryan F Keeley
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Matthew R Kondoff
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Breanna I Kussy
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Marannda K Lane
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Stephanie Lawler
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Brittany A Leigh
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Courtney Lewis
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Lygia M Lostal
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Devon Marking
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Paola A Mancera
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Evan C McClenthan
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Emily A McIntyre
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Jessica A Mine
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Swapnil Modi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Brittney D Moore
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - William A Morgan
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Kaleigh M Nelson
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Kimmy N Nguyen
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Nicholas Ogburn
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - David G Parrino
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Anangamanjari D Pedapudi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Rebecca P Pelham
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Amanda M Preece
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Elizabeth A Rampersad
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Jason C Richardson
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Christina M Rodgers
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Brent L Schaffer
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Nancy E Sheridan
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Michael R Solone
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Zachery R Staley
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Maki Tabuchi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Ramond J Waide
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Pauline W Wanjugi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Suzanne Young
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Alicia Clum
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | - Manoj Pillay
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - T B K Reddy
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Nicole Shapiro
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Neha Varghese
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Rich Boden
- School of Biological & Marine Sciences, University of Plymouth, Drake Circus, Plymouth, UK.,Sustainable Earth Institute, University of Plymouth, Drake Circus, Plymouth, UK
| | | | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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38
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Vitlin Gruber A, Feiz L. Rubisco Assembly in the Chloroplast. Front Mol Biosci 2018; 5:24. [PMID: 29594130 PMCID: PMC5859369 DOI: 10.3389/fmolb.2018.00024] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/27/2018] [Indexed: 01/13/2023] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the rate-limiting step in the Calvin-Benson cycle, which transforms atmospheric carbon into a biologically useful carbon source. The slow catalytic rate of Rubisco and low substrate specificity necessitate the production of high levels of this enzyme. In order to engineer a more efficient plant Rubisco, we need to better understand its folding and assembly process. Form I Rubisco, found in green algae and vascular plants, is a hexadecamer composed of 8 large subunits (RbcL), encoded by the chloroplast genome and 8 small, nuclear-encoded subunits (RbcS). Unlike its cyanobacterial homolog, which can be reconstituted in vitro or in E. coli, assisted by bacterial chaperonins (GroEL-GroES) and the RbcX chaperone, biogenesis of functional chloroplast Rubisco requires Cpn60-Cpn20, the chloroplast homologs of GroEL-GroES, and additional auxiliary factors, including Rubisco accumulation factor 1 (Raf1), Rubisco accumulation factor 2 (Raf2) and Bundle sheath defective 2 (Bsd2). The discovery and characterization of these factors paved the way for Arabidopsis Rubisco assembly in E. coli. In the present review, we discuss the uniqueness of hetero-oligomeric chaperonin complex for RbcL folding, as well as the sequential or concurrent actions of the post-chaperonin chaperones in holoenzyme assembly. The exact stages at which each assembly factor functions are yet to be determined. Expression of Arabidopsis Rubisco in E. coli provided some insight regarding the potential roles for Raf1 and RbcX in facilitating RbcL oligomerization, for Bsd2 in stabilizing the oligomeric core prior to holoenzyme assembly, and for Raf2 in interacting with both RbcL and RbcS. In the long term, functional characterization of each known factor along with the potential discovery and characterization of additional factors will set the stage for designing more efficient plants, with a greater biomass, for use in biofuels and sustenance.
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Affiliation(s)
- Anna Vitlin Gruber
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Leila Feiz
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
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Martin WF, Bryant DA, Beatty JT. A physiological perspective on the origin and evolution of photosynthesis. FEMS Microbiol Rev 2018; 42:205-231. [PMID: 29177446 PMCID: PMC5972617 DOI: 10.1093/femsre/fux056] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/20/2017] [Indexed: 12/22/2022] Open
Abstract
The origin and early evolution of photosynthesis are reviewed from an ecophysiological perspective. Earth's first ecosystems were chemotrophic, fueled by geological H2 at hydrothermal vents and, required flavin-based electron bifurcation to reduce ferredoxin for CO2 fixation. Chlorophyll-based phototrophy (chlorophototrophy) allowed autotrophs to generate reduced ferredoxin without electron bifurcation, providing them access to reductants other than H2. Because high-intensity, short-wavelength electromagnetic radiation at Earth's surface would have been damaging for the first chlorophyll (Chl)-containing cells, photosynthesis probably arose at hydrothermal vents under low-intensity, long-wavelength geothermal light. The first photochemically active pigments were possibly Zn-tetrapyrroles. We suggest that (i) after the evolution of red-absorbing Chl-like pigments, the first light-driven electron transport chains reduced ferredoxin via a type-1 reaction center (RC) progenitor with electrons from H2S; (ii) photothioautotrophy, first with one RC and then with two, was the bridge between H2-dependent chemolithoautotrophy and water-splitting photosynthesis; (iii) photothiotrophy sustained primary production in the photic zone of Archean oceans; (iv) photosynthesis arose in an anoxygenic cyanobacterial progenitor; (v) Chl a is the ancestral Chl; and (vi), anoxygenic chlorophototrophic lineages characterized so far acquired, by horizontal gene transfer, RCs and Chl biosynthesis with or without autotrophy, from the architects of chlorophototrophy-the cyanobacterial lineage.
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Affiliation(s)
- William F Martin
- Institute for Molecular Evolution, University of Düsseldorf, D-40225 Düsseldorf, Germany
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
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40
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Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota. ISME JOURNAL 2018; 12:1021-1031. [PMID: 29445130 DOI: 10.1038/s41396-018-0060-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 12/12/2017] [Accepted: 01/10/2018] [Indexed: 12/21/2022]
Abstract
Thorarchaeota are a new archaeal phylum within the Asgard superphylum, whose ancestors have been proposed to play possible ecological roles in cellular evolution. However, little is known about the lifestyles of these uncultured archaea. To provide a better resolution of the ecological roles and metabolic capacity of Thorarchaeota, we obtained Thorarchaeota genomes reconstructed from metagenomes of different depth layers in mangrove and mudflat sediments. These genomes from deep anoxic layers suggest the presence of Thorarchaeota with the potential to degrade organic matter, fix inorganic carbon, reduce sulfur/sulfate and produce acetate. In particular, Thorarchaeota may be involved in ethanol production, nitrogen fixation, nitrite reduction, and arsenic detoxification. Interestingly, these Thorarchaeotal genomes are inferred to contain the tetrahydromethanopterin and tetrahydrofolate Wood-Ljungdahl (WL) pathways for CO2 reduction, and the latter WL pathway appears to have originated from bacteria. These archaea are predicted to be able to use various inorganic and organic carbon sources, possessing genes inferred to encode ribulose bisphosphate carboxylase-like proteins (normally without RuBisCO activity) and a near-complete Calvin-Benson-Bassham cycle. The existence of eukaryotic selenocysteine insertion sequences and many genes for proteins previously considered eukaryote-specific in Thorarchaeota genomes provide new insights into their evolutionary roles in the origin of eukaryotic cellular complexity. Resolving the metabolic capacities of these enigmatic archaea and their origins will enhance our understanding of the origins of eukaryotes and their roles in ecosystems.
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41
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Lin MT, Hanson MR. Red algal Rubisco fails to accumulate in transplastomic tobacco expressing Griffithsia monilis RbcL and RbcS genes. PLANT DIRECT 2018; 2:e00045. [PMID: 31245711 PMCID: PMC6508576 DOI: 10.1002/pld3.45] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/28/2018] [Accepted: 01/30/2018] [Indexed: 05/03/2023]
Abstract
In C3 plants, the carbon fixation step catalyzed by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) represents a major rate-limiting step due to the competing oxygenation reaction, which leads to the energy-intensive photorespiration and lowers the overall photosynthetic efficiency. Hence, there is great biotechnological interest in replacing the Rubisco in C3 crops with a more efficient enzyme. The Rubisco enzymes from red algae are among the most attractive choices due to their remarkable preference for carboxylation over oxygenation reaction. However, the biogenesis of Rubisco is extremely complex. The Rubisco enzymes in plants, algae, and cyanobacteria are made up of eight large and eight small subunits. The folding of the large subunits and the assembly of the large subunits with the small subunits to form a functional holoenzyme require specific chaperonin complexes and assembly factors. As a result, previous success in expressing foreign Rubisco in plants has been limited to Rubisco large subunits from closely related plant species and simpler bacterial enzymes. In our previous work, we successfully replaced the Rubisco in tobacco with a cyanobacterial enzyme, which was able to support the phototrophic growth of the transgenic plants. In this work, we used the same approach to express the Rubisco subunits from the red alga Griffithsia monilis in tobacco chloroplasts in the absence of the tobacco Rubisco large subunit. Although the red algal Rubisco genes are being transcribed in tobacco chloroplasts, the transgenic plants lack functional Rubisco and can only grow in a medium containing sucrose. Our results suggest that co-expression of compatible chaperones will be necessary for successful assembly of red algal Rubisco in plants.
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Affiliation(s)
- Myat T. Lin
- Department of Molecular Biology and GeneticsCornell UniversityIthacaNYUSA
| | - Maureen R. Hanson
- Department of Molecular Biology and GeneticsCornell UniversityIthacaNYUSA
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Ślesak I, Ślesak H, Kruk J. RubisCO Early Oxygenase Activity: A Kinetic and Evolutionary Perspective. Bioessays 2017; 39. [PMID: 28976010 DOI: 10.1002/bies.201700071] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/10/2017] [Indexed: 11/09/2022]
Abstract
RubisCO (D-ribulose 1,5-bisphosphate carboxylase/oxygenase) is Earth's main enzyme responsible for CO2 fixation via carboxylation of ribulose-1,5-bisphosphate (RuBP) into organic matter. Besides the carboxylation reaction, RubisCO also catalyzes the oxygenation of RuBP by O2 , which is probably as old as its carboxylation properties. Based on molecular phylogeny, the occurrence of the reactive oxygen species (ROS)-removing system and kinetic properties of different RubisCO forms, we postulated that RubisCO oxygenase activity appeared in local microoxic areas, yet before the appearance of oxygenic photosynthesis. Here, in reviewing the literature, we present a novel hypothesis: the RubisCO early oxygenase activity hypothesis. This hypothesis may be compared with the exaptation hypothesis, according to which latent RubisCO oxygenase properties emerged later during the oxygenation of the Earth's atmosphere. The reconstruction of ancestral RubisCO forms using ancestral sequence reconstruction (ASR) techniques, as a promising way for testing of RubisCO early oxygenase activity hypothesis, is presented.
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Affiliation(s)
- Ireneusz Ślesak
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, Kraków 30-239, Poland
| | - Halina Ślesak
- Institute of Botany, Jagiellonian University, Gronostajowa 9, Kraków 30-387, Poland
| | - Jerzy Kruk
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland
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Kacar B, Hanson‐Smith V, Adam ZR, Boekelheide N. Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree. GEOBIOLOGY 2017; 15:628-640. [PMID: 28670785 PMCID: PMC5575542 DOI: 10.1111/gbi.12243] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 05/09/2017] [Indexed: 05/04/2023]
Abstract
Ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO, or Rubisco) catalyzes a key reaction by which inorganic carbon is converted into organic carbon in the metabolism of many aerobic and anaerobic organisms. Across the broader Rubisco protein family, homologs exhibit diverse biochemical characteristics and metabolic functions, but the evolutionary origins of this diversity are unclear. Evidence of the timing of Rubisco family emergence and diversification of its different forms has been obscured by a meager paleontological record of early Earth biota, their subcellular physiology and metabolic components. Here, we use computational models to reconstruct a Rubisco family phylogenetic tree, ancestral amino acid sequences at branching points on the tree, and protein structures for several key ancestors. Analysis of historic substitutions with respect to their structural locations shows that there were distinct periods of amino acid substitution enrichment above background levels near and within its oxygen-sensitive active site and subunit interfaces over the divergence between Form III (associated with anoxia) and Form I (associated with oxia) groups in its evolutionary history. One possible interpretation is that these periods of substitutional enrichment are coincident with oxidative stress exerted by the rise of oxygenic photosynthesis in the Precambrian era. Our interpretation implies that the periods of Rubisco substitutional enrichment inferred near the transition from anaerobic Form III to aerobic Form I ancestral sequences predate the acquisition of Rubisco by fully derived cyanobacterial (i.e., dual photosystem-bearing, oxygen-evolving) clades. The partitioning of extant lineages at high clade levels within our Rubisco phylogeny indicates that horizontal transfer of Rubisco is a relatively infrequent event. Therefore, it is possible that the mutational enrichment periods between the Form III and Form I common ancestral sequences correspond to the adaptation of key oxygen-sensitive components of Rubisco prior to, or coincident with, the Great Oxidation Event.
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Affiliation(s)
- B. Kacar
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
| | - V. Hanson‐Smith
- Department of Microbiology and ImmunologyUniversity of California San FranciscoSan FranciscoCAUSA
| | - Z. R. Adam
- Department of Earth and Planetary SciencesHarvard UniversityCambridgeMAUSA
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Erb TJ, Zarzycki J. A short history of RubisCO: the rise and fall (?) of Nature's predominant CO 2 fixing enzyme. Curr Opin Biotechnol 2017; 49:100-107. [PMID: 28843191 DOI: 10.1016/j.copbio.2017.07.017] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/26/2017] [Accepted: 07/26/2017] [Indexed: 11/18/2022]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is arguably one of the most abundant proteins in the biosphere and a key enzyme in the global carbon cycle. Although RubisCO has been intensively studied, its evolutionary origins and rise as Nature's most dominant carbon dioxide (CO2)-fixing enzyme still remain in the dark. In this review we will bring together biochemical, structural, physiological, microbiological, as well as phylogenetic data to speculate on the evolutionary roots of the CO2-fixation reaction of RubisCO, the emergence of RubisCO-based autotrophic CO2-fixation in the context of the Calvin-Benson-Bassham cycle, and the further evolution of RubisCO into the 'RubisCOsome', a complex of various proteins assembling and interacting with the enzyme to improve its operational capacity (functionality) under different biological and environmental conditions.
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Affiliation(s)
- Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry and Synthetic Metabolism, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany.
| | - Jan Zarzycki
- Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry and Synthetic Metabolism, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
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Yang J, Yin L, Lessner FH, Nakayasu ES, Payne SH, Fixen KR, Gallagher L, Harwood CS. Genes essential for phototrophic growth by a purple alphaproteobacterium. Environ Microbiol 2017; 19:3567-3578. [PMID: 28677146 DOI: 10.1111/1462-2920.13852] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 06/13/2017] [Accepted: 06/28/2017] [Indexed: 12/01/2022]
Abstract
Tn-seq was used to identify genes essential for phototrophic growth by the purple bacterium Rhodopseudomonas palustris. About 167 genes required for anaerobic growth on acetate in light were identified, 35 of which are annotated as photosynthesis genes. The essentiality of many of these genes by analysing the phenotypes of independently generated mutants that had altered pigmentation was verified. Three genes were identified, two possibly involved in biogenesis of the membrane-bound photosynthetic apparatus and one for phosphatidylcholine biosynthesis, that were not known to be essential for phototrophic growth. Site-directed mutagenesis was used to show that the NADH:quinone oxidoreductase complex IE was essential for phototrophic growth under strictly anaerobic conditions and appeared to play a role in reverse electron transport to generate NADH. A homologous NADH:quinone oxidoreductase complex IA likely operates in the opposite direction to oxidize NADH. The operation of the two enzymes in opposition would allow R. palustris to maintain redox balance. As a complement to the genetic data, proteomics experiments were carried out in which it was found that 408 proteins were present in significantly higher amounts in cells grown anaerobically in light compared with aerobically. Among these were proteins encoded by subset of the phototrophic growth-essential genes.
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Affiliation(s)
- Jianming Yang
- Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.,Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Liang Yin
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Faith H Lessner
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Samuel H Payne
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kathryn R Fixen
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Larry Gallagher
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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Quasem I, Achille AN, Caddick BA, Carter TA, Daniels C, Delaney JA, Delic V, Denton KA, Duran MC, Fatica MK, Ference CM, Galkiewicz JP, Garcia AM, Hendrick JD, Horton SA, Kun MS, Koch PW, Lee TM, McCabe CR, McHale S, McDaniel LD, Menning DM, Menning KJ, Mirzaei-Souderjani H, Mostajabian S, Nicholson DA, Nugent CK, Osman NP, Pappas DI, Rocha AM, Rosario K, Rubelmann H, Schwartz JA, Seeley KW, Staley CM, Wallace EM, Wong TM, Zielinski BL, Hanson TE, Scott KM. Peculiar citric acid cycle of hydrothermal vent chemolithoautotroph Hydrogenovibrio crunogenus, and insights into carbon metabolism by obligate autotrophs. FEMS Microbiol Lett 2017; 364:3958794. [DOI: 10.1093/femsle/fnx148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/10/2017] [Indexed: 12/24/2022] Open
Affiliation(s)
- Ishtiaque Quasem
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Alexandra N. Achille
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Brittany A. Caddick
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Travis A. Carter
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Camille Daniels
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Jennifer A. Delaney
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Vedad Delic
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Kimberly A. Denton
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Martina C. Duran
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Marianne K. Fatica
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | | | - Julie P. Galkiewicz
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Ana M. Garcia
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | | | - Steven A. Horton
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Mey S. Kun
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Phoebe W. Koch
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Tien Min Lee
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Christie R. McCabe
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Sean McHale
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Lauren D. McDaniel
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Damian M. Menning
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Kristy J. Menning
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | | | - Salina Mostajabian
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - David A. Nicholson
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Courtney K. Nugent
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Nicholas P. Osman
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Desiree I. Pappas
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Andrea M. Rocha
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Karyna Rosario
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Haydn Rubelmann
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Julie A. Schwartz
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Kent W. Seeley
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Christopher M. Staley
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Elizabeth M. Wallace
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Terianne M. Wong
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Brian L. Zielinski
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Thomas E. Hanson
- School of Marine Science and Policy, Delaware Biotechnology Institute, and Department of Biological Sciences, University of Delaware, Newark, DE 19711, USA
| | - Kathleen M. Scott
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
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Shen C, Dupont CL, Hopkinson BM. The diversity of CO2-concentrating mechanisms in marine diatoms as inferred from their genetic content. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3937-3948. [PMID: 28510761 PMCID: PMC5853954 DOI: 10.1093/jxb/erx163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/24/2017] [Indexed: 05/24/2023]
Abstract
Marine diatoms are one of the most ecologically significant primary producers in the ocean. Most diatoms use a CO2-concentrating mechanism (CCM) to overcome the scarcity of CO2 in the ocean and limitations of the carbon-fixing enzyme Rubisco. However, the CCMs in model diatoms differ substantially in their genetic make-up and structural organization. To assess the extent of CCM diversity in marine diatoms more generally, we analyzed genome and transcriptome data from 31 diatom strains to identify putative CCM genes, examine the overall CCM architecture, and study CCM development in the context of the evolutionary history of these diatoms. Key CCM genes [carbonic anhydrases (CAs) and solute carrier 4 (SLC4) bicarbonate transporters] identified in the diatoms were placed into groups of likely orthologs by sequence similarity (OrthoMCL) and phylogenetic methods. These analyses indicated that diatoms seem to share similar HCO3- transporters, but possess a variety of CAs that have either undergone extensive diversification within the diatom lineage or have been acquired through horizontal gene transfer. Hierarchical clustering of the diatom species based on their CCM gene content suggests that CCM development is largely congruent with evolution of diatom species, despite some notable differences in CCM genes even among closely related species.
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Affiliation(s)
- Chen Shen
- Qingdao Institute of BioEnergy and BioProcess Technology, Chinese Academy of Sciences, Qingdao, China
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | | | - Brian M Hopkinson
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
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Boden R, Scott KM, Williams J, Russel S, Antonen K, Rae AW, Hutt LP. An evaluation of Thiomicrospira, Hydrogenovibrio and Thioalkalimicrobium: reclassification of four species of Thiomicrospira to each Thiomicrorhabdus gen. nov. and Hydrogenovibrio, and reclassification of all four species of Thioalkalimicrobium to Thiomicrospira. Int J Syst Evol Microbiol 2017; 67:1140-1151. [DOI: 10.1099/ijsem.0.001855] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rich Boden
- Sustainable Earth Institute, University of Plymouth, Drake Circus, Plymouth, UK
- School of Biological & Marine Sciences, University of Plymouth, Drake Circus, Plymouth, UK
| | - Kathleen M Scott
- Department of Integrative Biology, University of South Florida, East Fowler Avenue, Tampa, FL, USA
| | - John Williams
- Department of Integrative Biology, University of South Florida, East Fowler Avenue, Tampa, FL, USA
| | - Sydney Russel
- Department of Integrative Biology, University of South Florida, East Fowler Avenue, Tampa, FL, USA
| | - Kirsten Antonen
- Department of Integrative Biology, University of South Florida, East Fowler Avenue, Tampa, FL, USA
| | - Alex W Rae
- School of Biological & Marine Sciences, University of Plymouth, Drake Circus, Plymouth, UK
| | - Lee P Hutt
- Sustainable Earth Institute, University of Plymouth, Drake Circus, Plymouth, UK
- School of Biological & Marine Sciences, University of Plymouth, Drake Circus, Plymouth, UK
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49
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Bracher A, Whitney SM, Hartl FU, Hayer-Hartl M. Biogenesis and Metabolic Maintenance of Rubisco. ANNUAL REVIEW OF PLANT BIOLOGY 2017; 68:29-60. [PMID: 28125284 DOI: 10.1146/annurev-arplant-043015-111633] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) mediates the fixation of atmospheric CO2 in photosynthesis by catalyzing the carboxylation of the 5-carbon sugar ribulose-1,5-bisphosphate (RuBP). Rubisco is a remarkably inefficient enzyme, fixing only 2-10 CO2 molecules per second. Efforts to increase crop yields by bioengineering Rubisco remain unsuccessful, owing in part to the complex cellular machinery required for Rubisco biogenesis and metabolic maintenance. The large subunit of Rubisco requires the chaperonin system for folding, and recent studies have shown that assembly of hexadecameric Rubisco is mediated by specific assembly chaperones. Moreover, Rubisco function can be inhibited by a range of sugar-phosphate ligands, including RuBP. Metabolic repair depends on remodeling of Rubisco by the ATP-dependent Rubisco activase and hydrolysis of inhibitory sugar phosphates by specific phosphatases. Here, we review our present understanding of the structure and function of these auxiliary factors and their utilization in efforts to engineer more catalytically efficient Rubisco enzymes.
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Affiliation(s)
- Andreas Bracher
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany ; , ,
| | - Spencer M Whitney
- Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601, Australia;
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany ; , ,
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany ; , ,
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Proteomic and Mutant Analysis of the CO 2 Concentrating Mechanism of Hydrothermal Vent Chemolithoautotroph Thiomicrospira crunogena. J Bacteriol 2017; 199:JB.00871-16. [PMID: 28115547 DOI: 10.1128/jb.00871-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/12/2017] [Indexed: 12/21/2022] Open
Abstract
Many autotrophic microorganisms are likely to adapt to scarcity in dissolved inorganic carbon (DIC; CO2 + HCO3- + CO32-) with CO2 concentrating mechanisms (CCM) that actively transport DIC across the cell membrane to facilitate carbon fixation. Surprisingly, DIC transport has been well studied among cyanobacteria and microalgae only. The deep-sea vent gammaproteobacterial chemolithoautotroph Thiomicrospira crunogena has a low-DIC inducible CCM, though the mechanism for uptake is unclear, as homologs to cyanobacterial transporters are absent. To identify the components of this CCM, proteomes of T. crunogena cultivated under low- and high-DIC conditions were compared. Fourteen proteins, including those comprising carboxysomes, were at least 4-fold more abundant under low-DIC conditions. One of these proteins was encoded by Tcr_0854; strains carrying mutated copies of this gene, as well as the adjacent Tcr_0853, required elevated DIC for growth. Strains carrying mutated copies of Tcr_0853 and Tcr_0854 overexpressed carboxysomes and had diminished ability to accumulate intracellular DIC. Based on reverse transcription (RT)-PCR, Tcr_0853 and Tcr_0854 were cotranscribed and upregulated under low-DIC conditions. The Tcr_0853-encoded protein was predicted to have 13 transmembrane helices. Given the mutant phenotypes described above, Tcr_0853 and Tcr_0854 may encode a two-subunit DIC transporter that belongs to a previously undescribed transporter family, though it is widespread among autotrophs from multiple phyla.IMPORTANCE DIC uptake and fixation by autotrophs are the primary input of inorganic carbon into the biosphere. The mechanism for dissolved inorganic carbon uptake has been characterized only for cyanobacteria despite the importance of DIC uptake by autotrophic microorganisms from many phyla among the Bacteria and Archaea In this work, proteins necessary for dissolved inorganic carbon utilization in the deep-sea vent chemolithoautotroph T. crunogena were identified, and two of these may be able to form a novel transporter. Homologs of these proteins are present in 14 phyla in Bacteria and also in one phylum of Archaea, the Euryarchaeota Many organisms carrying these homologs are autotrophs, suggesting a role in facilitating dissolved inorganic carbon uptake and fixation well beyond the genus Thiomicrospira.
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