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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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Metagenomic Approaches as a Tool to Unravel Promising Biocatalysts from Natural Resources: Soil and Water. Catalysts 2022. [DOI: 10.3390/catal12040385] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Natural resources are considered a promising source of microorganisms responsible for producing biocatalysts with great relevance in several industrial areas. However, a significant fraction of the environmental microorganisms remains unknown or unexploited due to the limitations associated with their cultivation in the laboratory through classical techniques. Metagenomics has emerged as an innovative and strategic approach to explore these unculturable microorganisms through the analysis of DNA extracted from environmental samples. In this review, a detailed discussion is presented on the application of metagenomics to unravel the biotechnological potential of natural resources for the discovery of promising biocatalysts. An extensive bibliographic survey was carried out between 2010 and 2021, covering diverse metagenomic studies using soil and/or water samples from different types and locations. The review comprises, for the first time, an overview of the worldwide metagenomic studies performed in soil and water and provides a complete and global vision of the enzyme diversity associated with each specific environment.
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3
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Davidi D, Shamshoum M, Guo Z, Bar‐On YM, Prywes N, Oz A, Jablonska J, Flamholz A, Wernick DG, Antonovsky N, de Pins B, Shachar L, Hochhauser D, Peleg Y, Albeck S, Sharon I, Mueller‐Cajar O, Milo R. Highly active rubiscos discovered by systematic interrogation of natural sequence diversity. EMBO J 2020; 39:e104081. [PMID: 32500941 PMCID: PMC7507306 DOI: 10.15252/embj.2019104081] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 04/30/2020] [Accepted: 05/07/2020] [Indexed: 11/09/2022] Open
Abstract
CO2 is converted into biomass almost solely by the enzyme rubisco. The poor carboxylation properties of plant rubiscos have led to efforts that made it the most kinetically characterized enzyme, yet these studies focused on < 5% of its natural diversity. Here, we searched for fast-carboxylating variants by systematically mining genomic and metagenomic data. Approximately 33,000 unique rubisco sequences were identified and clustered into ≈ 1,000 similarity groups. We then synthesized, purified, and biochemically tested the carboxylation rates of 143 representatives, spanning all clusters of form-II and form-II/III rubiscos. Most variants (> 100) were active in vitro, with the fastest having a turnover number of 22 ± 1 s-1 -sixfold faster than the median plant rubisco and nearly twofold faster than the fastest measured rubisco to date. Unlike rubiscos from plants and cyanobacteria, the fastest variants discovered here are homodimers and exhibit a much simpler folding and activation kinetics. Our pipeline can be utilized to explore the kinetic space of other enzymes of interest, allowing us to get a better view of the biosynthetic potential of the biosphere.
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Affiliation(s)
- Dan Davidi
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
Department of GeneticsHarvard Medical SchoolBostonMAUSA
| | - Melina Shamshoum
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Zhijun Guo
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Yinon M Bar‐On
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Noam Prywes
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Aia Oz
- Migal Galilee Research InstituteKiryat ShmonaIsrael
- Tel Hai CollegeUpper GalileeIsrael
| | - Jagoda Jablonska
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Avi Flamholz
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - David G Wernick
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
BASF Enzymes LLCSan DiegoCAUSA
| | - Niv Antonovsky
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
Laboratory of Genetically Encoded Small MoleculesThe Rockefeller UniversityNew YorkNYUSA
| | - Benoit de Pins
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Lior Shachar
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Dina Hochhauser
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Yoav Peleg
- Department of Life Sciences Core FacilitiesWeizmann Institute of ScienceRehovotIsrael
| | - Shira Albeck
- Department of Life Sciences Core FacilitiesWeizmann Institute of ScienceRehovotIsrael
| | - Itai Sharon
- Migal Galilee Research InstituteKiryat ShmonaIsrael
- Tel Hai CollegeUpper GalileeIsrael
| | | | - Ron Milo
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
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Selection of Cyanobacterial ( Synechococcus sp. Strain PCC 6301) RubisCO Variants with Improved Functional Properties That Confer Enhanced CO 2-Dependent Growth of Rhodobacter capsulatus, a Photosynthetic Bacterium. mBio 2019; 10:mBio.01537-19. [PMID: 31337726 PMCID: PMC6650557 DOI: 10.1128/mbio.01537-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RubisCO catalysis has a significant impact on mitigating greenhouse gas accumulation and CO2 conversion to food, fuel, and other organic compounds required to sustain life. Because RubisCO-dependent CO2 fixation is severely compromised by oxygen inhibition and other physiological constraints, improving RubisCO’s kinetic properties to enhance growth in the presence of atmospheric O2 levels has been a longstanding goal. In this study, RubisCO variants with superior structure-functional properties were selected which resulted in enhanced growth of an autotrophic host organism (R. capsulatus), indicating that RubisCO function was indeed growth limiting. It is evident from these results that genetically engineered RubisCO with kinetically enhanced properties can positively impact growth rates in primary producers. Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a ubiquitous enzyme that catalyzes the conversion of atmospheric CO2 into organic carbon in primary producers. All naturally occurring RubisCOs have low catalytic turnover rates and are inhibited by oxygen. Evolutionary adaptations of the enzyme and its host organisms to changing atmospheric oxygen concentrations provide an impetus to artificially evolve RubisCO variants under unnatural selective conditions. A RubisCO deletion strain of the nonsulfur purple photosynthetic bacterium Rhodobacter capsulatus was previously used as a heterologous host for directed evolution and suppressor selection studies that led to the identification of a conserved hydrophobic region near the active site where amino acid substitutions selectively impacted the enzyme’s sensitivity to O2. In this study, structural alignments, mutagenesis, suppressor selection, and growth complementation with R. capsulatus under anoxic or oxygenic conditions were used to analyze the importance of semiconserved residues in this region of Synechococcus RubisCO. RubisCO mutant substitutions were identified that provided superior CO2-dependent growth capabilities relative to the wild-type enzyme. Kinetic analyses of the mutant enzymes indicated that enhanced growth performance was traceable to differential interactions of the enzymes with CO2 and O2. Effective residue substitutions also appeared to be localized to two other conserved hydrophobic regions of the holoenzyme. Structural comparisons and similarities indicated that regions identified in this study may be targeted for improvement in RubisCOs from other sources, including crop plants.
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Seeking active RubisCOs from the currently uncultured microbial majority colonizing deep-sea hydrothermal vent environments. ISME JOURNAL 2019; 13:2475-2488. [PMID: 31182769 DOI: 10.1038/s41396-019-0439-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 04/18/2019] [Accepted: 05/03/2019] [Indexed: 12/22/2022]
Abstract
Almost all the inorganic carbon on Earth is converted into biomass via the Calvin-Benson-Bassham (CBB) cycle. Here, the central carboxylation reaction is catalyzed by ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), which can be found in numerous primary producers including plants, algae, cyanobacteria, and many autotrophic bacteria. Although RubisCO possesses a crucial role in global biomass production, it is not a perfect catalyst. Therefore, research interest persists on accessing the full potential of yet unexplored RubisCOs. We recently developed an activity-based screen suited to seek active recombinant RubisCOs from the environment-independent of the native host's culturability. Here, we applied this screen to twenty pre-selected genomic fosmid clones from six cultured proteobacteria to demonstrate that a broad range of phylogenetically distinct RubisCOs can be targeted. We then screened 12,500 metagenomic fosmid clones from six distinct hydrothermal vents and identified forty active RubisCOs. Additional sequence-based screening uncovered eight further RubisCOs, which could then also be detected by a modified version of the screen. Seven were active form III RubisCOs from yet uncultured Archaea. This indicates the potential of the activity-based screen to detect RubisCO enzymes even from organisms that would not be expected to be targeted.
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6
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Liu D, Ramya RCS, Mueller-Cajar O. Surveying the expanding prokaryotic Rubisco multiverse. FEMS Microbiol Lett 2018; 364:3983162. [PMID: 28854711 DOI: 10.1093/femsle/fnx156] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/19/2017] [Indexed: 11/12/2022] Open
Abstract
The universal, but catalytically modest, CO2-fixing enzyme Rubisco is currently experiencing intense interest by researchers aiming to enhance crop photosynthesis. These efforts are mostly focused on the highly conserved hexadecameric enzyme found in land plants. In comparison, prokaryotic organisms harbor a far greater diversity in Rubisco forms. Recent work towards improving our appreciation of microbial Rubisco properties and harnessing their potential is surveyed. New structural models are providing informative glimpses into catalytic subtleties and diverse oligomeric states. Ongoing characterization is informing us about the conservation of constraints, such as sugar phosphate inhibition and the associated dependence on Rubisco activase helper proteins. Prokaryotic Rubiscos operate under a far wider range of metabolic contexts than the photosynthetic function of higher plant enzymes. Relaxed selection pressures may have resulted in the exploration of a larger volume of sequence space than permitted in organisms performing oxygenic photosynthesis. To tap into the potential of microbial Rubiscos, in vivo selection systems are being used to discover functional metagenomic Rubiscos. Various directed evolution systems to optimize their function have been developed. It is anticipated that this approach will provide access to biotechnologically valuable enzymes that cannot be encountered in the higher plant Rubisco space.
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Affiliation(s)
- Di Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | | | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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7
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Böhnke S, Perner M. Unraveling RubisCO Form I and Form II Regulation in an Uncultured Organism from a Deep-Sea Hydrothermal Vent via Metagenomic and Mutagenesis Studies. Front Microbiol 2017; 8:1303. [PMID: 28747908 PMCID: PMC5506194 DOI: 10.3389/fmicb.2017.01303] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/28/2017] [Indexed: 12/04/2022] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) catalyzes the first major step of carbon fixation in the Calvin-Benson-Bassham (CBB) cycle. This autotrophic CO2 fixation cycle accounts for almost all the assimilated carbon on Earth. Due to the primary role that RubisCO plays in autotrophic carbon fixation, it is important to understand how its gene expression is regulated and the enzyme is activated. Since the majority of all microorganisms are currently not culturable, we used a metagenomic approach to identify genes and enzymes associated with RubisCO expression. The investigated metagenomic DNA fragment originates from the deep-sea hydrothermal vent field Nibelungen at 8°18′ S along the Mid-Atlantic Ridge. It is 13,046 bp and resembles genes from Thiomicrospira crunogena. The fragment encodes nine open reading frames (ORFs) which include two types of RubisCO, form I (CbbL/S) and form II (CbbM), two LysR transcriptional regulators (LysR1 and LysR2), two von Willebrand factor type A (CbbO-m and CbbO-1), and two AAA+ ATPases (CbbQ-m and CbbQ-1), expected to function as RubisCO activating enzymes. In silico analyses uncovered several putative LysR binding sites and promoter structures. Functions of some of these DNA motifs were experimentally confirmed. For example, according to mobility shift assays LysR1’s binding ability to the intergenic region of lysR1 and cbbL appears to be intensified when CbbL or LysR2 are present. Binding of LysR2 upstream of cbbM appears to be intensified if CbbM is present. Our study suggests that CbbQ-m and CbbO-m activate CbbL and that LysR1 and LysR2 proteins promote CbbQ-m/CbbO-m expression. CbbO-1 seems to activate CbbM and CbbM itself appears to contribute to intensifying LysR’s binding ability and thus its own transcriptional regulation. CbbM furthermore appears to impair cbbL expression. A model summarizes the findings and predicts putative interactions of the different proteins influencing RubisCO gene regulation and expression.
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Affiliation(s)
- Stefanie Böhnke
- Molecular Biology of Microbial Consortia, Biocenter Klein Flottbek, University of HamburgHamburg, Germany
| | - Mirjam Perner
- Molecular Biology of Microbial Consortia, Biocenter Klein Flottbek, University of HamburgHamburg, Germany
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8
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Erb TJ, Zarzycki J. Biochemical and synthetic biology approaches to improve photosynthetic CO 2-fixation. Curr Opin Chem Biol 2016; 34:72-79. [PMID: 27400232 DOI: 10.1016/j.cbpa.2016.06.026] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 01/08/2023]
Abstract
There is an urgent need to improve agricultural productivity to secure future food and biofuel supply. Here, we summarize current approaches that aim at improving photosynthetic CO2-fixation. We critically review, compare and comment on the four major lines of research towards this aim, which focus on (i) improving RubisCO, the CO2-fixing enzyme in photosynthesis, (ii) implementing CO2-concentrating mechanisms, (iii) establishing synthetic photorespiration bypasses, and (iv) engineering synthetic CO2-fixation pathways.
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Affiliation(s)
- Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Biochemistry & Synthetic Biology of Microbial Metabolism Group, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, 35043 Marburg, Germany.
| | - Jan Zarzycki
- Max Planck Institute for Terrestrial Microbiology, Biochemistry & Synthetic Biology of Microbial Metabolism Group, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
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9
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Hanson TE. Back to the future: function-first metagenomics returns to the fore. Environ Microbiol 2016; 18:1094-5. [DOI: 10.1111/1462-2920.13260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 02/09/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas E. Hanson
- School of Marine Science and Policy, Department of Biological Sciences, and Delaware Biotechnology Institute; University of Delaware; Newark DE 19716 USA
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10
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Varaljay VA, Satagopan S, North JA, Witte B, Dourado MN, Anantharaman K, Arbing MA, McCann SH, Oremland RS, Banfield JF, Wrighton KC, Tabita FR. Functional metagenomic selection of ribulose 1, 5-bisphosphate carboxylase/oxygenase from uncultivated bacteria. Environ Microbiol 2016; 18:1187-99. [PMID: 26617072 PMCID: PMC10035430 DOI: 10.1111/1462-2920.13138] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/17/2015] [Accepted: 11/17/2015] [Indexed: 01/29/2023]
Abstract
Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a critical yet severely inefficient enzyme that catalyses the fixation of virtually all of the carbon found on Earth. Here, we report a functional metagenomic selection that recovers physiologically active RubisCO molecules directly from uncultivated and largely unknown members of natural microbial communities. Selection is based on CO2 -dependent growth in a host strain capable of expressing environmental deoxyribonucleic acid (DNA), precluding the need for pure cultures or screening of recombinant clones for enzymatic activity. Seventeen functional RubisCO-encoded sequences were selected using DNA extracted from soil and river autotrophic enrichments, a photosynthetic biofilm and a subsurface groundwater aquifer. Notably, three related form II RubisCOs were recovered which share high sequence similarity with metagenomic scaffolds from uncultivated members of the Gallionellaceae family. One of the Gallionellaceae RubisCOs was purified and shown to possess CO2 /O2 specificity typical of form II enzymes. X-ray crystallography determined that this enzyme is a hexamer, only the second form II multimer ever solved and the first RubisCO structure obtained from an uncultivated bacterium. Functional metagenomic selection leverages natural biological diversity and billions of years of evolution inherent in environmental communities, providing a new window into the discovery of CO2 -fixing enzymes not previously characterized.
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Affiliation(s)
- Vanessa A. Varaljay
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Sriram Satagopan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Justin A. North
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Brian Witte
- The Botanical Research Institute of Texas, Fort Worth, TX 76107, USA
| | | | - Karthik Anantharaman
- Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA
| | - Mark A. Arbing
- Protein Expression Technology Center, UCLA-DOE Institute, University of California, Los Angeles, CA 90095, USA
| | | | | | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA
| | - Kelly C. Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - F. Robert Tabita
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- For correspondence. ; Tel. +1 614 292 4297; Fax: +1 614 292 6337
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11
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A function-based screen for seeking RubisCO active clones from metagenomes: novel enzymes influencing RubisCO activity. ISME JOURNAL 2014; 9:735-45. [PMID: 25203835 DOI: 10.1038/ismej.2014.163] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/15/2014] [Accepted: 08/11/2014] [Indexed: 11/08/2022]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a key enzyme of the Calvin cycle, which is responsible for most of Earth's primary production. Although research on RubisCO genes and enzymes in plants, cyanobacteria and bacteria has been ongoing for years, still little is understood about its regulation and activation in bacteria. Even more so, hardly any information exists about the function of metagenomic RubisCOs and the role of the enzymes encoded on the flanking DNA owing to the lack of available function-based screens for seeking active RubisCOs from the environment. Here we present the first solely activity-based approach for identifying RubisCO active fosmid clones from a metagenomic library. We constructed a metagenomic library from hydrothermal vent fluids and screened 1056 fosmid clones. Twelve clones exhibited RubisCO activity and the metagenomic fragments resembled genes from Thiomicrospira crunogena. One of these clones was further analyzed. It contained a 35.2 kb metagenomic insert carrying the RubisCO gene cluster and flanking DNA regions. Knockouts of twelve genes and two intergenic regions on this metagenomic fragment demonstrated that the RubisCO activity was significantly impaired and was attributed to deletions in genes encoding putative transcriptional regulators and those believed to be vital for RubisCO activation. Our new technique revealed a novel link between a poorly characterized gene and RubisCO activity. This screen opens the door to directly investigating RubisCO genes and respective enzymes from environmental samples.
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Bauwe H, Hagemann M, Kern R, Timm S. Photorespiration has a dual origin and manifold links to central metabolism. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:269-75. [PMID: 22284850 DOI: 10.1016/j.pbi.2012.01.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 12/27/2011] [Accepted: 01/05/2012] [Indexed: 05/19/2023]
Abstract
Photorespiration is a Janus-headed metabolic process: it makes oxygenic photosynthesis possible by scavenging its major toxic by-product, 2-phosphoglycolate, but also leads to high losses of freshly assimilated CO(2) from most land plants. Photorespiration has been often classified as a wasteful process but is now increasingly appreciated as a key ancillary component of photosynthesis and therefore the global carbon cycle. As such, the photorespiratory cycle is one of the major highways for the flow of carbon in the terrestrial biosphere. Recent research revealed that this important pathway originated as a partner of oxygenic photosynthesis billions of years ago and is multiply linked to other pathways of central metabolism of contemporary land plants.
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Affiliation(s)
- Hermann Bauwe
- University of Rostock, Department of Plant Physiology, Rostock, Germany.
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13
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Dittmar T, Zänker KS. Horizontal gene transfers with or without cell fusions in all categories of the living matter. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 714:5-89. [PMID: 21506007 PMCID: PMC7120942 DOI: 10.1007/978-94-007-0782-5_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This article reviews the history of widespread exchanges of genetic segments initiated over 3 billion years ago, to be part of their life style, by sphero-protoplastic cells, the ancestors of archaea, prokaryota, and eukaryota. These primordial cells shared a hostile anaerobic and overheated environment and competed for survival. "Coexist with, or subdue and conquer, expropriate its most useful possessions, or symbiose with it, your competitor" remain cellular life's basic rules. This author emphasizes the role of viruses, both in mediating cell fusions, such as the formation of the first eukaryotic cell(s) from a united crenarchaeon and prokaryota, and the transfer of host cell genes integrated into viral (phages) genomes. After rising above the Darwinian threshold, rigid rules of speciation and vertical inheritance in the three domains of life were established, but horizontal gene transfers with or without cell fusions were never abolished. The author proves with extensive, yet highly selective documentation, that not only unicellular microorganisms, but the most complex multicellular entities of the highest ranks resort to, and practice, cell fusions, and donate and accept horizontally (laterally) transferred genes. Cell fusions and horizontally exchanged genetic materials remain the fundamental attributes and inherent characteristics of the living matter, whether occurring accidentally or sought after intentionally. These events occur to cells stagnating for some 3 milliard years at a lower yet amazingly sophisticated level of evolution, and to cells achieving the highest degree of differentiation, and thus functioning in dependence on the support of a most advanced multicellular host, like those of the human brain. No living cell is completely exempt from gene drains or gene insertions.
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Affiliation(s)
- Thomas Dittmar
- Inst. Immunologie, Universität Witten/Herdecke, Stockumer Str. 10, Witten, 58448 Germany
| | - Kurt S. Zänker
- Institute of Immunologie, University of Witten/Herdecke, Stockumer Str. 10, Witten, 58448 Germany
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14
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Hügler M, Sievert SM. Beyond the Calvin cycle: autotrophic carbon fixation in the ocean. ANNUAL REVIEW OF MARINE SCIENCE 2011; 3:261-89. [PMID: 21329206 DOI: 10.1146/annurev-marine-120709-142712] [Citation(s) in RCA: 334] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Organisms capable of autotrophic metabolism assimilate inorganic carbon into organic carbon. They form an integral part of ecosystems by making an otherwise unavailable form of carbon available to other organisms, a central component of the global carbon cycle. For many years, the doctrine prevailed that the Calvin-Benson-Bassham (CBB) cycle is the only biochemical autotrophic CO2 fixation pathway of significance in the ocean. However, ecological, biochemical, and genomic studies carried out over the last decade have not only elucidated new pathways but also shown that autotrophic carbon fixation via pathways other than the CBB cycle can be significant. This has ramifications for our understanding of the carbon cycle and energy flow in the ocean. Here, we review the recent discoveries in the field of autotrophic carbon fixation, including the biochemistry and evolution of the different pathways, as well as their ecological relevance in various oceanic ecosystems.
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Affiliation(s)
- Michael Hügler
- Microbiology Department, Water Technology Center, 76139 Karlsruhe, Germany.
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