1
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Zhao YX, Xiang X, Liu XP. The biochemical characterization of a TatD nuclease from Thermus thermophilus. Protein Expr Purif 2024; 223:106557. [PMID: 39009198 DOI: 10.1016/j.pep.2024.106557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/17/2024]
Abstract
Nucleases play pivotal roles in DNA repair and apoptosis. Moreover, they have various applications in biotechnology and industry. Among nucleases, TatD has been characterized as an exonuclease with various biological functions in different organisms. Here, we biochemically characterized the potential TatD nuclease from Thermus thermophilus. The tatD gene from T. thermophilus was cloned, then the recombinant TatD nuclease was expressed and purified. Our results revealed that the TthTatD nuclease could degrade both single-stranded and double-stranded DNA, and its activity is dependent on the divalent metal ions Mg2+ and Mn2+. Remarkably, the activity of TthTatD nuclease is highest at 37 °C and decreases with increasing temperature. TthTatD is not a thermostable enzyme, even though it is from a thermophilic bacterium. Based on the sequence similarity and molecular docking of the DNA substrate into the modeled TthTatD structure, several key conserved residues were identified and their roles were confirmed by analyzing the enzymatic activities of the site-directed mutants. The residues E86 and H149 play key roles in binding metal ions, residues R124/K126 and K211/R212 had a critical role in binding DNA substrate. Our results confirm the enzymatic properties of TthTatD and provide a primary basis for its possible application in biotechnology.
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Affiliation(s)
- Yi-Xuan Zhao
- SJTU Yazhou Bay Institute of Deepsea Sci-Tech, Yongyou Industrial Park, Sanya, 572024, China
| | - Xiao Xiang
- SJTU Yazhou Bay Institute of Deepsea Sci-Tech, Yongyou Industrial Park, Sanya, 572024, China; State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai, 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences (Ministry of Education), Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai, 200240, China; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai, 200240, China.
| | - Xi-Peng Liu
- SJTU Yazhou Bay Institute of Deepsea Sci-Tech, Yongyou Industrial Park, Sanya, 572024, China; State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai, 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences (Ministry of Education), Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai, 200240, China.
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2
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Zhang Z, Su H, Li Q, Li M. Transcriptome Profiling Reveals the Response of Seed Germination of Peganum harmala to Drought Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:1649. [PMID: 38931081 PMCID: PMC11207268 DOI: 10.3390/plants13121649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/06/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024]
Abstract
Peganum harmala L. is a perennial herbaceous plant that plays critical roles in protecting the ecological environment in arid, semi-arid, and desert areas. Although the seed germination characteristics of P. harmala in response to environmental factors (i.e., drought, temperature, and salt) have been investigated, the response mechanism of seed germination to drought conditions has not yet been revealed. In this study, the changes in the physiological characteristics and transcriptional profiles in seed germination were examined under different polyethylene glycol (PEG) concentrations (0-25%). The results show that the seed germination rate was significantly inhibited with an increase in the PEG concentration. Totals of 3726 and 10,481 differentially expressed genes (DEGs) were, respectively, generated at 5% and 25% PEG vs. the control (C), with 1642 co-expressed DEGs, such as drought stress (15), stress response (175), and primary metabolism (261). The relative expression levels (RELs) of the key genes regulating seed germination in response to drought stress were in accordance with the physiological changes. These findings will pave the way to increase the seed germination rate of P. harmala in drought conditions.
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Affiliation(s)
- Zhen Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (Z.Z.); (H.S.)
| | - Hongyan Su
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (Z.Z.); (H.S.)
| | - Qingen Li
- Station of Forestry and Grassland, Alxa Right Banner 737300, China;
| | - Mengfei Li
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (Z.Z.); (H.S.)
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3
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Thorpe T, Marshall JR, Turner NJ. Multifunctional Biocatalysts for Organic Synthesis. J Am Chem Soc 2024; 146:7876-7884. [PMID: 38489244 PMCID: PMC10979396 DOI: 10.1021/jacs.3c09542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 03/17/2024]
Abstract
Biocatalysis is becoming an indispensable tool in organic synthesis due to high enzymatic catalytic efficiency as well as exquisite chemo- and stereoselectivity. Some biocatalysts display great promiscuity including a broad substrate scope as well as the ability to catalyze more than one type of transformation. These promiscuous activities have been applied individually to efficiently access numerous valuable target molecules. However, systems in which enzymes possessing multiple different catalytic activities are applied in the synthesis are less well developed. Such multifunctional biocatalysts (MFBs) would simplify chemical synthesis by reducing the number of operational steps and enzyme count, as well as simplifying the sequence space that needs to be engineered to develop an efficient biocatalyst. In this Perspective, we highlight recently reported MFBs focusing on their synthetic utility and mechanism. We also offer insight into their origin as well as comment on potential strategies for their discovery and engineering.
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Affiliation(s)
- Thomas
W. Thorpe
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester, United Kingdom, M1
7DN
| | - James R. Marshall
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester, United Kingdom, M1
7DN
| | - Nicholas J. Turner
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester, United Kingdom, M1
7DN
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4
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Wang Y, Liu W, Chen J, Li Z, Hu Y, Fan Z, Yan L, Liu J, Zhou Y, Jiang W, Rui H, Dai L. Overexpression of the FBA and TPI genes promotes high production of HDMF in Zygosaccharomyces rouxii. Front Microbiol 2024; 15:1366021. [PMID: 38577687 PMCID: PMC10993695 DOI: 10.3389/fmicb.2024.1366021] [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: 01/05/2024] [Accepted: 02/29/2024] [Indexed: 04/06/2024] Open
Abstract
4-Hydroxy-2,5-dimethyl-3 (2H)-furanone (HDMF) is widely used in the food industry as a spice and flavoring agent with high market demand. In this study, fructose-1,6-bisphosphate aldolase (FBA) and triose phosphate isomerase (TPI) were overexpressed in Zygosaccharomyces rouxii in the form of single and double genes, respectively, via electroporation. High-yield HDMF-engineered yeast strains were constructed by combining the analysis of gene expression levels obtained by real-time fluorescence quantitative PCR technology and HDMF production measured by HPLC. The results showed that there was a significant positive correlation between the production of HDMF and the expression levels of the FBA and TPI genes in yeast; the expression levels of the FBA and TPI genes were also positively correlated (p < 0.05). Compared with the wild type (WT), the engineered strains F10-D, T17-D, and TF15-A showed marked increases in HDMF production and FBA and TPI gene expression (p < 0.05) and exhibited great genetic stability with no obvious differences in biomass or colony morphology. In addition, the exogenous addition of d-fructose promoted the growth of Z. rouxii. Among the engineered strains, when fermented in YPD media supplemented with d-fructose for 5 days, TF15-A (overexpressing the FBA and TPI genes) generated the highest HDMF production of 13.39 mg/L, which is 1.91 times greater than that of the wild-type strain. The results above indicated that FBA and TPI, which are key enzymes involved in the process of HDMF biosynthesis by Z. rouxii, positively regulate the synthesis of HDMF at the transcriptional level. d-fructose can be used as a precursor for the biosynthesis of HDMF by engineered yeast in industrial production.
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Affiliation(s)
- Yanhong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wei Liu
- Heilongjiang Agricultural Economy Vocational College, Mudanjiang, China
| | - Jingyao Chen
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhijiang Li
- College of Food Science, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yijia Hu
- College of Food Science, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zixiang Fan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Liangyuan Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jiahui Liu
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yuao Zhou
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wei Jiang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Haiying Rui
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing, China
| | - Lingyan Dai
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, China
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5
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Hudson EP. The Calvin Benson cycle in bacteria: New insights from systems biology. Semin Cell Dev Biol 2024; 155:71-83. [PMID: 37002131 DOI: 10.1016/j.semcdb.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/21/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023]
Abstract
The Calvin Benson cycle in phototrophic and chemolithoautotrophic bacteria has ecological and biotechnological importance, which has motivated study of its regulation. I review recent advances in our understanding of how the Calvin Benson cycle is regulated in bacteria and the technologies used to elucidate regulation and modify it, and highlight differences between and photoautotrophic and chemolithoautotrophic models. Systems biology studies have shown that in oxygenic phototrophic bacteria, Calvin Benson cycle enzymes are extensively regulated at post-transcriptional and post-translational levels, with multiple enzyme activities connected to cellular redox status through thioredoxin. In chemolithoautotrophic bacteria, regulation is primarily at the transcriptional level, with effector metabolites transducing cell status, though new methods should now allow facile, proteome-wide exploration of biochemical regulation in these models. A biotechnological objective is to enhance CO2 fixation in the cycle and partition that carbon to a product of interest. Flux control of CO2 fixation is distributed over multiple enzymes, and attempts to modulate gene Calvin cycle gene expression show a robust homeostatic regulation of growth rate, though the synthesis rates of products can be significantly increased. Therefore, de-regulation of cycle enzymes through protein engineering may be necessary to increase fluxes. Non-canonical Calvin Benson cycles, if implemented with synthetic biology, could have reduced energy demand and enzyme loading, thus increasing the attractiveness of these bacteria for industrial applications.
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Affiliation(s)
- Elton P Hudson
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
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6
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Bei Q, Reitz T, Schädler M, Hodgskiss LH, Peng J, Schnabel B, Buscot F, Eisenhauer N, Schleper C, Heintz-Buschart A. Metabolic potential of Nitrososphaera-associated clades. THE ISME JOURNAL 2024; 18:wrae086. [PMID: 38742714 PMCID: PMC11131427 DOI: 10.1093/ismejo/wrae086] [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: 12/07/2023] [Revised: 02/13/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024]
Abstract
Soil ammonia-oxidizing archaea (AOA) play a crucial role in converting ammonia to nitrite, thereby mobilizing reactive nitrogen species into their soluble form, with a significant impact on nitrogen losses from terrestrial soils. Yet, our knowledge regarding their diversity and functions remains limited. In this study, we reconstructed 97 high-quality AOA metagenome-assembled genomes (MAGs) from 180 soil samples collected in Central Germany during 2014-2019 summers. These MAGs were affiliated with the order Nitrososphaerales and clustered into four family-level clades (NS-α/γ/δ/ε). Among these MAGs, 75 belonged to the most abundant but least understood δ-clade. Within the δ-clade, the amoA genes in three MAGs from neutral soils showed a 99.5% similarity to the fosmid clone 54d9, which has served as representative of the δ-clade for the past two decades since even today no cultivated representatives are available. Seventy-two MAGs constituted a distinct δ sub-clade, and their abundance and expression activity were more than twice that of other MAGs in slightly acidic soils. Unlike the less abundant clades (α, γ, and ε), the δ-MAGs possessed multiple highly expressed intracellular and extracellular carbohydrate-active enzymes responsible for carbohydrate binding (CBM32) and degradation (GH5), along with highly expressed genes involved in ammonia oxidation. Together, these results suggest metabolic versatility of uncultured soil AOA and a potential mixotrophic or chemolithoheterotrophic lifestyle among 54d9-like AOA.
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Affiliation(s)
- Qicheng Bei
- Department of Soil Ecology, Helmholtz Centre for Environmental Research – UFZ, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, United States
| | - Thomas Reitz
- Department of Soil Ecology, Helmholtz Centre for Environmental Research – UFZ, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Martin Schädler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Department of Community Ecology, Helmholtz Centre for Environmental Research – UFZ, 06120 Halle (Saale), Germany
| | - Logan H Hodgskiss
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria
| | - Jingjing Peng
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Beatrix Schnabel
- Department of Soil Ecology, Helmholtz Centre for Environmental Research – UFZ, 06120 Halle (Saale), Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz Centre for Environmental Research – UFZ, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, 04103 Leipzig, Germany
| | - Christa Schleper
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria
| | - Anna Heintz-Buschart
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
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7
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Mrnjavac N, Wimmer JLE, Brabender M, Schwander L, Martin WF. The Moon-Forming Impact and the Autotrophic Origin of Life. Chempluschem 2023; 88:e202300270. [PMID: 37812146 PMCID: PMC7615287 DOI: 10.1002/cplu.202300270] [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: 06/05/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023]
Abstract
The Moon-forming impact vaporized part of Earth's mantle, and turned the rest into a magma ocean, from which carbon dioxide degassed into the atmosphere, where it stayed until water rained out to form the oceans. The rain dissolved CO2 and made it available to react with transition metal catalysts in the Earth's crust so as to ultimately generate the organic compounds that form the backbone of microbial metabolism. The Moon-forming impact was key in building a planet with the capacity to generate life in that it converted carbon on Earth into a homogeneous and accessible substrate for organic synthesis. Today all ecosystems, without exception, depend upon primary producers, organisms that fix CO2 . According to theories of autotrophic origin, it has always been that way, because autotrophic theories posit that the first forms of life generated all the molecules needed to build a cell from CO2 , forging a direct line of continuity between Earth's initial CO2 -rich atmosphere and the first microorganisms. By modern accounts these were chemolithoautotrophic archaea and bacteria that initially colonized the crust and still inhabit that environment today.
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Affiliation(s)
- Natalia Mrnjavac
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Jessica L. E. Wimmer
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Max Brabender
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Loraine Schwander
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - William F. Martin
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
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8
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Nogal N, Sanz-Sánchez M, Vela-Gallego S, Ruiz-Mirazo K, de la Escosura A. The protometabolic nature of prebiotic chemistry. Chem Soc Rev 2023; 52:7359-7388. [PMID: 37855729 PMCID: PMC10614573 DOI: 10.1039/d3cs00594a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/20/2023]
Abstract
The field of prebiotic chemistry has been dedicated over decades to finding abiotic routes towards the molecular components of life. There is nowadays a handful of prebiotically plausible scenarios that enable the laboratory synthesis of most amino acids, fatty acids, simple sugars, nucleotides and core metabolites of extant living organisms. The major bottleneck then seems to be the self-organization of those building blocks into systems that can self-sustain. The purpose of this tutorial review is having a close look, guided by experimental research, into the main synthetic pathways of prebiotic chemistry, suggesting how they could be wired through common intermediates and catalytic cycles, as well as how recursively changing conditions could help them engage in self-organized and dissipative networks/assemblies (i.e., systems that consume chemical or physical energy from their environment to maintain their internal organization in a dynamic steady state out of equilibrium). In the article we also pay attention to the implications of this view for the emergence of homochirality. The revealed connectivity between those prebiotic routes should constitute the basis for a robust research program towards the bottom-up implementation of protometabolic systems, taken as a central part of the origins-of-life problem. In addition, this approach should foster further exploration of control mechanisms to tame the combinatorial explosion that typically occurs in mixtures of various reactive precursors, thus regulating the functional integration of their respective chemistries into self-sustaining protocellular assemblies.
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Affiliation(s)
- Noemí Nogal
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Marcos Sanz-Sánchez
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Sonia Vela-Gallego
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Kepa Ruiz-Mirazo
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
- Department of Philosophy, University of the Basque Country, Leioa, Spain
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Campus de Cantoblanco, 28049, Madrid, Spain
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9
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Russell MJ. A self-sustaining serpentinization mega-engine feeds the fougerite nanoengines implicated in the emergence of guided metabolism. Front Microbiol 2023; 14:1145915. [PMID: 37275164 PMCID: PMC10236563 DOI: 10.3389/fmicb.2023.1145915] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/22/2023] [Indexed: 06/07/2023] Open
Abstract
The demonstration by Ivan Barnes et al. that the serpentinization of fresh Alpine-type ultramafic rocks results in the exhalation of hot alkaline fluids is foundational to the submarine alkaline vent theory (AVT) for life's emergence to its 'improbable' thermodynamic state. In AVT, such alkaline fluids ≤ 150°C, bearing H2 > CH4 > HS--generated and driven convectively by a serpentinizing exothermic mega-engine operating in the ultramafic crust-exhale into the iron-rich, CO2> > > NO3--bearing Hadean ocean to result in hydrothermal precipitate mounds comprising macromolecular ferroferric-carbonate oxyhydroxide and minor sulfide. As the nanocrystalline minerals fougerite/green rust and mackinawite (FeS), they compose the spontaneously precipitated inorganic membranes that keep the highly contrasting solutions apart, thereby maintaining redox and pH disequilibria. They do so in the form of fine chimneys and chemical gardens. The same disequilibria drive the reduction of CO2 to HCOO- or CO, and the oxidation of CH4 to a methyl group-the two products reacting to form acetate in a sequence antedating the 'energy-producing' acetyl coenzyme-A pathway. Fougerite is a 2D-layered mineral in which the hydrous interlayers themselves harbor 2D solutions, in effect constricted to ~ 1D by preferentially directed electron hopping/tunneling, and proton Gröthuss 'bucket-brigading' when subject to charge. As a redox-driven nanoengine or peristaltic pump, fougerite forces the ordered reduction of nitrate to ammonium, the amination of pyruvate and oxalate to alanine and glycine, and their condensation to short peptides. In turn, these peptides have the flexibility to sequester the founding inorganic iron oxyhydroxide, sulfide, and pyrophosphate clusters, to produce metal- and phosphate-dosed organic films and cells. As the feed to the hydrothermal mound fails, the only equivalent sustenance on offer to the first autotrophs is the still mildly serpentinizing upper crust beneath. While the conditions here are very much less bountiful, they do offer the similar feed and disequilibria the survivors are accustomed to. Sometime during this transition, a replicating non-ribosomal guidance system is discovered to provide the rules to take on the incrementally changing surroundings. The details of how these replicating apparatuses emerged are the hard problem, but by doing so the progenote archaea and bacteria could begin to colonize what would become the deep biosphere. Indeed, that the anaerobic nitrate-respiring methanotrophic archaea and the deep-branching Acetothermia presently comprise a portion of that microbiome occupying serpentinizing rocks offers circumstantial support for this notion. However, the inescapable, if jarring conclusion is drawn that, absent fougerite/green rust, there would be no structured channelway to life.
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Affiliation(s)
- Michael J. Russell
- Dipartimento di Chimica, Università degli Studi di Torino, Torino, Italy
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10
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Wozniak K, Brzezinski K. Biological Catalysis and Information Storage Have Relied on N-Glycosyl Derivatives of β-D-Ribofuranose since the Origins of Life. Biomolecules 2023; 13:biom13050782. [PMID: 37238652 DOI: 10.3390/biom13050782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/24/2023] [Accepted: 04/29/2023] [Indexed: 05/28/2023] Open
Abstract
Most naturally occurring nucleotides and nucleosides are N-glycosyl derivatives of β-d-ribose. These N-ribosides are involved in most metabolic processes that occur in cells. They are essential components of nucleic acids, forming the basis for genetic information storage and flow. Moreover, these compounds are involved in numerous catalytic processes, including chemical energy production and storage, in which they serve as cofactors or coribozymes. From a chemical point of view, the overall structure of nucleotides and nucleosides is very similar and simple. However, their unique chemical and structural features render these compounds versatile building blocks that are crucial for life processes in all known organisms. Notably, the universal function of these compounds in encoding genetic information and cellular catalysis strongly suggests their essential role in the origins of life. In this review, we summarize major issues related to the role of N-ribosides in biological systems, especially in the context of the origin of life and its further evolution, through the RNA-based World(s), toward the life we observe today. We also discuss possible reasons why life has arisen from derivatives of β-d-ribofuranose instead of compounds based on other sugar moieties.
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Affiliation(s)
- Katarzyna Wozniak
- Department of Structural Biology of Prokaryotic Organisms, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-074 Poznan, Poland
| | - Krzysztof Brzezinski
- Department of Structural Biology of Prokaryotic Organisms, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-074 Poznan, Poland
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11
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Paladhi S, Park SJ, Hwang IS, Park JH, Bae HY, Jadhav AP, Song CE. Biomimetic Catalytic Retro-Aldol Reaction Using a Cation-Binding Catalyst: A Promising Route to Axially Chiral Biaryl Aldehydes. Org Lett 2023; 25:2713-2717. [PMID: 37052359 DOI: 10.1021/acs.orglett.3c00825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Here we describe a biomimetic catalytic retro-aldol reaction of racemic α-substituted β-hydroxy ketones utilizing a chiral oligoEG cation-binding catalyst as a type-II aldolase mimic. Our investigation of various aldol substrates has demonstrated that our biomimetic retro-aldol protocol enables rapid access to highly enantiomerically enriched aldols with a selectivity factor (s) of up to 70. Additionally, we have demonstrated the synthetic strategy's feasibility for accessing diverse and valuable axially chiral aldehydes.
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Affiliation(s)
- Sushovan Paladhi
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Korea
- Department of Chemistry, Thakur Prasad Singh (T.P.S.) College, Patna 800001, India
| | - Si Joon Park
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Korea
| | - In-Soo Hwang
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Korea
| | - Jin Hyun Park
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Korea
| | - Han Yong Bae
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Korea
| | - Amol P Jadhav
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Korea
| | - Choong Eui Song
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Korea
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12
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Rao YZ, Li YX, Li ZW, Qu YN, Qi YL, Jiao JY, Shu WS, Hua ZS, Li WJ. Metagenomic Discovery of " Candidatus Parvarchaeales"-Related Lineages Sheds Light on Adaptation and Diversification from Neutral-Thermal to Acidic-Mesothermal Environments. mSystems 2023; 8:e0125222. [PMID: 36943058 PMCID: PMC10134863 DOI: 10.1128/msystems.01252-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
"Candidatus Parvarchaeales" microbes, representing a DPANN archaeal group with limited metabolic potential and reliance on hosts for their growth, were initially found in acid mine drainage (AMD). Due to the lack of representatives, however, their ecological roles and adaptation to extreme habitats such as AMD as well as how they diverge across the lineage remain largely unexplored. By applying genome-resolved metagenomics, 28 Parvarchaeales-associated metagenome-assembled genomes (MAGs) representing two orders and five genera were recovered. Among them, we identified three new genera and proposed the names "Candidatus Jingweiarchaeum," "Candidatus Haiyanarchaeum," and "Candidatus Rehaiarchaeum," with the former two belonging to a new order, "Candidatus Jingweiarchaeales." Further analyses of the metabolic potentials revealed substantial niche differentiation between Jingweiarchaeales and Parvarchaeales. Jingweiarchaeales may rely on fermentation, salvage pathways, partial glycolysis, and the pentose phosphate pathway (PPP) for energy conservation reservation, while the metabolic potentials of Parvarchaeales might be more versatile. Comparative genomic analyses suggested that Jingweiarchaeales favor habitats with higher temperatures and that Parvarchaeales are better adapted to acidic environments. We further revealed that the thermal adaptation of these lineages, especially Haiyanarchaeum, might rely on genomic features such as the usage of specific amino acids, genome streamlining, and hyperthermophile featured genes such as rgy. Notably, the adaptation of Parvarchaeales to acidic environments was possibly driven by horizontal gene transfer (HGT). The reconstruction of ancestral states demonstrated that both may have originated from thermal and neutral environments and later spread to mesothermal and acidic environments. These evolutionary processes may also be accompanied by adaptation to oxygen-rich environments via HGT. IMPORTANCE "Candidatus Parvarchaeales" microbes may represent a lineage uniquely distributed in extreme environments such as AMD and hot springs. However, little is known about the strategies and processes of how they adapted to these extreme environments. By the discovery of potential new order-level lineages, "Ca. Jingweiarchaeales," and in-depth comparative genomic analysis, we unveiled the functional differentiation of these lineages. Furthermore, we show that the adaptation of these lineages to high-temperature and acidic environments was driven by different strategies, with the former relying more on genomic characteristics such as genome streamlining and amino acid compositions and the latter relying more on the acquisition of genes associated with acid tolerance. Finally, by the reconstruction of the ancestral states of the optimal growth temperature (OGT) and isoelectric point (pI), we showed the potential evolutionary process of Parvarchaeales-related lineages with regard to the shift from the high-temperature environment of their common ancestors to low-temperature (potentially acidic) environments.
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Affiliation(s)
- Yang-Zhi Rao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Yu-Xian Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, People's Republic of China
| | - Ze-Wei Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, People's Republic of China
| | - Yan-Ni Qu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Yan-Ling Qi
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, People's Republic of China
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13
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Römling U. Is biofilm formation intrinsic to the origin of life? Environ Microbiol 2023; 25:26-39. [PMID: 36655713 PMCID: PMC10086821 DOI: 10.1111/1462-2920.16179] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 01/21/2023]
Abstract
Biofilms are multicellular, often surface-associated, communities of autonomous cells. Their formation is the natural mode of growth of up to 80% of microorganisms living on this planet. Biofilms refractory towards antimicrobial agents and the actions of the immune system due to their tolerance against multiple environmental stresses. But how did biofilm formation arise? Here, I argue that the biofilm lifestyle has its foundation already in the fundamental, surface-triggered chemical reactions and energy preserving mechanisms that enabled the development of life on earth. Subsequently, prototypical biofilm formation has evolved and diversified concomitantly in composition, cell morphology and regulation with the expansion of prokaryotic organisms and their radiation by occupation of diverse ecological niches. This ancient origin of biofilm formation thus mirrors the harnessing environmental conditions that have been the rule rather than the exception in microbial life. The subsequent emergence of the association of microbes, including recent human pathogens, with higher organisms can be considered as the entry into a nutritional and largely stress-protecting heaven. Nevertheless, basic mechanisms of biofilm formation have surprisingly been conserved and refunctionalized to promote sustained survival in new environments.
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Affiliation(s)
- Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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14
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Zhang CS, Li M, Wang Y, Li X, Zong Y, Long S, Zhang M, Feng JW, Wei X, Liu YH, Zhang B, Wu J, Zhang C, Lian W, Ma T, Tian X, Qu Q, Yu Y, Xiong J, Liu DT, Wu Z, Zhu M, Xie C, Wu Y, Xu Z, Yang C, Chen J, Huang G, He Q, Huang X, Zhang L, Sun X, Liu Q, Ghafoor A, Gui F, Zheng K, Wang W, Wang ZC, Yu Y, Zhao Q, Lin SY, Wang ZX, Piao HL, Deng X, Lin SC. The aldolase inhibitor aldometanib mimics glucose starvation to activate lysosomal AMPK. Nat Metab 2022; 4:1369-1401. [PMID: 36217034 PMCID: PMC9584815 DOI: 10.1038/s42255-022-00640-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/16/2022] [Indexed: 01/20/2023]
Abstract
The activity of 5'-adenosine monophosphate-activated protein kinase (AMPK) is inversely correlated with the cellular availability of glucose. When glucose levels are low, the glycolytic enzyme aldolase is not bound to fructose-1,6-bisphosphate (FBP) and, instead, signals to activate lysosomal AMPK. Here, we show that blocking FBP binding to aldolase with the small molecule aldometanib selectively activates the lysosomal pool of AMPK and has beneficial metabolic effects in rodents. We identify aldometanib in a screen for aldolase inhibitors and show that it prevents FBP from binding to v-ATPase-associated aldolase and activates lysosomal AMPK, thereby mimicking a cellular state of glucose starvation. In male mice, aldometanib elicits an insulin-independent glucose-lowering effect, without causing hypoglycaemia. Aldometanib also alleviates fatty liver and nonalcoholic steatohepatitis in obese male rodents. Moreover, aldometanib extends lifespan and healthspan in both Caenorhabditis elegans and mice. Taken together, aldometanib mimics and adopts the lysosomal AMPK activation pathway associated with glucose starvation to exert physiological roles, and might have potential as a therapeutic for metabolic disorders in humans.
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Affiliation(s)
- Chen-Song Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Mengqi Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Yu Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Xiaoyang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Yue Zong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Shating Long
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Mingliang Zhang
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jin-Wei Feng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Xiaoyan Wei
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Yan-Hui Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Baoding Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Jianfeng Wu
- Laboratory Animal Research Centre, Xiamen University, Fujian, China
| | - Cixiong Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Wenhua Lian
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Teng Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Xiao Tian
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Qi Qu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Yaxin Yu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Jinye Xiong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Dong-Tai Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Zhenhua Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Mingxia Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Changchuan Xie
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Yaying Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Zheni Xu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Chunyan Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Junjie Chen
- Analysis and Measurement Centre, School of Pharmaceutical Sciences, Xiamen University, Fujian, China
| | - Guohong Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Qingxia He
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xi Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Lei Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Xiufeng Sun
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Qingfeng Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Abdul Ghafoor
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Fu Gui
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Kaili Zheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Wen Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Liaoning, China
| | - Zhi-Chao Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Liaoning, China
| | - Yong Yu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Qingliang Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Shu-Yong Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China
| | - Zhi-Xin Wang
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hai-Long Piao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Liaoning, China
| | - Xianming Deng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China.
| | - Sheng-Cai Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, China.
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15
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Kohtz AJ, Jay ZJ, Lynes MM, Krukenberg V, Hatzenpichler R. Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments. ISME COMMUNICATIONS 2022; 2:86. [PMID: 37938354 PMCID: PMC9723716 DOI: 10.1038/s43705-022-00175-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/03/2022] [Accepted: 09/08/2022] [Indexed: 11/09/2023]
Abstract
Geothermal environments, including terrestrial hot springs and deep-sea hydrothermal sediments, often contain many poorly understood lineages of archaea. Here, we recovered ten metagenome-assembled genomes (MAGs) from geothermal sediments and propose that they constitute a new archaeal class within the TACK superphylum, "Candidatus Culexarchaeia", named after the Culex Basin in Yellowstone National Park. Culexarchaeia harbor distinct sets of proteins involved in key cellular processes that are either phylogenetically divergent or are absent from other closely related TACK lineages, with a particular divergence in cell division and cytoskeletal proteins. Metabolic reconstruction revealed that Culexarchaeia have the capacity to metabolize a wide variety of organic and inorganic substrates. Notably, Culexarchaeia encode a unique modular, membrane associated, and energy conserving [NiFe]-hydrogenase complex that potentially interacts with heterodisulfide reductase (Hdr) subunits. Comparison of this [NiFe]-hydrogenase complex with similar complexes from other archaea suggests that interactions between membrane associated [NiFe]-hydrogenases and Hdr may be more widespread than previously appreciated in both methanogenic and non-methanogenic lifestyles. The analysis of Culexarchaeia further expands our understanding of the phylogenetic and functional diversity of lineages within the TACK superphylum and the ecology, physiology, and evolution of these organisms in extreme environments.
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Affiliation(s)
- Anthony J Kohtz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Mackenzie M Lynes
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Viola Krukenberg
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA.
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
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16
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Cai M, Duan C, Zhang X, Pan J, Liu Y, Zhang C, Li M. Genomic and transcriptomic dissection of Theionarchaea in marine ecosystem. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1222-1234. [PMID: 34668130 DOI: 10.1007/s11427-021-1996-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/17/2021] [Indexed: 11/24/2022]
Abstract
Theionarchaea is a recently described archaeal class within the Euryarchaeota. While it is widely distributed in sediment ecosystems, little is known about its metabolic potential and ecological features. Here, we used metagenomics and metatranscriptomics to characterize 12 theionarchaeal metagenome-assembled genomes, which were further divided into two subgroups, from coastal mangrove sediments of China and seawater columns of the Yap Trench. Genomic analysis revealed that apart from the canonical sulfhydrogenase, Theionarchaea harbor genes encoding heliorhodopsin, group 4 [NiFe]-hydrogenase, and flagellin, in which genes for heliorhodopsin and group 4 [NiFe]-hydrogenase were transcribed in mangrove sediment. Further, the theionarchaeal substrate spectrum may be broader than previously reported as revealed by metagenomics and metatranscriptomics, and the potential carbon substrates include detrital proteins, hemicellulose, ethanol, and CO2. The genes for organic substrate metabolism (mainly detrital protein and amino acid metabolism genes) have relatively higher transcripts in the top sediment layers in mangrove wetlands. In addition, co-occurrence analysis suggested that the degradation of these organic compounds by Theionarchaea might be processed in syntrophy with fermenters (e.g., Chloroflexi) and methanogens. Collectively, these observations expand the current knowledge of the metabolic potential of Theionarchaea, and shed light on the metabolic strategies and roles of these archaea in the marine ecosystems.
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Affiliation(s)
- Mingwei Cai
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Changhai Duan
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, 518060, China
| | - Xinxu Zhang
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Jie Pan
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Yang Liu
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Cuijing Zhang
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Meng Li
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, 518060, China.
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17
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Kalapos MP, de Bari L. Hidden biochemical fossils reveal an evolutionary trajectory for glycolysis in the prebiotic era. FEBS Lett 2022; 596:1955-1968. [DOI: 10.1002/1873-3468.14408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/08/2022] [Accepted: 05/13/2022] [Indexed: 11/09/2022]
Affiliation(s)
| | - Lidia de Bari
- Institute of Biomembranes Bioenergetics and Molecular Biotechnologies Bari Italy
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18
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Wimmer JLE, Xavier JC, Vieira ADN, Pereira DPH, Leidner J, Sousa FL, Kleinermanns K, Preiner M, Martin WF. Energy at Origins: Favorable Thermodynamics of Biosynthetic Reactions in the Last Universal Common Ancestor (LUCA). Front Microbiol 2021; 12:793664. [PMID: 34966373 PMCID: PMC8710812 DOI: 10.3389/fmicb.2021.793664] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/24/2021] [Indexed: 12/02/2022] Open
Abstract
Though all theories for the origin of life require a source of energy to promote primordial chemical reactions, the nature of energy that drove the emergence of metabolism at origins is still debated. We reasoned that evidence for the nature of energy at origins should be preserved in the biochemical reactions of life itself, whereby changes in free energy, ΔG, which determine whether a reaction can go forward or not, should help specify the source. By calculating values of ΔG across the conserved and universal core of 402 individual reactions that synthesize amino acids, nucleotides and cofactors from H2, CO2, NH3, H2S and phosphate in modern cells, we find that 95-97% of these reactions are exergonic (ΔG ≤ 0 kJ⋅mol-1) at pH 7-10 and 80-100°C under nonequilibrium conditions with H2 replacing biochemical reductants. While 23% of the core's reactions involve ATP hydrolysis, 77% are ATP-independent, thermodynamically driven by ΔG of reactions involving carbon bonds. We identified 174 reactions that are exergonic by -20 to -300 kJ⋅mol-1 at pH 9 and 80°C and that fall into ten reaction types: six pterin dependent alkyl or acyl transfers, ten S-adenosylmethionine dependent alkyl transfers, four acyl phosphate hydrolyses, 14 thioester hydrolyses, 30 decarboxylations, 35 ring closure reactions, 31 aromatic ring formations, and 44 carbon reductions by reduced nicotinamide, flavins, ferredoxin, or formate. The 402 reactions of the biosynthetic core trace to the last universal common ancestor (LUCA), and reveal that synthesis of LUCA's chemical constituents required no external energy inputs such as electric discharge, UV-light or phosphide minerals. The biosynthetic reactions of LUCA uncover a natural thermodynamic tendency of metabolism to unfold from energy released by reactions of H2, CO2, NH3, H2S, and phosphate.
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Affiliation(s)
- Jessica L. E. Wimmer
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Joana C. Xavier
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andrey d. N. Vieira
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Delfina P. H. Pereira
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jacqueline Leidner
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Filipa L. Sousa
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Karl Kleinermanns
- Department of Chemistry, Institute of Physical Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Martina Preiner
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - William F. Martin
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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19
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Nazarbek G, Kutzhanova A, Nurtay L, Mu C, Kazybay B, Li X, Ma C, Amin A, Xie Y. Nano-evolution and protein-based enzymatic evolution predicts novel types of natural product nanozymes of traditional Chinese medicine: cases of herbzymes of Taishan-Huangjing ( Rhizoma polygonati) and Goji ( Lycium chinense). NANOSCALE ADVANCES 2021; 3:6728-6738. [PMID: 36132653 PMCID: PMC9418865 DOI: 10.1039/d1na00475a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/09/2021] [Indexed: 06/01/2023]
Abstract
Nanozymes and natural product-derived herbzymes have been identified in different types of enzymes simulating the natural protein-based enzyme function. How to explore and predict enzyme types of novel nanozymes when synthesized remains elusive. An informed analysis might be useful for the prediction. Here, we applied a protein-evolution analysis method to predict novel types of enzymes with experimental validation. First, reported nanozymes were analyzed by chemical classification and nano-evolution. We found that nanozymes are predominantly classified as protein-based EC1 oxidoreductase. In comparison, we analyzed the evolution of protein-based natural enzymes by a phylogenetic tree and the most conserved enzymes were found to be peroxidase and lyase. Therefore, the natural products of Rhizoma polygonati and Goji herbs were analyzed to explore and test the potent new types of natural nanozymes/herbzymes using the simplicity simulation of natural protein enzyme evolution as they contain these conserved enzyme types. The experimental validation showed that the natural products from the total extract of nanoscale traditional Chinese medicine Huangjing (RP, Rhizoma polygonati) from Mount-Tai (Taishan) exhibit fructose-bisphosphate aldolase of lyase while nanoscale Goji (Lycium chinense) extract exhibits peroxidase activities. Thus, the bioinformatics analysis would provide an additional tool for the virtual discovery of natural product nanozymes.
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Affiliation(s)
- Guldan Nazarbek
- Biology Department, Nazarbayev University 53 Kabanbay Batyr Ave 010000 Nur-Sultan Kazakhstan +7 7172694686
| | - Aidana Kutzhanova
- Biology Department, Nazarbayev University 53 Kabanbay Batyr Ave 010000 Nur-Sultan Kazakhstan +7 7172694686
| | - Lazzat Nurtay
- Biology Department, Nazarbayev University 53 Kabanbay Batyr Ave 010000 Nur-Sultan Kazakhstan +7 7172694686
| | - Chenglin Mu
- Sino-German Joint Research Center on Agricultural Biology, State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University Tai'an 271018 China
| | - Bexultan Kazybay
- Biology Department, Nazarbayev University 53 Kabanbay Batyr Ave 010000 Nur-Sultan Kazakhstan +7 7172694686
| | - Xugang Li
- Sino-German Joint Research Center on Agricultural Biology, State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University Tai'an 271018 China
| | - Cuiping Ma
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology Qingdao 266042 China
| | - Amr Amin
- Biology Department, UAE University Al Ain 15551 UAE
- The College, The University of Chicago Chicago IL 60637 USA
| | - Yingqiu Xie
- Biology Department, Nazarbayev University 53 Kabanbay Batyr Ave 010000 Nur-Sultan Kazakhstan +7 7172694686
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20
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Fujioka T, Numoto N, Akama H, Shilpa K, Oka M, Roy PK, Krishna Y, Ito N, Baker D, Oda M, Tanaka F. Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions. Chembiochem 2021; 23:e202100435. [PMID: 34698422 DOI: 10.1002/cbic.202100435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/26/2021] [Indexed: 11/07/2022]
Abstract
Natural aldolase enzymes and created retro-aldolase protein catalysts often catalyze both aldol and retro-aldol reactions depending on the concentrations of the reactants and the products. Here, we report that the directionality of protein catalysts can be altered by replacing one amino acid. The protein catalyst derived from a scaffold of a previously reported retro-aldolase catalyst, catalyzed aldol reactions more efficiently than the previously reported retro-aldolase catalyst. The retro-aldolase catalyst efficiently catalyzed the retro-aldol reaction but was less efficient in catalyzing the aldol reaction. The results indicate that protein catalysts with varying levels of directionality in usually reversibly catalyzed aldol and retro-aldol reactions can be generated from the same protein scaffold.
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Affiliation(s)
- Toshifumi Fujioka
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto, 606-8522, Japan.,Current address: Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Nobutaka Numoto
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Hiroyuki Akama
- Chemistry and Chemical Bioengineering Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan.,Current address: Research Center for Infection Control, Omura Satoshi Memorial Institute, Kitasato University Shirokane, Tokyo, 108-8641, Japan
| | - Kola Shilpa
- Chemistry and Chemical Bioengineering Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Michiko Oka
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto, 606-8522, Japan
| | - Prodip K Roy
- Chemistry and Chemical Bioengineering Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Yarkali Krishna
- Chemistry and Chemical Bioengineering Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Nobutoshi Ito
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - David Baker
- Department of Biochemistry, Institute for Protein Design and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto, 606-8522, Japan
| | - Fujie Tanaka
- Chemistry and Chemical Bioengineering Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
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21
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Cai T, Sun H, Qiao J, Zhu L, Zhang F, Zhang J, Tang Z, Wei X, Yang J, Yuan Q, Wang W, Yang X, Chu H, Wang Q, You C, Ma H, Sun Y, Li Y, Li C, Jiang H, Wang Q, Ma Y. Cell-free chemoenzymatic starch synthesis from carbon dioxide. Science 2021; 373:1523-1527. [PMID: 34554807 DOI: 10.1126/science.abh4049] [Citation(s) in RCA: 170] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Tao Cai
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Hongbing Sun
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Jing Qiao
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Leilei Zhu
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Fan Zhang
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Jie Zhang
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Zijing Tang
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xinlei Wei
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jiangang Yang
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qianqian Yuan
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wangyin Wang
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xue Yang
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Huanyu Chu
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qian Wang
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chun You
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Hongwu Ma
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yuanxia Sun
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yin Li
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Can Li
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Huifeng Jiang
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qinhong Wang
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanhe Ma
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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22
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Lewis AM, Recalde A, Bräsen C, Counts JA, Nussbaum P, Bost J, Schocke L, Shen L, Willard DJ, Quax TEF, Peeters E, Siebers B, Albers SV, Kelly RM. The biology of thermoacidophilic archaea from the order Sulfolobales. FEMS Microbiol Rev 2021; 45:fuaa063. [PMID: 33476388 PMCID: PMC8557808 DOI: 10.1093/femsre/fuaa063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.
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Affiliation(s)
- April M Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Alejandra Recalde
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Christopher Bräsen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - James A Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Phillip Nussbaum
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Jan Bost
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Larissa Schocke
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Lu Shen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Daniel J Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Tessa E F Quax
- Archaeal Virus–Host Interactions, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sonja-Verena Albers
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
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23
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Pirovich DB, Da’dara AA, Skelly PJ. Multifunctional Fructose 1,6-Bisphosphate Aldolase as a Therapeutic Target. Front Mol Biosci 2021; 8:719678. [PMID: 34458323 PMCID: PMC8385298 DOI: 10.3389/fmolb.2021.719678] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/31/2021] [Indexed: 01/01/2023] Open
Abstract
Fructose 1,6-bisphosphate aldolase is a ubiquitous cytosolic enzyme that catalyzes the fourth step of glycolysis. Aldolases are classified into three groups: Class-I, Class-IA, and Class-II; all classes share similar structural features but low amino acid identity. Apart from their conserved role in carbohydrate metabolism, aldolases have been reported to perform numerous non-enzymatic functions. Here we review the myriad "moonlighting" functions of this classical enzyme, many of which are centered on its ability to bind to an array of partner proteins that impact cellular scaffolding, signaling, transcription, and motility. In addition to the cytosolic location, aldolase has been found the extracellular surface of several pathogenic bacteria, fungi, protozoans, and metazoans. In the extracellular space, the enzyme has been reported to perform virulence-enhancing moonlighting functions e.g., plasminogen binding, host cell adhesion, and immunomodulation. Aldolase's importance has made it both a drug target and vaccine candidate. In this review, we note the several inhibitors that have been synthesized with high specificity for the aldolases of pathogens and cancer cells and have been shown to inhibit classical enzyme activity and moonlighting functions. We also review the many trials in which recombinant aldolases have been used as vaccine targets against a wide variety of pathogenic organisms including bacteria, fungi, and metazoan parasites. Most of such trials generated significant protection from challenge infection, correlated with antigen-specific cellular and humoral immune responses. We argue that refinement of aldolase antigen preparations and expansion of immunization trials should be encouraged to promote the advancement of promising, protective aldolase vaccines.
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Affiliation(s)
- David B. Pirovich
- Molecular Helminthology Laboratory, Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States
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24
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Abstract
DPANN is known as highly diverse, globally widespread, and mostly ectosymbiotic archaeal superphylum. However, this group of archaea was overlooked for a long time, and there were limited in-depth studies reported. In this investigation, 41 metagenome-assembled genomes (MAGs) belonging to the DPANN superphylum were recovered (18 MAGs had average nucleotide identity [ANI] values of <95% and a percentage of conserved proteins [POCP] of >50%, while 14 MAGs showed a POCP of <50%), which were analyzed comparatively with 515 other published DPANN genomes. Mismatches to known 16S rRNA gene primers were identified among 16S rRNA genes of DPANN archaea. Numbers of gene families lost (mostly related to energy and amino acid metabolism) were over three times greater than those gained in the evolution of DPANN archaea. Lateral gene transfer (LGT; ∼45.5% was cross-domain) had facilitated niche adaption of the DPANN archaea, ensuring a delicate equilibrium of streamlined genomes with efficient niche-adaptive strategies. For instance, LGT-derived cytochrome bd ubiquinol oxidase and arginine deiminase in the genomes of “Candidatus Micrarchaeota” could help them better adapt to aerobic acidic mine drainage habitats. In addition, most DPANN archaea acquired enzymes for biosynthesis of extracellular polymeric substances (EPS) and transketolase/transaldolase for the pentose phosphate pathway from Bacteria. IMPORTANCE The domain Archaea is a key research model for gaining insights into the origin and evolution of life, as well as the relevant biogeochemical processes. The discovery of nanosized DPANN archaea has overthrown many aspects of microbiology. However, the DPANN superphylum still contains a vast genetic novelty and diversity that need to be explored. Comprehensively comparative genomic analysis on the DPANN superphylum was performed in this study, with an attempt to illuminate its metabolic potential, ecological distribution and evolutionary history. Many interphylum differences within the DPANN superphylum were found. For example, Altiarchaeota had the biggest genome among DPANN phyla, possessing many pathways missing in other phyla, such as formaldehyde assimilation and the Wood-Ljungdahl pathway. In addition, LGT acted as an important force to provide DPANN archaeal genetic flexibility that permitted the occupation of diverse niches. This study has advanced our understanding of the diversity and genome evolution of archaea.
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25
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Functional compartmentalization and metabolic separation in a prokaryotic cell. Proc Natl Acad Sci U S A 2021; 118:2022114118. [PMID: 34161262 DOI: 10.1073/pnas.2022114118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The prokaryotic cell is traditionally seen as a "bag of enzymes," yet its organization is much more complex than in this simplified view. By now, various microcompartments encapsulating metabolic enzymes or pathways are known for Bacteria These microcompartments are usually small, encapsulating and concentrating only a few enzymes, thus protecting the cell from toxic intermediates or preventing unwanted side reactions. The hyperthermophilic, strictly anaerobic Crenarchaeon Ignicoccus hospitalis is an extraordinary organism possessing two membranes, an inner and an energized outer membrane. The outer membrane (termed here outer cytoplasmic membrane) harbors enzymes involved in proton gradient generation and ATP synthesis. These two membranes are separated by an intermembrane compartment, whose function is unknown. Major information processes like DNA replication, RNA synthesis, and protein biosynthesis are located inside the "cytoplasm" or central cytoplasmic compartment. Here, we show by immunogold labeling of ultrathin sections that enzymes involved in autotrophic CO2 assimilation are located in the intermembrane compartment that we name (now) a peripheric cytoplasmic compartment. This separation may protect DNA and RNA from reactive aldehydes arising in the I. hospitalis carbon metabolism. This compartmentalization of metabolic pathways and information processes is unprecedented in the prokaryotic world, representing a unique example of spatiofunctional compartmentalization in the second domain of life.
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26
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Thomas SC, Payne D, Tamadonfar KO, Seymour CO, Jiao JY, Murugapiran SK, Lai D, Lau R, Bowen BP, Silva LP, Louie KB, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Eloe-Fadrosh E, Hamilton TL, Dijkstra P, Dodsworth JA, Northen TR, Li WJ, Hedlund BP. Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan. Front Microbiol 2021; 12:632731. [PMID: 34017316 PMCID: PMC8129789 DOI: 10.3389/fmicb.2021.632731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/02/2021] [Indexed: 01/21/2023] Open
Abstract
Thermoflexus hugenholtzii JAD2T, the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2T and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii JAD2T and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing “Candidatus Thermoflexus japonica,” “Candidatus Thermoflexus tengchongensis,” and “Candidatus Thermoflexus sinensis.” Genomics was integrated with targeted exometabolomics and 13C metabolic probing of T. hugenholtzii. The Thermoflexus genomes each code for complete central carbon metabolic pathways and an unusually high abundance and diversity of peptidases, particularly Metallo- and Serine peptidase families, along with ABC transporters for peptides and some amino acids. The T. hugenholtzii JAD2T exometabolome provided evidence of extracellular proteolytic activity based on the accumulation of free amino acids. However, several neutral and polar amino acids appear not to be utilized, based on their accumulation in the medium and the lack of annotated transporters. Adenine and adenosine were scavenged, and thymine and nicotinic acid were released, suggesting interdependency with other organisms in situ. Metabolic probing of T. hugenholtzii JAD2T using 13C-labeled compounds provided evidence of oxidation of glucose, pyruvate, cysteine, and citrate, and functioning glycolytic, tricarboxylic acid (TCA), and oxidative pentose-phosphate pathways (PPPs). However, differential use of position-specific 13C-labeled compounds showed that glycolysis and the TCA cycle were uncoupled. Thus, despite the high abundance of Thermoflexus in sediments of some geothermal systems, they appear to be highly focused on chemoorganotrophy, particularly protein degradation, and may interact extensively with other microorganisms in situ.
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Affiliation(s)
- Scott C Thomas
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Devon Payne
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Kevin O Tamadonfar
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Cale O Seymour
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Jian-Yu Jiao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Senthil K Murugapiran
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States.,Department of Plant and Microbial Biology, The BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Dengxun Lai
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Rebecca Lau
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Benjamin P Bowen
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Leslie P Silva
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Katherine B Louie
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcel Huntemann
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Alicia Clum
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Alex Spunde
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Manoj Pillay
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Krishnaveni Palaniappan
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Neha Varghese
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Mikhailova
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - I-Min Chen
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Dimitrios Stamatis
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - T B K Reddy
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ronan O'Malley
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Chris Daum
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nicole Shapiro
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Ivanova
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nikos C Kyrpides
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Tanja Woyke
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Emiley Eloe-Fadrosh
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trinity L Hamilton
- Department of Plant and Microbial Biology, The BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Paul Dijkstra
- Department of Biological Sciences, Center of Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, United States
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, United States
| | - Trent R Northen
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, United States
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27
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Metagenomic Insights into the Metabolic and Ecological Functions of Abundant Deep-Sea Hydrothermal Vent DPANN Archaea. Appl Environ Microbiol 2021; 87:AEM.03009-20. [PMID: 33608296 PMCID: PMC8091004 DOI: 10.1128/aem.03009-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/13/2021] [Indexed: 02/04/2023] Open
Abstract
DPANN archaea show high distribution in the hydrothermal system, although they display small genome size and some incomplete biological processes. Exploring their metabolism is helpful to understand how such small forms of life adapt to this unique environment and what ecological roles they play. Due to their unique metabolism and important ecological roles, deep-sea hydrothermal archaea have attracted great scientific interest. Among these archaea, DPANN superphylum archaea are widely distributed in hydrothermal vent environments. However, DPANN metabolism and ecology remain largely unknown. In this study, we assembled 20 DPANN genomes among 43 reconstructed genomes obtained from deep-sea hydrothermal vent sediments. Phylogenetic analysis suggests 6 phyla, comprised of Aenigmarchaeota, Diapherotrites, Nanoarchaeota, Pacearchaeota, Woesearchaeota, and a new candidate phylum we have designated Kexuearchaeota. These are included in the 20 DPANN archaeal members, indicating their broad diversity in this special environment. Analyses of their metabolism reveal deficiencies due to their reduced genome size, including gluconeogenesis and de novo nucleotide and amino acid biosynthesis. However, DPANN archaea possess alternate strategies to address these deficiencies. DPANN archaea also have the potential to assimilate nitrogen and sulfur compounds, indicating an important ecological role in the hydrothermal vent system. IMPORTANCE DPANN archaea show high distribution in the hydrothermal system, although they display small genome size and some incomplete biological processes. Exploring their metabolism is helpful to understand how such small forms of life adapt to this unique environment and what ecological roles they play. In this study, we obtained 20 high-quality metagenome-assembled genomes (MAGs) corresponding to 6 phyla of the DPANN group (Aenigmarchaeota, Diapherotrites, Nanoarchaeota, Pacearchaeota, Woesearchaeota, and a new candidate phylum designated Kexuearchaeota). Further metagenomic analyses provided insights on the metabolism and ecological functions of DPANN archaea to adapt to deep-sea hydrothermal environments. Our study contributes to a deeper understanding of their special lifestyles and should provide clues to cultivate this important archaeal group in the future.
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Xavier JC, Gerhards RE, Wimmer JLE, Brueckner J, Tria FDK, Martin WF. The metabolic network of the last bacterial common ancestor. Commun Biol 2021; 4:413. [PMID: 33772086 PMCID: PMC7997952 DOI: 10.1038/s42003-021-01918-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/26/2021] [Indexed: 02/03/2023] Open
Abstract
Bacteria are the most abundant cells on Earth. They are generally regarded as ancient, but due to striking diversity in their metabolic capacities and widespread lateral gene transfer, the physiology of the first bacteria is unknown. From 1089 reference genomes of bacterial anaerobes, we identified 146 protein families that trace to the last bacterial common ancestor, LBCA, and form the conserved predicted core of its metabolic network, which requires only nine genes to encompass all universal metabolites. Our results indicate that LBCA performed gluconeogenesis towards cell wall synthesis, and had numerous RNA modifications and multifunctional enzymes that permitted life with low gene content. In accordance with recent findings for LUCA and LACA, analyses of thousands of individual gene trees indicate that LBCA was rod-shaped and the first lineage to diverge from the ancestral bacterial stem was most similar to modern Clostridia, followed by other autotrophs that harbor the acetyl-CoA pathway.
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Affiliation(s)
- Joana C Xavier
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany.
| | - Rebecca E Gerhards
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany
| | - Jessica L E Wimmer
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany
| | - Julia Brueckner
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany
| | - Fernando D K Tria
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany
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Vuillemin A, Kerrigan Z, D'Hondt S, Orsi WD. Exploring the abundance, metabolic potential and gene expression of subseafloor Chloroflexi in million-year-old oxic and anoxic abyssal clay. FEMS Microbiol Ecol 2020; 96:fiaa223. [PMID: 33150943 PMCID: PMC7688785 DOI: 10.1093/femsec/fiaa223] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/03/2020] [Indexed: 01/31/2023] Open
Abstract
Chloroflexi are widespread in subsurface environments, and recent studies indicate that they represent a major fraction of the communities in subseafloor sediment. Here, we compare the abundance, diversity, metabolic potential and gene expression of Chloroflexi from three abyssal sediment cores from the western North Atlantic Gyre (water depth >5400 m) covering up to 15 million years of sediment deposition, where Chloroflexi were found to represent major components of the community at all sites. Chloroflexi communities die off in oxic red clay over 10-15 million years, and gene expression was below detection. In contrast, Chloroflexi abundance and gene expression at the anoxic abyssal clay site increase below the seafloor and peak in 2-3 million-year-old sediment, indicating a comparably higher activity. Metatranscriptomes from the anoxic site reveal increased expression of Chloroflexi genes involved in cell wall biogenesis, protein turnover, inorganic ion transport, defense mechanisms and prophages. Phylogenetic analysis shows that these Chloroflexi are closely related to homoacetogenic subseafloor clades and actively transcribe genes involved in sugar fermentations, gluconeogenesis and Wood-Ljungdahl pathway in the subseafloor. Concomitant expression of cell division genes indicates that these putative homoacetogenic Chloroflexi are actively growing in these million-year-old anoxic abyssal sediments.
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Affiliation(s)
- Aurèle Vuillemin
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Strasse 10, 80333 Munich, Germany
| | - Zak Kerrigan
- Graduate School of Oceanography, University of Rhode Island, Narragansett Bay Campus, 215 South Ferry Road, Narragansett, RI 02882, USA
| | - Steven D'Hondt
- Graduate School of Oceanography, University of Rhode Island, Narragansett Bay Campus, 215 South Ferry Road, Narragansett, RI 02882, USA
| | - William D Orsi
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Strasse 10, 80333 Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Richard-Wagner-Strasse 10, 80333 Munich, Germany
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Metabolic Diversity and Evolutionary History of the Archaeal Phylum " Candidatus Micrarchaeota" Uncovered from a Freshwater Lake Metagenome. Appl Environ Microbiol 2020; 86:AEM.02199-20. [PMID: 32978130 DOI: 10.1128/aem.02199-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/18/2020] [Indexed: 12/19/2022] Open
Abstract
Acidophilic archaea of the archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) group from the uncultured candidate phylum "Candidatus Micrarchaeota" have small genomes and cell sizes and are known to be metabolically dependent and physically associated with their Thermoplasmatales hosts. However, phylogenetically diverse "Ca Micrarchaeota" are widely distributed in various nonacidic environments, and it remains uncertain because of the lack of complete genomes whether they are also devoted to a partner-dependent lifestyle. Here, we obtained nine metagenome-assembled genomes of "Ca Micrarchaeota" from the sediments of a meromictic freshwater lake, including a complete, closed 1.2 Mbp genome of "Ca Micrarchaeota" Sv326, an archaeon phylogenetically distant from the ARMAN lineage. Genome analysis revealed that, contrary to ARMAN "Ca Micrarchaeota," the Sv326 archaeon has complete glycolytic pathways and ATP generation mechanisms in substrate phosphorylation reactions, the capacities to utilize some sugars and amino acids as substrates, and pathways for de novo nucleotide biosynthesis but lacked an aerobic respiratory chain. We suppose that Sv326 is a free-living scavenger rather than an obligate parasite/symbiont. Comparative analysis of "Ca Micrarchaeota" genomes representing different order-level divisions indicated that evolution of the "Ca Micrarchaeota" from a free-living "Candidatus Diapherotrites"-like ancestor involved losses of important metabolic pathways in different lineages and gains of specific functions in the course of adaptation to a partner-dependent lifestyle and specific environmental conditions. The ARMAN group represents the most pronounced case of genome reduction and gene loss, while the Sv326 lineage appeared to be rather close to the ancestral state of the "Ca Micrarchaeota" in terms of metabolic potential.IMPORTANCE The recently described superphylum DPANN includes several phyla of uncultivated archaea with small cell sizes, reduced genomes, and limited metabolic capabilities. One of these phyla, "Ca Micrarchaeota," comprises an enigmatic group of archaea found in acid mine drainage environments, the archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) group. Analysis of their reduced genomes revealed the absence of key metabolic pathways consistent with their partner-associated lifestyle, and physical associations of ARMAN cells with their hosts were documented. However, "Ca Micrarchaeota" include several lineages besides the ARMAN group found in nonacidic environments, and none of them have been characterized. Here, we report a complete genome of "Ca Micrarchaeota" from a non-ARMAN lineage. Analysis of this genome revealed the presence of metabolic capacities lost in ARMAN genomes that could enable a free-living lifestyle. These results expand our understanding of genetic diversity, lifestyle, and evolution of "Ca Micrarchaeota."
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Ghosh S, Das M, Basu S, Adhikari J. Gluconeogenic fructose-1,6-bisphosphatase from the mature sporocarps of common aquatic ferns: partial purification and basic characterization of this enzyme from Marsilea minuta (Polypodiopsida). UKRAINIAN BOTANICAL JOURNAL 2020. [DOI: 10.15407/ukrbotj77.05.386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The present communication reports substantial activity of gluconeogenic fructose-1,6-bisphosphatase (FBPase; EC 3.1.3.11) in three common heterosporous aquatic ferns (Marsilea minuta, Salvinia natans, and Azolla pinnata) and also describes a protocol for its partial purification from mature sporocarps of Marsilea minuta. The cytosolic FBPase, obtained from Marsilea minuta, Salvinia natans, and Azolla pinnata was recognized as gluconeogenic enzyme due to its drastic catabolic inactivation in presence of externally administered glucose and its insensitivity towards photosynthetic light illumination. Cytosolic gluconeogenic FBPase was partially purified from mature sporocarps of Marsilea minuta to about 22-fold over homogenate following low-speed centrifugation (11, 400 × g), 30–80% ammonium sulfate fractionation followed by subsequent chromatography using matrices like CM-Cellulose, Sephadex G-200, and Ultrogel AcA 34. The profile of partially purified FBPase in PAGE under non-denaturing condition was recorded. The enzyme activity increased linearly with respect to protein concentration to about 100 µg and with respect to time up to 75 minutes. Temperature optimum was found at 35 °C. The effect of substrate concentration and kinetic analyses for FBPase were carried out using D-fructose-1,6-bisphosphate (D-FBP, the substrate) in the range of 0.0 to 1.0 mM at an interval of 0.1 mM concentration. The Km value for D-FBP of FBPase was 0.06129 mM and Vmax was 4525 nmole Pi released (mg)-1 protein h-1 as determined by nonlinear regression kinetics using Prism 8 software (Graph Pad). The enzyme was functional in a constricted pH range of 7.0 to 8.0, giving maxima at pH 7.5. This cytosolic enzyme was significantly stimulated by Mg2+ and strongly inhibited by Hg2+, Cu2+ and Zn2+.
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Dombrowski N, Williams TA, Sun J, Woodcroft BJ, Lee JH, Minh BQ, Rinke C, Spang A. Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution. Nat Commun 2020; 11:3939. [PMID: 32770105 PMCID: PMC7414124 DOI: 10.1038/s41467-020-17408-w] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/25/2020] [Indexed: 01/08/2023] Open
Abstract
The recently discovered DPANN archaea are a potentially deep-branching, monophyletic radiation of organisms with small cells and genomes. However, the monophyly and early emergence of the various DPANN clades and their role in life's evolution are debated. Here, we reconstructed and analysed genomes of an uncharacterized archaeal phylum (Candidatus Undinarchaeota), revealing that its members have small genomes and, while potentially being able to conserve energy through fermentation, likely depend on partner organisms for the acquisition of certain metabolites. Our phylogenomic analyses robustly place Undinarchaeota as an independent lineage between two highly supported 'DPANN' clans. Further, our analyses suggest that DPANN have exchanged core genes with their hosts, adding to the difficulty of placing DPANN in the tree of life. This pattern can be sufficiently dominant to allow identifying known symbiont-host clades based on routes of gene transfer. Together, our work provides insights into the origins and evolution of DPANN and their hosts.
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Affiliation(s)
- Nina Dombrowski
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB, Den Burg, The Netherlands
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Jiarui Sun
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Benjamin J Woodcroft
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jun-Hoe Lee
- Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden
| | - Bui Quang Minh
- Research School of Computer Science and Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB, Den Burg, The Netherlands.
- Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden.
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Muchowska KB, Varma SJ, Moran J. Nonenzymatic Metabolic Reactions and Life's Origins. Chem Rev 2020; 120:7708-7744. [PMID: 32687326 DOI: 10.1021/acs.chemrev.0c00191] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prebiotic chemistry aims to explain how the biochemistry of life as we know it came to be. Most efforts in this area have focused on provisioning compounds of importance to life by multistep synthetic routes that do not resemble biochemistry. However, gaining insight into why core metabolism uses the molecules, reactions, pathways, and overall organization that it does requires us to consider molecules not only as synthetic end goals. Equally important are the dynamic processes that build them up and break them down. This perspective has led many researchers to the hypothesis that the first stage of the origin of life began with the onset of a primitive nonenzymatic version of metabolism, initially catalyzed by naturally occurring minerals and metal ions. This view of life's origins has come to be known as "metabolism first". Continuity with modern metabolism would require a primitive version of metabolism to build and break down ketoacids, sugars, amino acids, and ribonucleotides in much the same way as the pathways that do it today. This review discusses metabolic pathways of relevance to the origin of life in a manner accessible to chemists, and summarizes experiments suggesting several pathways might have their roots in prebiotic chemistry. Finally, key remaining milestones for the protometabolic hypothesis are highlighted.
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Affiliation(s)
| | - Sreejith J Varma
- University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France
| | - Joseph Moran
- University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France
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Cader MZ, de Almeida Rodrigues RP, West JA, Sewell GW, Md-Ibrahim MN, Reikine S, Sirago G, Unger LW, Iglesias-Romero AB, Ramshorn K, Haag LM, Saveljeva S, Ebel JF, Rosenstiel P, Kaneider NC, Lee JC, Lawley TD, Bradley A, Dougan G, Modis Y, Griffin JL, Kaser A. FAMIN Is a Multifunctional Purine Enzyme Enabling the Purine Nucleotide Cycle. Cell 2020; 180:278-295.e23. [PMID: 31978345 PMCID: PMC6978800 DOI: 10.1016/j.cell.2019.12.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 11/18/2019] [Accepted: 12/12/2019] [Indexed: 12/11/2022]
Abstract
Mutations in FAMIN cause arthritis and inflammatory bowel disease in early childhood, and a common genetic variant increases the risk for Crohn's disease and leprosy. We developed an unbiased liquid chromatography-mass spectrometry screen for enzymatic activity of this orphan protein. We report that FAMIN phosphorolytically cleaves adenosine into adenine and ribose-1-phosphate. Such activity was considered absent from eukaryotic metabolism. FAMIN and its prokaryotic orthologs additionally have adenosine deaminase, purine nucleoside phosphorylase, and S-methyl-5′-thioadenosine phosphorylase activity, hence, combine activities of the namesake enzymes of central purine metabolism. FAMIN enables in macrophages a purine nucleotide cycle (PNC) between adenosine and inosine monophosphate and adenylosuccinate, which consumes aspartate and releases fumarate in a manner involving fatty acid oxidation and ATP-citrate lyase activity. This macrophage PNC synchronizes mitochondrial activity with glycolysis by balancing electron transfer to mitochondria, thereby supporting glycolytic activity and promoting oxidative phosphorylation and mitochondrial H+ and phosphate recycling. An unbiased LC-MS screen reveals FAMIN as a purine nucleoside enzyme FAMIN combines adenosine phosphorylase with ADA-, PNP-, and MTAP-like activities FAMIN enables a purine nucleotide cycle (PNC) preventing cytoplasmic acidification The FAMIN-dependent PNC balances the glycolysis-mitochondrial redox interface
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Affiliation(s)
- M Zaeem Cader
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Rodrigo Pereira de Almeida Rodrigues
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - James A West
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK
| | - Gavin W Sewell
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Muhammad N Md-Ibrahim
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Stephanie Reikine
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Giuseppe Sirago
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Lukas W Unger
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Ana Belén Iglesias-Romero
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Katharina Ramshorn
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Lea-Maxie Haag
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Svetlana Saveljeva
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Jana-Fabienne Ebel
- Institute of Clinical Molecular Biology, Christian Albrechts University, Campus Kiel, 24105 Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian Albrechts University, Campus Kiel, 24105 Kiel, Germany
| | - Nicole C Kaneider
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - James C Lee
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | | | - Allan Bradley
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Yorgo Modis
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Julian L Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK
| | - Arthur Kaser
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.
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Martin WF. Older Than Genes: The Acetyl CoA Pathway and Origins. Front Microbiol 2020; 11:817. [PMID: 32655499 PMCID: PMC7325901 DOI: 10.3389/fmicb.2020.00817] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/06/2020] [Indexed: 11/13/2022] Open
Abstract
For decades, microbiologists have viewed the acetyl CoA pathway and organisms that use it for H2-dependent carbon and energy metabolism, acetogens and methanogens, as ancient. Classical evidence and newer evidence indicating the antiquity of the acetyl CoA pathway are summarized here. The acetyl CoA pathway requires approximately 10 enzymes, roughly as many organic cofactors, and more than 500 kDa of combined subunit molecular mass to catalyze the conversion of H2 and CO2 to formate, acetate, and pyruvate in acetogens and methanogens. However, a single hydrothermal vent alloy, awaruite (Ni3Fe), can convert H2 and CO2 to formate, acetate, and pyruvate under mild hydrothermal conditions on its own. The chemical reactions of H2 and CO2 to pyruvate thus have a natural tendency to occur without enzymes, given suitable inorganic catalysts. This suggests that the evolution of the enzymatic acetyl CoA pathway was preceded by-and patterned along-a route of naturally occurring exergonic reactions catalyzed by transition metal minerals that could activate H2 and CO2 by chemisorption. The principle of forward (autotrophic) pathway evolution from preexisting non-enzymatic reactions is generalized to the concept of patterned evolution of pathways. In acetogens, exergonic reduction of CO2 by H2 generates acyl phosphates by highly reactive carbonyl groups undergoing attack by inert inorganic phosphate. In that ancient reaction of biochemical energy conservation, the energy behind formation of the acyl phosphate bond resides in the carbonyl, not in phosphate. The antiquity of the acetyl CoA pathway is usually seen in light of CO2 fixation; its role in primordial energy coupling via acyl phosphates and substrate-level phosphorylation is emphasized here.
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Affiliation(s)
- William F. Martin
- Institute for Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
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36
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Gan N, Guan H, Huang Y, Yu T, Fu J, Nakayasu ES, Puvar K, Das C, Wang D, Ouyang S, Luo Z. Legionella pneumophila regulates the activity of UBE2N by deamidase-mediated deubiquitination. EMBO J 2020; 39:e102806. [PMID: 31825121 PMCID: PMC7024838 DOI: 10.15252/embj.2019102806] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 12/21/2022] Open
Abstract
The Legionella pneumophila effector MavC induces ubiquitination of the E2 ubiquitin-conjugating enzyme UBE2N by transglutamination, thereby abolishing its function in the synthesis of K63 -type polyubiquitin chains. The inhibition of UBE2N activity creates a conundrum because this E2 enzyme is important in multiple signaling pathways, including some that are important for intracellular L. pneumophila replication. Here, we show that prolonged inhibition of UBE2N activity by MavC restricts intracellular bacterial replication and that the activity of UBE2N is restored by MvcA, an ortholog of MavC (50% identity) with ubiquitin deamidase activity. MvcA functions to deubiquitinate UBE2N-Ub using the same catalytic triad required for its deamidase activity. Structural analysis of the MvcA-UBE2N-Ub complex reveals a crucial role of the insertion domain in MvcA in substrate recognition. Our study establishes a deubiquitination mechanism catalyzed by a deamidase, which, together with MavC, imposes temporal regulation of the activity of UBE2N during L. pneumophila infection.
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Affiliation(s)
- Ninghai Gan
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Hongxin Guan
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationThe Key Laboratory of Innate Immune Biology of Fujian ProvinceBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Yini Huang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationThe Key Laboratory of Innate Immune Biology of Fujian ProvinceBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Ting Yu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationThe Key Laboratory of Innate Immune Biology of Fujian ProvinceBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Jiaqi Fu
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Ernesto S Nakayasu
- Biological Science DivisionPacific Northwest National LaboratoryRichlandWAUSA
| | - Kedar Puvar
- Department of ChemistryPurdue UniversityWest LafayetteINUSA
| | | | - Dongmei Wang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationThe Key Laboratory of Innate Immune Biology of Fujian ProvinceBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Songying Ouyang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationThe Key Laboratory of Innate Immune Biology of Fujian ProvinceBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Zhao‐Qing Luo
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
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Meng D, Wang J, You C. The properties of the linker in a mini-scaffoldin influence the catalytic efficiency of scaffoldin-mediated enzyme complexes. Enzyme Microb Technol 2020; 133:109460. [DOI: 10.1016/j.enzmictec.2019.109460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/27/2019] [Accepted: 10/31/2019] [Indexed: 10/25/2022]
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38
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Form III RubisCO-mediated transaldolase variant of the Calvin cycle in a chemolithoautotrophic bacterium. Proc Natl Acad Sci U S A 2019; 116:18638-18646. [PMID: 31451656 DOI: 10.1073/pnas.1904225116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Calvin-Benson-Bassham (CBB) cycle assimilates CO2 for the primary production of organic matter in all plants and algae, as well as in some autotrophic bacteria. The key enzyme of the CBB cycle, ribulose-bisphosphate carboxylase/oxygenase (RubisCO), is a main determinant of de novo organic matter production on Earth. Of the three carboxylating forms of RubisCO, forms I and II participate in autotrophy, and form III so far has been associated only with nucleotide and nucleoside metabolism. Here, we report that form III RubisCO functions in the CBB cycle in the thermophilic chemolithoautotrophic bacterium Thermodesulfobium acidiphilum, a phylum-level lineage representative. We further show that autotrophic CO2 fixation in T. acidiphilum is accomplished via the transaldolase variant of the CBB cycle, which has not been previously demonstrated experimentally and has been considered unlikely to occur. Thus, this work reveals a distinct form of the key pathway of CO2 fixation.
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Abstract
There is a lot of controversy in the origin and early evolution of life field, but most people agree that at the advent of genetically coded protein synthesis, cells must have had access to ribonucleotides, amino acids, lipids and some sort of energy source. However, the provenance of these materials is a contentious issue — did early life obtain its building blocks prefabricated from the environment, or did it synthesise them from feedstocks such as CO2 and N2? In the first case, synthesis conditions need not have been compatible with life and any kind of reaction network that furnished the building blocks — and not much else — could have provisioned the subsequent origin and early evolution of life. In the second case, synthesis must have been under life-compatible conditions, with the reaction network either along the same lines as extant biology or along different ones. On the basis of experimental evidence, we will argue in favour of prefabrication and against synthesis by life in its nascent state, especially synthesis that resembles extant biosynthesis, which we suggest would have been well-nigh impossible without biological catalysts.
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40
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Thomas SC, Tamadonfar KO, Seymour CO, Lai D, Dodsworth JA, Murugapiran SK, Eloe-Fadrosh EA, Dijkstra P, Hedlund BP. Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures. Front Microbiol 2019; 10:1427. [PMID: 31333598 PMCID: PMC6624737 DOI: 10.3389/fmicb.2019.01427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 06/05/2019] [Indexed: 12/02/2022] Open
Abstract
Temperature is a primary driver of microbial community composition and taxonomic diversity; however, it is unclear to what extent temperature affects characteristics of central carbon metabolic pathways (CCMPs) at the community level. In this study, 16S rRNA gene amplicon and metagenome sequencing were combined with 13C-labeled metabolite probing of the CCMPs to assess community carbon metabolism along a temperature gradient (60–95°C) in Great Boiling Spring, NV. 16S rRNA gene amplicon diversity was inversely proportional to temperature, and Archaea were dominant at higher temperatures. KO richness and diversity were also inversely proportional to temperature, yet CCMP genes were similarly represented across the temperature gradient and many individual metagenome-assembled genomes had complete pathways. In contrast, genes encoding cellulosomes and many genes involved in plant matter degradation and photosynthesis were absent at higher temperatures. In situ13C-CO2 production from labeled isotopomer pairs of glucose, pyruvate, and acetate suggested lower relative oxidative pentose phosphate pathway activity and/or fermentation at 60°C, and a stable or decreased maintenance energy demand at higher temperatures. Catabolism of 13C-labeled citrate, succinate, L-alanine, L-serine, and L-cysteine was observed at 85°C, demonstrating broad heterotrophic activity and confirming functioning of the TCA cycle. Together, these results suggest that temperature-driven losses in biodiversity and gene content in geothermal systems may not alter CCMP function or maintenance energy demands at a community level.
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Affiliation(s)
- Scott C Thomas
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Kevin O Tamadonfar
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Cale O Seymour
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Dengxun Lai
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, United States
| | | | - Emiley A Eloe-Fadrosh
- Department of Energy Joint Genome Institute, Joint Genome Institute, Walnut Creek, CA, United States
| | - Paul Dijkstra
- Department of Biological Sciences, Center of Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, United States
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
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41
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Jaffe AL, Castelle CJ, Dupont CL, Banfield JF. Lateral Gene Transfer Shapes the Distribution of RuBisCO among Candidate Phyla Radiation Bacteria and DPANN Archaea. Mol Biol Evol 2019; 36:435-446. [PMID: 30544151 PMCID: PMC6389311 DOI: 10.1093/molbev/msy234] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is considered to be the most abundant enzyme on Earth. Despite this, its full diversity and distribution across the domains of life remain to be determined. Here, we leverage a large set of bacterial, archaeal, and viral genomes recovered from the environment to expand our understanding of existing RuBisCO diversity and the evolutionary processes responsible for its distribution. Specifically, we report a new type of RuBisCO present in Candidate Phyla Radiation (CPR) bacteria that is related to the archaeal Form III enzyme and contains the amino acid residues necessary for carboxylase activity. Genome-level metabolic analyses supported the inference that these RuBisCO function in a CO2-incorporating pathway that consumes nucleotides. Importantly, some Gottesmanbacteria (CPR) also encode a phosphoribulokinase that may augment carbon metabolism through a partial Calvin–Benson–Bassham cycle. Based on the scattered distribution of RuBisCO and its discordant evolutionary history, we conclude that this enzyme has been extensively laterally transferred across the CPR bacteria and DPANN archaea. We also report RuBisCO-like proteins in phage genomes from diverse environments. These sequences cluster with proteins in the Beckwithbacteria (CPR), implicating phage as a possible mechanism of RuBisCO transfer. Finally, we synthesize our metabolic and evolutionary analyses to suggest that lateral gene transfer of RuBisCO may have facilitated major shifts in carbon metabolism in several important bacterial and archaeal lineages.
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Affiliation(s)
- Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA.,Chan Zuckerberg Biohub, San Francisco, CA
| | | | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA.,Chan Zuckerberg Biohub, San Francisco, CA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA
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42
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Toxvaerd S. A Prerequisite for Life. J Theor Biol 2019; 474:48-51. [PMID: 31059714 DOI: 10.1016/j.jtbi.2019.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/28/2019] [Accepted: 05/02/2019] [Indexed: 11/28/2022]
Abstract
The complex physicochemical structures and chemical reactions in living organism have some common features: (1) The life processes take place in the cytosol in the cells, which, from a physicochemical point of view is an emulsion of biomolecules in a dilute aqueous suspension. (2) All living systems are homochiral with respect to the units of amino acids and carbohydrates, but (some) proteins are chiral unstable in the cytosol. (3) And living organism are mortal. These three common features together give a prerequisite for the prebiotic self-assembly at the start of the Abiogenesis. Here we argue, that it all together indicates, that the prebiotic self-assembly of structures and reactions took place in a more saline environment, whereby the homochirality of proteins not only could be obtained, but also preserved. A more saline environment for the prebiotic self-assembly of organic molecules and establishment of biochemical reactions could have been the hydrothermal vents.
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Affiliation(s)
- Søren Toxvaerd
- Department of Science and Environment, Roskilde University, Postbox 260, Roskilde DK-4000, Denmark.
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43
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Haferkamp P, Tjaden B, Shen L, Bräsen C, Kouril T, Siebers B. The Carbon Switch at the Level of Pyruvate and Phosphoenolpyruvate in Sulfolobus solfataricus P2. Front Microbiol 2019; 10:757. [PMID: 31031731 PMCID: PMC6474364 DOI: 10.3389/fmicb.2019.00757] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/26/2019] [Indexed: 01/26/2023] Open
Abstract
Sulfolobus solfataricus P2 grows on different carbohydrates as well as alcohols, peptides and amino acids. Carbohydrates such as D-glucose or D-galactose are degraded via the modified, branched Entner–Doudoroff (ED) pathway whereas growth on peptides requires the Embden–Meyerhof–Parnas (EMP) pathway for gluconeogenesis. As for most hyperthermophilic Archaea an important control point is established at the level of triosephophate conversion, however, the regulation at the level of pyruvate/phosphoenolpyruvate conversion was not tackled so far. Here we describe the cloning, expression, purification and characterization of the pyruvate kinase (PK, SSO0981) and the phosphoenolpyruvate synthetase (PEPS, SSO0883) of Sul. solfataricus. The PK showed only catabolic activity [catalytic efficiency (PEP): 627.95 mM-1s-1, 70°C] with phosphoenolpyruvate as substrate and ADP as phosphate acceptor and was allosterically inhibited by ATP and isocitrate (Ki 0.8 mM). The PEPS was reversible, however, exhibited preferred activity in the gluconeogenic direction [catalytic efficiency (pyruvate): 1.04 mM-1s-1, 70°C] and showed some inhibition by AMP and α-ketoglutarate. The gene SSO2829 annotated as PEPS/pyruvate:phosphate dikinase (PPDK) revealed neither PEPS nor PPDK activity. Our studies suggest that the energy charge of the cell as well as the availability of building blocks in the citric acid cycle and the carbon/nitrogen balance plays a major role in the Sul. solfataricus carbon switch. The comparison of regulatory features of well-studied hyperthermophilic Archaea reveals a close link and sophisticated coordination between the respective sugar kinases and the kinetic and regulatory properties of the enzymes at the level of PEP-pyruvate conversion.
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Affiliation(s)
- Patrick Haferkamp
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Centre for Water and Environmental Research, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Britta Tjaden
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Centre for Water and Environmental Research, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Lu Shen
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Centre for Water and Environmental Research, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Centre for Water and Environmental Research, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Theresa Kouril
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Centre for Water and Environmental Research, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.,Department of Biochemistry, University of Stellenbosch, Stellenbosch, South Africa
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Centre for Water and Environmental Research, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
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44
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Türkowsky D, Jehmlich N, Diekert G, Adrian L, von Bergen M, Goris T. An integrative overview of genomic, transcriptomic and proteomic analyses in organohalide respiration research. FEMS Microbiol Ecol 2019; 94:4830072. [PMID: 29390082 DOI: 10.1093/femsec/fiy013] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 01/24/2018] [Indexed: 02/06/2023] Open
Abstract
Organohalide respiration (OHR) is a crucial process in the global halogen cycle and of interest for bioremediation. However, investigations on OHR are hampered by the restricted genetic accessibility and the poor growth yields of many organohalide-respiring bacteria (OHRB). Therefore, genomics, transcriptomics and proteomics are often used to investigate OHRB. In general, these gene expression studies are more useful when the data of the different 'omics' approaches are integrated and compared among a wide range of cultivation conditions and ideally involve several closely related OHRB. Despite the availability of a couple of proteomic and transcriptomic datasets dealing with OHRB, such approaches are currently not covered in reviews. Therefore, we here present an integrative and comparative overview of omics studies performed with the OHRB Sulfurospirillum multivorans, Dehalococcoides mccartyi, Desulfitobacterium spp. and Dehalobacter restrictus. Genes, transcripts, proteins and the regulatory and biochemical processes involved in OHR are discussed, and a comprehensive view on the unusual metabolism of D. mccartyi, which is one of the few bacteria possibly using a quinone-independent respiratory chain, is provided. Several 'omics'-derived theories on OHRB, e.g. the organohalide-respiratory chain, hydrogen metabolism, corrinoid biosynthesis or one-carbon metabolism are critically discussed on the basis of this integrative approach.
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Affiliation(s)
- Dominique Türkowsky
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, Germany
| | - Tobias Goris
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
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45
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Sorokin DY, Messina E, La Cono V, Ferrer M, Ciordia S, Mena MC, Toshchakov SV, Golyshin PN, Yakimov MM. Sulfur Respiration in a Group of Facultatively Anaerobic Natronoarchaea Ubiquitous in Hypersaline Soda Lakes. Front Microbiol 2018; 9:2359. [PMID: 30333814 PMCID: PMC6176080 DOI: 10.3389/fmicb.2018.02359] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 09/14/2018] [Indexed: 11/21/2022] Open
Abstract
The ubiquity of strictly anaerobic sulfur-respiring haloarchaea in hypersaline systems with circumneutral pH has shaken a traditional concept of this group as predominantly aerobic heterotrophs. Here, we demonstrated that this functional group of haloarchaea also has its representatives in hypersaline alkaline lakes. Sediments from various hypersaline soda lakes showed high activity of sulfur reduction only partially inhibited by antibiotics. Eight pure cultures of sulfur-reducing natronoarchaea were isolated from such sediments using formate and butyrate as electron donors and sulfur as an electron acceptor. Unlike strict anaerobic haloarchaea, these novel sulfur-reducing natronoarchaea are facultative anaerobes, whose metabolic capabilities were inferred from cultivation experiments and genomic/proteomic reconstruction. While sharing many physiological traits with strict anaerobic haloarchaea, following metabolic distinctions make these new organisms be successful in both anoxic and aerobic habitats: the recruiting of heme-copper quinol oxidases as terminal electron sink in aerobic respiratory chain and the utilization of formate, hydrogen or short-chain fatty acids as electron donors during anaerobic growth with elemental sulfur. Obtained results significantly advance the emerging concept of halo(natrono)archaea as important players in the anaerobic sulfur and carbon cycling in various salt-saturated habitats.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Enzo Messina
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Violetta La Cono
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Manuel Ferrer
- Institute of Catalysis, Spanish National Research Council, Madrid, Spain
| | - Sergio Ciordia
- Proteomics Unit, National Center for Biotechnology, Spanish National Research Council, Madrid, Spain
| | - Maria C Mena
- Proteomics Unit, National Center for Biotechnology, Spanish National Research Council, Madrid, Spain
| | - Stepan V Toshchakov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Peter N Golyshin
- School of Biological Sciences and The Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Michail M Yakimov
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy.,Immanuel Kant Baltic Federal University, Kaliningrad, Russia
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46
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Russell MJ. Green Rust: The Simple Organizing 'Seed' of All Life? Life (Basel) 2018; 8:E35. [PMID: 30150570 PMCID: PMC6161180 DOI: 10.3390/life8030035] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 06/28/2018] [Accepted: 08/14/2018] [Indexed: 01/18/2023] Open
Abstract
Korenaga and coworkers presented evidence to suggest that the Earth's mantle was dry and water filled the ocean to twice its present volume 4.3 billion years ago. Carbon dioxide was constantly exhaled during the mafic to ultramafic volcanic activity associated with magmatic plumes that produced the thick, dense, and relatively stable oceanic crust. In that setting, two distinct and major types of sub-marine hydrothermal vents were active: ~400 °C acidic springs, whose effluents bore vast quantities of iron into the ocean, and ~120 °C, highly alkaline, and reduced vents exhaling from the cooler, serpentinizing crust some distance from the heads of the plumes. When encountering the alkaline effluents, the iron from the plume head vents precipitated out, forming mounds likely surrounded by voluminous exhalative deposits similar to the banded iron formations known from the Archean. These mounds and the surrounding sediments, comprised micro or nano-crysts of the variable valence FeII/FeIII oxyhydroxide known as green rust. The precipitation of green rust, along with subsidiary iron sulfides and minor concentrations of nickel, cobalt, and molybdenum in the environment at the alkaline springs, may have established both the key bio-syntonic disequilibria and the means to properly make use of them-the elements needed to effect the essential inanimate-to-animate transitions that launched life. Specifically, in the submarine alkaline vent model for the emergence of life, it is first suggested that the redox-flexible green rust micro- and nano-crysts spontaneously precipitated to form barriers to the complete mixing of carbonic ocean and alkaline hydrothermal fluids. These barriers created and maintained steep ionic disequilibria. Second, the hydrous interlayers of green rust acted as engines that were powered by those ionic disequilibria and drove essential endergonic reactions. There, aided by sulfides and trace elements acting as catalytic promoters and electron transfer agents, nitrate could be reduced to ammonia and carbon dioxide to formate, while methane may have been oxidized to methyl and formyl groups. Acetate and higher carboxylic acids could then have been produced from these C1 molecules and aminated to amino acids, and thence oligomerized to offer peptide nests to phosphate and iron sulfides, and secreted to form primitive amyloid-bounded structures, leading conceivably to protocells.
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Affiliation(s)
- Michael J Russell
- Planetary Chemistry and Astrobiology, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109-8099, USA.
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47
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A Phosphofructokinase Homolog from Pyrobaculum calidifontis Displays Kinase Activity towards Pyrimidine Nucleosides and Ribose 1-Phosphate. J Bacteriol 2018; 200:JB.00284-18. [PMID: 29866806 DOI: 10.1128/jb.00284-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 05/17/2018] [Indexed: 01/22/2023] Open
Abstract
The genome of the hyperthermophilic archaeon Pyrobaculum calidifontis contains an open reading frame, Pcal_0041, annotated as encoding a PfkB family ribokinase, consisting of phosphofructokinase and pyrimidine kinase domains. Among the biochemically characterized enzymes, the Pcal_0041 protein was 37% identical to the phosphofructokinase (Ape_0012) from Aeropyrum pernix, which displayed kinase activity toward a broad spectrum of substrates, including sugars, sugar phosphates, and nucleosides, and 36% identical to a phosphofructokinase from Desulfurococcus amylolyticus To examine the biochemical function of the Pcal_0041 protein, we cloned and expressed the gene and purified the recombinant protein. Although the Pcal_0041 protein contained a putative phosphofructokinase domain, it exhibited only low levels of phosphofructokinase activity. The recombinant enzyme catalyzed the phosphorylation of nucleosides and, to a lower extent, sugars and sugar phosphates. Surprisingly, among the substrates tested, the highest activity was detected with ribose 1-phosphate (R1P), followed by cytidine and uridine. The catalytic efficiency (k cat/Km ) toward R1P was 11.5 mM-1 · s-1 ATP was the most preferred phosphate donor, followed by GTP. Activity measurements with cell extracts of P. calidifontis indicated the presence of nucleoside phosphorylase activity, which would provide the means to generate R1P from nucleosides. The study suggests that, in addition to the recently identified ADP-dependent ribose 1-phosphate kinase (R1P kinase) in Thermococcus kodakarensis that functions in the pentose bisphosphate pathway, R1P kinase is also present in members of the Crenarchaeota.IMPORTANCE The discovery of the pentose bisphosphate pathway in Thermococcus kodakarensis has clarified how this archaeon can degrade nucleosides. Homologs of the enzymes of this pathway are present in many members of the Thermococcales, suggesting that this metabolism occurs in these organisms. However, this is not the case in other archaea, and degradation mechanisms for nucleosides or ribose 1-phosphate are still unknown. This study reveals an important first step in understanding nucleoside metabolism in Crenarchaeota and identifies an ATP-dependent ribose 1-phosphate kinase in Pyrobaculum calidifontis The enzyme is structurally distinct from previously characterized archaeal members of the ribokinase family and represents a group of proteins found in many crenarchaea.
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48
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Wong HL, White RA, Visscher PT, Charlesworth JC, Vázquez-Campos X, Burns BP. Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes. ISME JOURNAL 2018; 12:2619-2639. [PMID: 29980796 DOI: 10.1038/s41396-018-0208-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 04/27/2018] [Accepted: 06/01/2018] [Indexed: 11/09/2022]
Abstract
The functional metagenomic potential of Shark Bay microbial mats was examined for the first time at a millimeter scale, employing shotgun sequencing of communities via the Illumina NextSeq 500 platform in conjunction with defined chemical analyses. A detailed functional metagenomic profile has elucidated key pathways and facilitated inference of critical microbial interactions. In addition, 87 medium-to-high-quality metagenome-assembled genomes (MAG) were assembled, including potentially novel bins under the deep-branching archaeal Asgard group (Thorarchaetoa and Lokiarchaeota). A range of pathways involved in carbon, nitrogen, sulfur, and phosphorus cycles were identified in mat metagenomes, with the Wood-Ljungdahl pathway over-represented and inferred as a major carbon fixation mode. The top five sets of genes were affiliated to sulfate assimilation (cysNC cysNCD, sat), methanogenesis (hdrABC), Wood-Ljungdahl pathways (cooS, coxSML), phosphate transport (pstB), and copper efflux (copA). Polyhydroxyalkanoate (PHA) synthase genes were over-represented at the surface, with PHA serving as a potential storage of fixed carbon. Sulfur metabolism genes were highly represented, in particular complete sets of genes responsible for both assimilatory and dissimilatory sulfate reduction. Pathways of environmental adaptation (UV, hypersalinity, oxidative stress, and heavy metal resistance) were also delineated, as well as putative viral defensive mechanisms (core genes of the CRISPR, BREX, and DISARM systems). This study provides new metagenome-based models of how biogeochemical cycles and adaptive responses may be partitioned in the microbial mats of Shark Bay.
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Affiliation(s)
- Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Richard Allen White
- Institute of Biological Chemistry, Washington State University, Pullman, USA
| | - Pieter T Visscher
- Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia.,Department of Marine Sciences, University of Connecticut, Storrs, CT, USA
| | - James C Charlesworth
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia. .,Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia.
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49
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Branscomb E, Russell MJ. Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis? Bioessays 2018; 40:e1700182. [DOI: 10.1002/bies.201700182] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 04/26/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Elbert Branscomb
- Department of Physics; Carl R. Woese Institute for Genomic Biology; University of Illinois; Urbana IL 61801 USA
| | - Michael J. Russell
- Planetary Chemistry and Astrobiology; Sec. 3225 MS:183-301; Jet Propulsion Laboratory; California Institute of Technology; Pasadena CA 91109-8099 USA
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Quehenberger J, Shen L, Albers SV, Siebers B, Spadiut O. Sulfolobus - A Potential Key Organism in Future Biotechnology. Front Microbiol 2017; 8:2474. [PMID: 29312184 PMCID: PMC5733018 DOI: 10.3389/fmicb.2017.02474] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/28/2017] [Indexed: 11/13/2022] Open
Abstract
Extremophilic organisms represent a potentially valuable resource for the development of novel bioprocesses. They can act as a source for stable enzymes and unique biomaterials. Extremophiles are capable of carrying out microbial processes and biotransformations under extremely hostile conditions. Extreme thermoacidophilic members of the well-characterized genus Sulfolobus are outstanding in their ability to thrive at both high temperatures and low pH. This review gives an overview of the biological system Sulfolobus including its central carbon metabolism and the development of tools for its genetic manipulation. We highlight findings of commercial relevance and focus on potential industrial applications. Finally, the current state of bioreactor cultivations is summarized and we discuss the use of Sulfolobus species in biorefinery applications.
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Affiliation(s)
- Julian Quehenberger
- Research Division Biochemical Engineering, Faculty of Technical Chemistry, Institute of Chemical, Environmental and Biological Engineering, Vienna University of Technology, Vienna, Austria
| | - Lu Shen
- Department of Molecular Enzyme Technology and Biochemistry, Faculty of Chemistry – Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II-Microbiology, Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Faculty of Chemistry – Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Oliver Spadiut
- Research Division Biochemical Engineering, Faculty of Technical Chemistry, Institute of Chemical, Environmental and Biological Engineering, Vienna University of Technology, Vienna, Austria
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