1
|
Biester A, Grahame DA, Drennan CL. Capturing a methanogenic carbon monoxide dehydrogenase/acetyl-CoA synthase complex via cryogenic electron microscopy. Proc Natl Acad Sci U S A 2024; 121:e2410995121. [PMID: 39361653 DOI: 10.1073/pnas.2410995121] [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: 06/01/2024] [Accepted: 08/27/2024] [Indexed: 10/05/2024] Open
Abstract
Approximately two-thirds of the estimated one-billion metric tons of methane produced annually by methanogens is derived from the cleavage of acetate. Acetate is broken down by a Ni-Fe-S-containing A-cluster within the enzyme acetyl-CoA synthase (ACS) to carbon monoxide (CO) and a methyl group (CH3+). The methyl group ultimately forms the greenhouse gas methane, whereas CO is converted to the greenhouse gas carbon dioxide (CO2) by a Ni-Fe-S-containing C-cluster within the enzyme carbon monoxide dehydrogenase (CODH). Although structures have been solved of CODH/ACS from acetogens, which use these enzymes to make acetate from CO2, no structure of a CODH/ACS from a methanogen has been reported. In this work, we use cryo-electron microscopy to reveal the structure of a methanogenic CODH and CODH/ACS from Methanosarcina thermophila (MetCODH/ACS). We find that the N-terminal domain of acetogenic ACS, which is missing in all methanogens, is replaced by a domain of CODH. This CODH domain provides a channel for CO to travel between the two catalytic Ni-Fe-S clusters. It generates the binding surface for ACS and creates a remarkably similar CO alcove above the A-cluster using residues from CODH rather than ACS. Comparison of our MetCODH/ACS structure with our MetCODH structure reveals a molecular mechanism to restrict gas flow from the CO channel when ACS departs, preventing CO escape into the cell. Overall, these long-awaited structures of a methanogenic CODH/ACS reveal striking functional similarities to their acetogenic counterparts despite a substantial difference in domain organization.
Collapse
Affiliation(s)
- Alison Biester
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - David A Grahame
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- HHMI, Massachusetts Institute of Technology, Cambridge, MA 02139
| |
Collapse
|
2
|
De Jesús JAC, Elghandour MMMY, Adegbeye MJ, Aguirre DL, Roque-Jimenez JA, Lackner M, Salem AZM. Nano-encapsulation of essential amino acids: ruminal methane, carbon monoxide, hydrogen sulfide and fermentation. AMB Express 2024; 14:109. [PMID: 39349779 PMCID: PMC11442736 DOI: 10.1186/s13568-024-01767-4] [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: 07/05/2024] [Accepted: 09/12/2024] [Indexed: 10/04/2024] Open
Abstract
This study aimed to evaluate the effect of nano-encapsulation of four essential amino acids (AA), threonine, methionine, tryptophan, and lysine on in vitro ruminal total gas, methane, carbon monoxide, and hydrogen sulfide production as well as the rumen fermentation profile in cattle. The highest (P < 0.001) rate and asymptotic gas production after 48 h of incubation was observed in the diets that had threonine, followed by lysine, methionine, and tryptophan. Asymptotic methane gas production decreased in the following order: threonine > lysine > tryptophan > methionine (P < 0.0001) and the rate of production per hour followed the same trend (P = 0.0259). CH4 parameters showed that in 4 h, 24 h, and 48 h of incubation the lowest methane production was obtained in the diet with methionine (P < 0.05) and the highest one in diet supplemented with threonine. Methane fractions showed that methionine-containing diets resulted in more (P < 0.05) metabolizable energy versus methane, followed by tryptophan-containing, and then lysine-containing diets. Methionine-fortified diets seem to be the most eco-friendly among those studied regarding methane output. However, based on methane, CO, and H2S output as well as the rumen fermentation profile nano-encapsulated lysine is recommended for use in ruminant nutrition.
Collapse
Affiliation(s)
- Jorge Adalberto Cayetano De Jesús
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, C.P. 50000,, Toluca, Estado de México, Mexico
| | | | - Moyosore Joseph Adegbeye
- Research Centre for Animal Husbandry, National Research and Innovation Agency, Cibinong Science Centre, Cibinong, Bogor 16915, Jl. Raya Jakarta-Bogor, Indonesia
| | - Daniel López Aguirre
- Facultad de Ingeniería y Ciencias, Universidad Autónoma de Tamaulipas, 87149, Ciudad Victoria, Tamaulipas, Mexico
| | | | - Maximilian Lackner
- Department of Industrial Engineering, University of Applied Sciences Technikum Wien, Hoechstaedtplatz 6, 1200, Vienna, Austria
| | - Abdelfattah Zeidan Mohamed Salem
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, C.P. 50000,, Toluca, Estado de México, Mexico.
| |
Collapse
|
3
|
Cossu M, Catlin D, Elliott SJ, Metcalf WW, Nair SK. Structural organization of pyruvate: ferredoxin oxidoreductase from the methanogenic archaeon Methanosarcina acetivorans. Structure 2024:S0969-2126(24)00328-9. [PMID: 39265575 DOI: 10.1016/j.str.2024.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/18/2024] [Accepted: 08/16/2024] [Indexed: 09/14/2024]
Abstract
Enzymes of the 2-oxoacid:ferredoxin oxidoreductase (OFOR) superfamily catalyze the reversible oxidation of 2-oxoacids to acyl-coenzyme A esters and carbon dioxide (CO2)using ferredoxin or flavodoxin as the redox partner. Although members of the family share primary sequence identity, a variety of domain and subunit arrangements are known. Here, we characterize the structure of a four-subunit family member: the pyruvate:ferredoxin oxidoreductase (PFOR) from the methane producing archaeon Methanosarcina acetivorans (MaPFOR). The 1.92 Å resolution crystal structure of MaPFOR shows a protein fold like those of single- or two-subunit PFORs that function in 2-oxoacid oxidation, including the location of the requisite thiamine pyrophosphate (TPP), and three [4Fe-4S] clusters. Of note, MaPFOR typically functions in the CO2 reductive direction, and structural comparisons to the pyruvate oxidizing PFORs show subtle differences in several regions of catalytical relevance. These studies provide a framework that may shed light on the biochemical mechanisms used to facilitate reductive pyruvate synthesis.
Collapse
Affiliation(s)
- Matteo Cossu
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Daniel Catlin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sean J Elliott
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - William W Metcalf
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
| |
Collapse
|
4
|
Bourgade B, Islam MA. Progresses and challenges of engineering thermophilic acetogenic cell factories. Front Microbiol 2024; 15:1476253. [PMID: 39282569 PMCID: PMC11392765 DOI: 10.3389/fmicb.2024.1476253] [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: 08/05/2024] [Accepted: 08/20/2024] [Indexed: 09/19/2024] Open
Abstract
Thermophilic acetogens are gaining recognition as potent microbial cell factories, leveraging their unique metabolic capabilities to drive the development of sustainable biotechnological processes. These microorganisms, thriving at elevated temperatures, exhibit robust carbon fixation abilities via the linear Wood-Ljungdahl pathway to efficiently convert C1 substrates, including syngas (CO, CO2 and H2) from industrial waste gasses, into acetate and biomass via the central metabolite acetyl-CoA. This review summarizes recent advancements in metabolic engineering and synthetic biology efforts that have expanded the range of products derived from thermophilic acetogens after briefly discussing their autotrophic metabolic diversity. These discussions highlight their potential in the sustainable bioproduction of industrially relevant compounds. We further review the remaining challenges for implementing efficient and complex strain engineering strategies in thermophilic acetogens, significantly limiting their use in an industrial context.
Collapse
Affiliation(s)
- Barbara Bourgade
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - M Ahsanul Islam
- Department of Chemical Engineering, Loughborough University, Loughborough, United Kingdom
| |
Collapse
|
5
|
Colman DR, Keller LM, Arteaga-Pozo E, Andrade-Barahona E, St Clair B, Shoemaker A, Cox A, Boyd ES. Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution. Nat Commun 2024; 15:7506. [PMID: 39209850 PMCID: PMC11362583 DOI: 10.1038/s41467-024-51841-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
The geosphere and the microbial biosphere have co-evolved for ~3.8 Ga, with many lines of evidence suggesting a hydrothermal habitat for life's origin. However, the extent that contemporary thermophiles and their hydrothermal habitats reflect those that likely existed on early Earth remains unknown. To address this knowledge gap, 64 geochemical analytes were measured and 1022 metagenome-assembled-genomes (MAGs) were generated from 34 chemosynthetic high-temperature springs in Yellowstone National Park and analysed alongside 444 MAGs from 35 published metagenomes. We used these data to evaluate co-variation in MAG taxonomy, metabolism, and phylogeny as a function of hot spring geochemistry. We found that cohorts of MAGs and their functions are discretely distributed across pH gradients that reflect different geochemical provinces. Acidic or circumneutral/alkaline springs harbor MAGs that branched later and are enriched in sulfur- and arsenic-based O2-dependent metabolic pathways that are inconsistent with early Earth conditions. In contrast, moderately acidic springs sourced by volcanic gas harbor earlier-branching MAGs that are enriched in anaerobic, gas-dependent metabolisms (e.g. H2, CO2, CH4 metabolism) that have been hypothesized to support early microbial life. Our results provide insight into the influence of redox state in the eco-evolutionary feedbacks between thermophiles and their habitats and suggest moderately acidic springs as early Earth analogs.
Collapse
Affiliation(s)
- Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
| | - Lisa M Keller
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Emilia Arteaga-Pozo
- Department of Chemistry and Geochemistry, Montana Technological University, Butte, MT, USA
| | - Eva Andrade-Barahona
- Department of Chemistry and Geochemistry, Montana Technological University, Butte, MT, USA
| | - Brian St Clair
- Department of Chemistry and Geochemistry, Montana Technological University, Butte, MT, USA
| | - Anna Shoemaker
- Department of Earth Sciences, Montana State University, Bozeman, MT, USA
| | - Alysia Cox
- Department of Chemistry and Geochemistry, Montana Technological University, Butte, MT, USA
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
| |
Collapse
|
6
|
Tian F, Wainaina JM, Howard-Varona C, Domínguez-Huerta G, Bolduc B, Gazitúa MC, Smith G, Gittrich MR, Zablocki O, Cronin DR, Eveillard D, Hallam SJ, Sullivan MB. Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans. MICROBIOME 2024; 12:159. [PMID: 39198891 PMCID: PMC11360552 DOI: 10.1186/s40168-024-01876-z] [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: 03/06/2024] [Accepted: 07/16/2024] [Indexed: 09/01/2024]
Abstract
BACKGROUND Prokaryotic microbes have impacted marine biogeochemical cycles for billions of years. Viruses also impact these cycles, through lysis, horizontal gene transfer, and encoding and expressing genes that contribute to metabolic reprogramming of prokaryotic cells. While this impact is difficult to quantify in nature, we hypothesized that it can be examined by surveying virus-encoded auxiliary metabolic genes (AMGs) and assessing their ecological context. RESULTS We systematically developed a global ocean AMG catalog by integrating previously described and newly identified AMGs and then placed this catalog into ecological and metabolic contexts relevant to ocean biogeochemistry. From 7.6 terabases of Tara Oceans paired prokaryote- and virus-enriched metagenomic sequence data, we increased known ocean virus populations to 579,904 (up 16%). From these virus populations, we then conservatively identified 86,913 AMGs that grouped into 22,779 sequence-based gene clusters, 7248 (~ 32%) of which were not previously reported. Using our catalog and modeled data from mock communities, we estimate that ~ 19% of ocean virus populations carry at least one AMG. To understand AMGs in their metabolic context, we identified 340 metabolic pathways encoded by ocean microbes and showed that AMGs map to 128 of them. Furthermore, we identified metabolic "hot spots" targeted by virus AMGs, including nine pathways where most steps (≥ 0.75) were AMG-targeted (involved in carbohydrate, amino acid, fatty acid, and nucleotide metabolism), as well as other pathways where virus-encoded AMGs outnumbered cellular homologs (involved in lipid A phosphates, phosphatidylethanolamine, creatine biosynthesis, phosphoribosylamine-glycine ligase, and carbamoyl-phosphate synthase pathways). CONCLUSIONS Together, this systematically curated, global ocean AMG catalog and analyses provide a valuable resource and foundational observations to understand the role of viruses in modulating global ocean metabolisms and their biogeochemical implications. Video Abstract.
Collapse
Affiliation(s)
- Funing Tian
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - James M Wainaina
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Cristina Howard-Varona
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
| | - Guillermo Domínguez-Huerta
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
- Centro Oceanográfico de Málaga (IEO-CSIC), Puerto Pesquero S/N, 29640, Fuengirola (Málaga), Spain
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
| | | | - Garrett Smith
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
| | - Marissa R Gittrich
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
| | - Dylan R Cronin
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
| | - Damien Eveillard
- Université de Nantes, CNRS, LS2N, Nantes, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara GO-SEE, Paris, France
| | - Steven J Hallam
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Genome Science and Technology Program, University of British Columbia, 2329 West Mall, Vancouver, BC, V6T 1Z4, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA.
- Center of Microbiome Science, Ohio State University, Columbus, OH, 43210, USA.
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA.
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
7
|
Schmitz LM, Kreitli N, Obermaier L, Weber N, Rychlik M, Angenent LT. Power-to-vitamins: producing folate (vitamin B 9) from renewable electric power and CO 2 with a microbial protein system. Trends Biotechnol 2024:S0167-7799(24)00177-X. [PMID: 39271416 DOI: 10.1016/j.tibtech.2024.06.014] [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: 06/06/2024] [Revised: 06/21/2024] [Accepted: 06/28/2024] [Indexed: 09/15/2024]
Abstract
We recently proposed a two-stage Power-to-Protein technology to produce microbial protein from renewable electric power and CO2. Two stages were operated in series: Clostridium ljungdahlii in Stage A to reduce CO2 with H2 into acetate, and Saccharomyces cerevisiae in Stage B to utilize O2 and produce microbial protein from acetate. Renewable energy can be used to power water electrolysis to produce H2 and O2. A drawback of Stage A was the need for continuous vitamin supplementation. In this study, by using the more robust thermophilic acetogen Thermoanaerobacter kivui instead of C. ljungdahlii, vitamin supplementation was no longer needed. Additionally, S. cerevisiae produced folate when grown with acetate as a sole carbon source, achieving a total folate concentration of 6.7 mg per 100 g biomass with an average biomass concentration of 3 g l-1. The developed Power-to-Vitamin system enables folate production from renewable power and CO2 with zero or negative net-carbon emissions.
Collapse
Affiliation(s)
- Lisa Marie Schmitz
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, 72074 Tübingen, Germany
| | - Nicolai Kreitli
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, 72074 Tübingen, Germany
| | - Lisa Obermaier
- Analytical Food Chemistry, Technical University of Munich, 85354 Freising, Germany
| | - Nadine Weber
- Analytical Food Chemistry, Technical University of Munich, 85354 Freising, Germany
| | - Michael Rychlik
- Analytical Food Chemistry, Technical University of Munich, 85354 Freising, Germany
| | - Largus T Angenent
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, 72074 Tübingen, Germany; AG Angenent, Max Planck Institute for Biology, Max Planck Ring 5, D-72076 Tübingen, Germany; Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10D, 8000Aarhus C, Denmark; The Novo Nordisk Foundation CO(2) Research Center (CORC), Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, C, Denmark; Cluster of Excellence - Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72074 Tübingen, Germany.
| |
Collapse
|
8
|
Mrnjavac N, Schwander L, Brabender M, Martin WF. Chemical Antiquity in Metabolism. Acc Chem Res 2024; 57:2267-2278. [PMID: 39083571 PMCID: PMC11339923 DOI: 10.1021/acs.accounts.4c00226] [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: 04/19/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 08/02/2024]
Abstract
ConspectusLife is an exergonic chemical reaction. The same was true when the very first cells emerged at life's origin. In order to live, all cells need a source of carbon, energy, and electrons to drive their overall reaction network (metabolism). In most cells, these are separate pathways. There is only one biochemical pathway that serves all three needs simultaneously: the acetyl-CoA pathway of CO2 fixation. In the acetyl-CoA pathway, electrons from H2 reduce CO2 to pyruvate for carbon supply, while methane or acetate synthesis are coupled to energy conservation as ATP. This simplicity and thermodynamic favorability prompted Georg Fuchs and Erhard Stupperich to propose in 1985 that the acetyl-CoA pathway might mark the origin of metabolism, at the same time that Steve Ragsdale and Harland Wood were uncovering catalytic roles for Fe, Co, and Ni in the enzymes of the pathway. Subsequent work has provided strong support for those proposals.In the presence of Fe, Co, and Ni in their native metallic state as catalysts, aqueous H2 and CO2 react specifically to formate, acetate, methane, and pyruvate overnight at 100 °C. These metals (and their alloys) thus replace the function of over 120 enzymes required for the conversion of H2 and CO2 to pyruvate via the pathway and its cofactors, an unprecedented set of findings in the study of biochemical evolution. The reactions require alkaline conditions, which promote hydrogen oxidation by proton removal and are naturally generated in serpentinizing (H2-producing) hydrothermal vents. Serpentinizing hydrothermal vents furthermore produce natural deposits of native Fe, Co, Ni, and their alloys. These are precisely the metals that reduce CO2 with H2 in the laboratory; they are also the metals found at the active sites of enzymes in the acetyl-CoA pathway. Iron, cobalt and nickel are relicts of the environments in which metabolism arose, environments that still harbor ancient methane- and acetate-producing autotrophs today. This convergence indicates bedrock-level antiquity for the acetyl-CoA pathway. In acetogens and methanogens growing on H2 as reductant, the acetyl-CoA pathway requires flavin-based electron bifurcation as a source of reduced ferredoxin (a 4Fe4S cluster-containing protein) in order to function. Recent findings show that H2 can reduce the 4Fe4S clusters of ferredoxin in the presence of native iron, uncovering an evolutionary precursor of flavin-based electron bifurcation and suggesting an origin of FeS-dependent electron transfer in proteins. Traditionally discussed as catalysts in early evolution, the most common function of FeS clusters in metabolism is one-electron transfer, also in radical SAM enzymes, a large and ancient enzyme family. The cofactors and active sites in enzymes of the acetyl-CoA pathway uncover chemical antiquity in metabolism involving metals, methyl groups, methyl transfer reactions, cobamides, pterins, GTP, S-adenosylmethionine, radical SAM enzymes, and carbon-metal bonds. The reaction sequence from H2 and CO2 to pyruvate on naturally deposited native metals is maximally simple. It requires neither nitrogen, sulfur, phosphorus, RNA, ion gradients, nor light. Solid-state metal catalysts tether the origin of metabolism to a H2-producing, serpentinizing hydrothermal vent.
Collapse
Affiliation(s)
- Natalia Mrnjavac
- Institute
of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Loraine Schwander
- Institute
of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Max Brabender
- Institute
of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - William F. Martin
- Institute
of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| |
Collapse
|
9
|
Stefanini R, Karekar S, Ale Enriquez F, Ahring B. Examining homoacetogens in feces from adult and juvenile kangaroos with the aim of finding competitive strains to hydrogenotrophic methanogens. Microbiol Spectr 2024; 12:e0318323. [PMID: 38904373 PMCID: PMC11302345 DOI: 10.1128/spectrum.03183-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/13/2024] [Indexed: 06/22/2024] Open
Abstract
We examined the microbial populations present in fecal samples of macropods capable of utilizing a mixture of hydrogen and carbon dioxide (70:30) percent. The feces samples were cultured under anaerobic conditions, and production of methane or acetic acids characteristic for methanogenesis and homoacetogenesis was measured. While the feces of adult macropods mainly produced methane from the substrate, the sample from a 2-month-old juvenile kangaroo only produced acetic acid and no methane. The stable highly enriched culture of the joey kangaroo was sequenced to examine the V3 and V4 regions of the 16S rRNA gene. The results showed that over 70% of gene copies belonged to the Clostridia class, with Paraclostridium and Blautia as the most predominant genera. The culture further showed the presence of Actinomyces spp., a genus which has only been identified in the GI tract of macropods in a few studies, and where none, to our knowledge, have been classified as homoacetogenic. The joey kangaroo mixed culture showed a doubling time of 3.54 h and a specific growth rate of 0.199/h, faster than what has been observed for homoacetogenic bacteria in general. IMPORTANCE Enteric methane emissions from cattle are a significant contributor to greenhouse gas emissions worldwide. Methane emissions not only contribute to climate change but also represent a loss of energy from the animal's diet. However, methanogens play an important role as hydrogen sink to rumen systems; without it, the performance of hydrolytic organisms diminishes. Therefore, effective strategies of methanogen inhibition would be enhanced in conjunction with the addition of alternative hydrogen sinks to the rumen. The significance of our research is to identify homoacetogens present in the GI tract of kangaroos and to present their performance in vitro, demonstrating their capability to serve as alternatives to rumen methanogens.
Collapse
Affiliation(s)
- Renan Stefanini
- Bioproducts, Sciences and Engineering Laboratory, Washington State University, Richland, Washington, USA
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington, USA
| | - Supriya Karekar
- Bioproducts, Sciences and Engineering Laboratory, Washington State University, Richland, Washington, USA
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington, USA
| | - Fuad Ale Enriquez
- Bioproducts, Sciences and Engineering Laboratory, Washington State University, Richland, Washington, USA
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, USA
| | - Birgitte Ahring
- Bioproducts, Sciences and Engineering Laboratory, Washington State University, Richland, Washington, USA
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington, USA
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, USA
| |
Collapse
|
10
|
Ruickoldt J, Jeoung JH, Rudolph MA, Lennartz F, Kreibich J, Schomäcker R, Dobbek H. Coupling CO 2 Reduction and Acetyl-CoA Formation: The Role of a CO Capturing Tunnel in Enzymatic Catalysis. Angew Chem Int Ed Engl 2024; 63:e202405120. [PMID: 38743001 DOI: 10.1002/anie.202405120] [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: 03/14/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
The bifunctional CO-dehydrogenase/acetyl-CoA synthase (CODH/ACS) complex couples the reduction of CO2 to the condensation of CO with a methyl moiety and CoA to acetyl-CoA. Catalysis occurs at two sites connected by a tunnel transporting the CO. In this study, we investigated how the bifunctional complex and its tunnel support catalysis using the CODH/ACS from Carboxydothermus hydrogenoformans as a model. Although CODH/ACS adapted to form a stable bifunctional complex with a secluded substrate tunnel, catalysis and CO transport is even more efficient when two monofunctional enzymes are coupled. Efficient CO channeling appears to be ensured by hydrophobic binding sites for CO, which act in a bucket-brigade fashion rather than as a simple tube. Tunnel remodeling showed that opening the tunnel increased activity but impaired directed transport of CO. Constricting the tunnel impaired activity and CO transport, suggesting that the tunnel evolved to sequester CO rather than to maximize turnover.
Collapse
Affiliation(s)
- Jakob Ruickoldt
- Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany
| | - Jae-Hun Jeoung
- Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany
| | - Maik Alexander Rudolph
- Technische Universität Berlin, Institut für Chemie - Technische Chemie, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Frank Lennartz
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Straße 15, 12489, Berlin, Germany
| | - Julian Kreibich
- Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany
| | - Reinhard Schomäcker
- Technische Universität Berlin, Institut für Chemie - Technische Chemie, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Holger Dobbek
- Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany
| |
Collapse
|
11
|
Kirschning A. Why pyridoxal phosphate could be a functional predecessor of thiamine pyrophosphate and speculations on a primordial metabolism. RSC Chem Biol 2024; 5:508-517. [PMID: 38846080 PMCID: PMC11151856 DOI: 10.1039/d4cb00016a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/15/2024] [Indexed: 06/09/2024] Open
Abstract
The account attempts to substantiate the hypothesis that, from an evolutionary perspective, the coenzyme couple pyridoxal phosphate and pyridoxamine phosphate preceded the coenzyme thiamine pyrophosphate and acted as its less efficient chemical analogue in some form of early metabolism. The analysis combines mechanism-based chemical reactivity with biosynthetic arguments and provides evidence that vestiges of "TPP-like reactivity" are still found for PLP today. From these thoughts, conclusions can be drawn about the key elements of a primordial form of metabolism, which includes the citric acid cycle, amino acid biosynthesis and the pentose phosphate pathway.
Collapse
Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B 30167 Hannover Germany
- Uppsala Biomedical Center (BMC), University Uppsala, Husargatan 3 752 37 Uppsala Sweden
| |
Collapse
|
12
|
Shomar H, Bokinsky G. Harnessing iron‑sulfur enzymes for synthetic biology. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119718. [PMID: 38574823 DOI: 10.1016/j.bbamcr.2024.119718] [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: 01/15/2024] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
Reactions catalysed by iron-sulfur (Fe-S) enzymes appear in a variety of biosynthetic pathways that produce valuable natural products. Harnessing these biosynthetic pathways by expression in microbial cell factories grown on an industrial scale would yield enormous economic and environmental benefits. However, Fe-S enzymes often become bottlenecks that limits the productivity of engineered pathways. As a consequence, achieving the production metrics required for industrial application remains a distant goal for Fe-S enzyme-dependent pathways. Here, we identify and review three core challenges in harnessing Fe-S enzyme activity, which all stem from the properties of Fe-S clusters: 1) limited Fe-S cluster supply within the host cell, 2) Fe-S cluster instability, and 3) lack of specialized reducing cofactor proteins often required for Fe-S enzyme activity, such as enzyme-specific flavodoxins and ferredoxins. We highlight successful methods developed for a variety of Fe-S enzymes and electron carriers for overcoming these difficulties. We use heterologous nitrogenase expression as a grand case study demonstrating how each of these challenges can be addressed. We predict that recent breakthroughs in protein structure prediction and design will prove well-suited to addressing each of these challenges. A reliable toolkit for harnessing Fe-S enzymes in engineered metabolic pathways will accelerate the development of industry-ready Fe-S enzyme-dependent biosynthesis pathways.
Collapse
Affiliation(s)
- Helena Shomar
- Institut Pasteur, université Paris Cité, Inserm U1284, Diversité moléculaire des microbes (Molecular Diversity of Microbes lab), 75015 Paris, France
| | - Gregory Bokinsky
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| |
Collapse
|
13
|
Wan S, Lai M, Gao X, Zhou M, Yang S, Li Q, Li F, Xia L, Tan Y. Recent progress in engineering Clostridium autoethanogenum to synthesize the biochemicals and biocommodities. Synth Syst Biotechnol 2024; 9:19-25. [PMID: 38205027 PMCID: PMC10776380 DOI: 10.1016/j.synbio.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/15/2023] [Accepted: 12/07/2023] [Indexed: 01/12/2024] Open
Abstract
Excessive mining and utilization fossil fuels has led to drastic environmental consequences, which will contribute to global warming and cause further climate change with severe consequences for the human population. The magnitude of these challenges requires several approaches to develop sustainable alternatives for chemicals and fuels production. In this context, biological processes, mainly microbial fermentation, have gained particular interest. For example, autotrophic gas-fermenting acetogenic bacteria are capable of converting CO, CO2 and H2 into biomass and multiple metabolites through Wood-Ljungdahl pathway, which can be exploited for large-scale fermentation processes to sustainably produce bulk biochemicals and biofuels (e.g. acetate and ethanol) from syngas. Clostridium autoethanogenum is one representative of these chemoautotrophic bacteria and considered as the model for the gas fermentation. Recently, the development of synthetic biology toolbox for this strain has enabled us to study and genetically improve their metabolic capability in gas fermentation. In this review, we will summarize the recent progress involved in the understanding of physiological mechanism and strain engineering for C. autoethanogenum, and provide our perspectives on the future development about the basic biology and engineering biology of this strain.
Collapse
Affiliation(s)
- Sai Wan
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
| | - Mingchi Lai
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xinyu Gao
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, Shandong, China
| | - Mingxin Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen, 518055, China
- Shenzhen Powered Carbon Biotechnology Co., Ltd, Shenzhen, 518055, China
| | - Song Yang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, Shandong, China
| | - Fuli Li
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
| | - Lin Xia
- Shenzhen Powered Carbon Biotechnology Co., Ltd, Shenzhen, 518055, China
| | - Yang Tan
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
| |
Collapse
|
14
|
Chaikitkaew S, Wongfaed N, Mamimin C, O-Thong S, Reungsang A. Conversion of carbon dioxide in biogas into acetic acid by Clostridium thailandense immobilized on porous support materials. Heliyon 2024; 10:e26378. [PMID: 38390190 PMCID: PMC10881430 DOI: 10.1016/j.heliyon.2024.e26378] [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: 09/13/2023] [Revised: 11/12/2023] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
This study aimed to convert CO2 in biogas into acetic acid using immobilized Clostridium thailandense cells on various support materials, including activated carbon, expanded clay, and coir. Immobilized cells and free cells were evaluated for their CO2 conversion ability into acetic acid using H2 as an electron donor at an H2 to CO2 in biogas ratio of 2:1 (v/v), 30 °C, 150 rpm. Results showed that immobilized cells on activated carbon increased CH4 content to 96.9% (v/v), and acetic acid production to 15.65 mmol/L within 96 h. These values outperformed free cells. The activated carbon-immobilized cells could be reused two times without losing efficacy in the purification of biogas and acetic acid production. This work indicates that using the immobilized cells offers a sustainable approach to biogas upgrading, reducing the environmental footprint of biogas production by increasing its energy content and purity.
Collapse
Affiliation(s)
- Srisuda Chaikitkaew
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand
- Research Group for Development of Microbial Hydrogen Production Process from Biomass, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Nantharat Wongfaed
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand
- Research Group for Development of Microbial Hydrogen Production Process from Biomass, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chonticha Mamimin
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand
- Research Group for Development of Microbial Hydrogen Production Process from Biomass, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sompong O-Thong
- Biofuel and Biocatalysis Innovation Research Unit, Nakhonsawan Campus, Mahidol University, Nakhonsawan, 60130, Thailand
| | - Alissara Reungsang
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand
- Research Group for Development of Microbial Hydrogen Production Process from Biomass, Khon Kaen University, Khon Kaen, 40002, Thailand
- Academy of Science, Royal Society of Thailand, Bangkok, 10300, Thailand
| |
Collapse
|
15
|
Zhang J, Li F, Liu D, Liu Q, Song H. Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production. Chem Soc Rev 2024; 53:1375-1446. [PMID: 38117181 DOI: 10.1039/d3cs00537b] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.
Collapse
Affiliation(s)
- Junqi Zhang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Feng Li
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Dingyuan Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Qijing Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| |
Collapse
|
16
|
Schoenmakers LLJ, Reydon TAC, Kirschning A. Evolution at the Origins of Life? Life (Basel) 2024; 14:175. [PMID: 38398684 PMCID: PMC10890241 DOI: 10.3390/life14020175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
The role of evolutionary theory at the origin of life is an extensively debated topic. The origin and early development of life is usually separated into a prebiotic phase and a protocellular phase, ultimately leading to the Last Universal Common Ancestor. Most likely, the Last Universal Common Ancestor was subject to Darwinian evolution, but the question remains to what extent Darwinian evolution applies to the prebiotic and protocellular phases. In this review, we reflect on the current status of evolutionary theory in origins of life research by bringing together philosophy of science, evolutionary biology, and empirical research in the origins field. We explore the various ways in which evolutionary theory has been extended beyond biology; we look at how these extensions apply to the prebiotic development of (proto)metabolism; and we investigate how the terminology from evolutionary theory is currently being employed in state-of-the-art origins of life research. In doing so, we identify some of the current obstacles to an evolutionary account of the origins of life, as well as open up new avenues of research.
Collapse
Affiliation(s)
- Ludo L. J. Schoenmakers
- Konrad Lorenz Institute for Evolution and Cognition Research (KLI), 3400 Klosterneuburg, Austria
| | - Thomas A. C. Reydon
- Institute of Philosophy, Centre for Ethics and Law in the Life Sciences (CELLS), Leibniz University Hannover, 30159 Hannover, Germany;
| | - Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, 30167 Hannover, Germany;
| |
Collapse
|
17
|
Kumar S, Tripathi A, Chakraborty I, Ghangrekar MM. Engineered nanomaterials for carbon capture and bioenergy production in microbial electrochemical technologies: A review. BIORESOURCE TECHNOLOGY 2023; 389:129809. [PMID: 37797801 DOI: 10.1016/j.biortech.2023.129809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023]
Abstract
The mounting threat of global warming, fuelled by industrialization and anthropogenic activities, is undeniable. In 2017, atmospheric carbon dioxide (CO2), the primary greenhouse gas, exceeded 410 ppm for the first time. Shockingly, on April 28, 2023, this figure surged even higher, reaching an alarming 425 ppm. Even though extensive research has been conducted on developing efficient carbon capture and storage technologies, most suffer from high costs, short lifespans, and significant environmental impacts. Recently, the use of engineered nanomaterials (ENM), particularly in microbial electrochemical technologies (METs), has gained momentum owing to their appropriate physicochemical properties and catalytic activity. By implementing ENM, the MET variants like microbial electrosynthesis (MES) and photosynthetic microbial fuel cells (pMFC) can enhance carbon capture efficiency with simultaneous bioenergy production and wastewater treatment. This review provides an overview of ENMs' role in carbon capture within MES and pMFC, highlighting advancements and charting future research directions.
Collapse
Affiliation(s)
- Santosh Kumar
- P. K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Akash Tripathi
- Department of Civil Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Indrajit Chakraborty
- Department of Civil Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Makarand M Ghangrekar
- P. K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; Department of Civil Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| |
Collapse
|
18
|
Bährle R, Böhnke S, Englhard J, Bachmann J, Perner M. Current status of carbon monoxide dehydrogenases (CODH) and their potential for electrochemical applications. BIORESOUR BIOPROCESS 2023; 10:84. [PMID: 38647803 PMCID: PMC10992861 DOI: 10.1186/s40643-023-00705-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/16/2023] [Indexed: 04/25/2024] Open
Abstract
Anthropogenic carbon dioxide (CO2) levels are rising to alarming concentrations in earth's atmosphere, causing adverse effects and global climate changes. In the last century, innovative research on CO2 reduction using chemical, photochemical, electrochemical and enzymatic approaches has been addressed. In particular, natural CO2 conversion serves as a model for many processes and extensive studies on microbes and enzymes regarding redox reactions involving CO2 have already been conducted. In this review we focus on the enzymatic conversion of CO2 to carbon monoxide (CO) as the chemical conversion downstream of CO production render CO particularly attractive as a key intermediate. We briefly discuss the different currently known natural autotrophic CO2 fixation pathways, focusing on the reversible reaction of CO2, two electrons and protons to CO and water, catalyzed by carbon monoxide dehydrogenases (CODHs). We then move on to classify the different type of CODHs, involved catalyzed chemical reactions and coupled metabolisms. Finally, we discuss applications of CODH enzymes in photochemical and electrochemical cells to harness CO2 from the environment transforming it into commodity chemicals.
Collapse
Affiliation(s)
- Rebecca Bährle
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany
| | - Stefanie Böhnke
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany
| | - Jonas Englhard
- Chemistry of Thin Film Materials, IZNF, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 3, 91058, Erlangen, Germany
| | - Julien Bachmann
- Chemistry of Thin Film Materials, IZNF, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 3, 91058, Erlangen, Germany
| | - Mirjam Perner
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany.
| |
Collapse
|
19
|
Chen X, Liu J, Zhu XY, Xue CX, Yao P, Fu L, Yang Z, Sun K, Yu M, Wang X, Zhang XH. Phylogenetically and metabolically diverse autotrophs in the world's deepest blue hole. ISME COMMUNICATIONS 2023; 3:117. [PMID: 37964026 PMCID: PMC10645885 DOI: 10.1038/s43705-023-00327-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023]
Abstract
The world's deepest yongle blue hole (YBH) is characterized by sharp dissolved oxygen (DO) gradients, and considerably low-organic-carbon and high-inorganic-carbon concentrations that may support active autotrophic communities. To understand metabolic strategies of autotrophic communities for obtaining carbon and energy spanning redox gradients, we presented finer characterizations of microbial community, metagenome and metagenome-assembled genomes (MAGs) in the YBH possessing oxic, hypoxic, essentially anoxic and completely anoxic zones vertically. Firstly, the YBH microbial composition and function shifted across the four zones, linking to different biogeochemical processes. The recovery of high-quality MAGs belonging to various uncultivated lineages reflected high novelty of the YBH microbiome. Secondly, carbon fixation processes and associated energy metabolisms varied with the vertical zones. The Calvin-Benson-Bassham (CBB) cycle was ubiquitous but differed in affiliated taxa at different zones. Various carbon fixation pathways were found in the hypoxic and essentially anoxic zones, including the 3-hyroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle affiliated to Nitrososphaeria, and Wood-Ljungdahl (WL) pathway affiliated to Planctomycetes, with sulfur oxidation and dissimilatory nitrate reduction as primary energy-conserving pathways. The completely anoxic zone harbored diverse taxa (Dehalococcoidales, Desulfobacterales and Desulfatiglandales) utilizing the WL pathway coupled with versatile energy-conserving pathways via sulfate reduction, fermentation, CO oxidation and hydrogen metabolism. Finally, most of the WL-pathway containing taxa displayed a mixotrophic lifestyle corresponding to flexible carbon acquisition strategies. Our result showed a vertical transition of microbial lifestyle from photo-autotrophy, chemoautotrophy to mixotrophy in the YBH, enabling a better understanding of carbon fixation processes and associated biogeochemical impacts with different oxygen availability.
Collapse
Affiliation(s)
- Xing Chen
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jiwen Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xiao-Yu Zhu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Chun-Xu Xue
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Liang Fu
- Sansha Track Ocean Coral Reef Conservation Research Institute, Sansha, 573199, China
| | - Zuosheng Yang
- College of Marine Geosciences, Ocean University of China, Qingdao, 266100, China
| | - Kai Sun
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Min Yu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xiaolei Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China.
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
| |
Collapse
|
20
|
Moon J, Schubert A, Poehlein A, Daniel R, Müller V. A new metabolic trait in an acetogen: Mixed acid fermentation of fructose in a methylene-tetrahydrofolate reductase mutant of Acetobacterium woodii. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:339-351. [PMID: 37150590 PMCID: PMC10472528 DOI: 10.1111/1758-2229.13160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/20/2023] [Indexed: 05/09/2023]
Abstract
To inactivate the Wood-Ljungdahl pathway in the acetogenic model bacterium Acetobacterium woodii, the genes metVF encoding two of the subunits of the methylene-tetrahydrofolate reductase were deleted. As expected, the mutant did not grow on C1 compounds and also not on lactate, ethanol or butanediol. In contrast to a mutant in which the first enzyme of the pathway (hydrogen-dependent CO2 reductase) had been genetically deleted, cells were able to grow on fructose, albeit with lower rates and yields than the wild-type. Growth was restored by addition of an external electron sink, glycine betaine + CO2 or caffeate. Resting cells pre-grown on fructose plus an external electron acceptor fermented fructose to two acetate and four hydrogen, that is, performed hydrogenogenesis. Cells pre-grown under fermentative conditions on fructose alone redirected carbon and electrons to form lactate, formate, ethanol as well as hydrogen. Apparently, growth on fructose alone induced enzymes for mixed acid fermentation (MAF). Transcriptome analyses revealed enzymes potentially involved in MAF and a quantitative model for MAF from fructose in A. woodii is presented.
Collapse
Affiliation(s)
- Jimyung Moon
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurtGermany
| | - Anja Schubert
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurtGermany
| | - Anja Poehlein
- Göttingen Genomics Laboratory, Institute for Microbiology and GeneticsGeorg August UniversityGöttingenGermany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute for Microbiology and GeneticsGeorg August UniversityGöttingenGermany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurtGermany
| |
Collapse
|
21
|
Sapountzaki E, Rova U, Christakopoulos P, Antonopoulou I. Renewable Hydrogen Production and Storage Via Enzymatic Interconversion of CO 2 and Formate with Electrochemical Cofactor Regeneration. CHEMSUSCHEM 2023; 16:e202202312. [PMID: 37165995 DOI: 10.1002/cssc.202202312] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/12/2023]
Abstract
The urgent need to reduce CO2 emissions has motivated the development of CO2 capture and utilization technologies. An emerging application is CO2 transformation into storage chemicals for clean energy carriers. Formic acid (FA), a valuable product of CO2 reduction, is an excellent hydrogen carrier. CO2 conversion to FA, followed by H2 release from FA, are conventionally chemically catalyzed. Biocatalysts offer a highly specific and less energy-intensive alternative. CO2 conversion to formate is catalyzed by formate dehydrogenase (FDH), which usually requires a cofactor to function. Several FDHs have been incorporated in bioelectrochemical systems where formate is produced by the biocathode and the cofactor is electrochemically regenerated. H2 production from formate is also catalyzed by several microorganisms possessing either formate hydrogenlyase or hydrogen-dependent CO2 reductase complexes. Combination of these two processes can lead to a CO2 -recycling cycle for H2 production, storage, and release with potentially lower environmental impact than conventional methods.
Collapse
Affiliation(s)
- Eleftheria Sapountzaki
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187, Luleå, Sweden
| | - Ulrika Rova
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187, Luleå, Sweden
| | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187, Luleå, Sweden
| | - Io Antonopoulou
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187, Luleå, Sweden
| |
Collapse
|
22
|
Katagiri S, Ohsugi Y, Shiba T, Yoshimi K, Nakagawa K, Nagasawa Y, Uchida A, Liu A, Lin P, Tsukahara Y, Iwata T, Tohara H. Homemade blenderized tube feeding improves gut microbiome communities in children with enteral nutrition. Front Microbiol 2023; 14:1215236. [PMID: 37680532 PMCID: PMC10482415 DOI: 10.3389/fmicb.2023.1215236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/09/2023] [Indexed: 09/09/2023] Open
Abstract
Enteral nutrition for children is supplied through nasogastric or gastrostomy tubes. Diet not only influences nutritional intake but also interacts with the composition and function of the gut microbiota. Homemade blenderized tube feeding has been administered to children receiving enteral nutrition, in addition to ready-made tube feeding. The purpose of this study was to evaluate the oral/gut microbial communities in children receiving enteral nutrition with or without homemade blenderized tube feeding. Among a total of 30 children, 6 receiving mainly ready-made tube feeding (RTF) and 5 receiving mainly homemade blenderized tube feeding (HBTF) were analyzed in this study. Oral and gut microbiota community profiles were evaluated through 16S rRNA sequencing of saliva and fecal samples. The α-diversity representing the number of observed features, Shannon index, and Chao1 in the gut were significantly increased in HBTF only in the gut microbiome but not in the oral microbiome. In addition, the relative abundances of the phylum Proteobacteria, class Gammaproteobacteria, and genus Escherichia-Shigella were significantly low, whereas that of the genus Ruminococcus was significantly high in the gut of children with HBTF, indicating HBTF altered the gut microbial composition and reducing health risks. Metagenome prediction showed enrichment of carbon fixation pathways in prokaryotes at oral and gut microbiomes in children receiving HBTF. In addition, more complex network structures were observed in the oral cavity and gut in the HBTF group than in the RTF group. In conclusion, HBTF not only provides satisfaction and enjoyment during meals with the family but also alters the gut microbial composition to a healthy state.
Collapse
Affiliation(s)
- Sayaka Katagiri
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yujin Ohsugi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takahiko Shiba
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA, United States
| | - Kanako Yoshimi
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kazuharu Nakagawa
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yuki Nagasawa
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Aritoshi Uchida
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Anhao Liu
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Peiya Lin
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yuta Tsukahara
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Haruka Tohara
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| |
Collapse
|
23
|
Zhang ZF, Liu LR, Pan YP, Pan J, Li M. Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments. MICROBIOME 2023; 11:188. [PMID: 37612768 PMCID: PMC10464287 DOI: 10.1186/s40168-023-01630-x] [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: 04/15/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND Mangrove wetlands are coastal ecosystems with important ecological features and provide habitats for diverse microorganisms with key roles in nutrient and biogeochemical cycling. However, the overall metabolic potentials and ecological roles of microbial community in mangrove sediment are remained unanswered. In current study, the microbial and metabolic profiles of prokaryotic and fungal communities in mangrove sediments were investigated using metagenomic analysis based on PacBio single-molecule real time (SMRT) and Illumina sequencing techniques. RESULTS Comparing to Illumina short reads, the incorporation of PacBio long reads significantly contributed to more contiguous assemblies, yielded more than doubled high-quality metagenome-assembled genomes (MAGs), and improved the novelty of the MAGs. Further metabolic reconstruction for recovered MAGs showed that prokaryotes potentially played an essential role in carbon cycling in mangrove sediment, displaying versatile metabolic potential for degrading organic carbons, fermentation, autotrophy, and carbon fixation. Mangrove fungi also functioned as a player in carbon cycling, potentially involved in the degradation of various carbohydrate and peptide substrates. Notably, a new candidate bacterial phylum named as Candidatus Cosmopoliota with a ubiquitous distribution is proposed. Genomic analysis revealed that this new phylum is capable of utilizing various types of organic substrates, anaerobic fermentation, and carbon fixation with the Wood-Ljungdahl (WL) pathway and the reverse tricarboxylic acid (rTCA) cycle. CONCLUSIONS The study not only highlights the advantages of HiSeq-PacBio Hybrid assembly for a more complete profiling of environmental microbiomes but also expands our understanding of the microbial diversity and potential roles of distinct microbial groups in biogeochemical cycling in mangrove sediment. Video Abstract.
Collapse
Affiliation(s)
- Zhi-Feng Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Present Address: Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Li-Rui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yue-Ping Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
| |
Collapse
|
24
|
Moon J, Waschinger LM, Müller V. Lactate formation from fructose or C1 compounds in the acetogen Acetobacterium woodii by metabolic engineering. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12637-7. [PMID: 37417977 PMCID: PMC10390620 DOI: 10.1007/s00253-023-12637-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 07/08/2023]
Abstract
Anaerobic, acetogenic bacteria are promising biocatalysts for a sustainable bioeconomy since they capture and convert carbon dioxide to acetic acid. Hydrogen is an intermediate in acetate formation from organic as well as C1 substrates. Here, we analyzed mutants of the model acetogen Acetobacterium woodii in which either one of the two hydrogenases or both together were genetically deleted. In resting cells of the double mutant, hydrogen formation from fructose was completely abolished and carbon was redirected largely to lactate. The lactate/fructose and lactate/acetate ratios were 1.24 and 2.76, respectively. We then tested for lactate formation from methyl groups (derived from glycine betaine) and carbon monoxide. Indeed, also under these conditions lactate and acetate were formed in equimolar amounts with a lactate/acetate ratio of 1.13. When the electron-bifurcating lactate dehydrogenase/ETF complex was genetically deleted, lactate formation was completely abolished. These experiments demonstrate the capability of A. woodii to produce lactate from fructose but also from promising C1 substrates, methyl groups and carbon monoxide. This adds an important milestone towards generation of a value chain leading from CO2 to value-added compounds. KEY POINTS: • Resting cells of the ΔhydBA/hdcr mutant of Acetobacterium woodii produced lactate from fructose or methyl groups + CO • Lactate formation from methyl groups + CO was completely abolished after deletion of lctBCD • Metabolic engineering of a homoacetogen to lactate formation gives a potential for industrial applications.
Collapse
Affiliation(s)
- Jimyung Moon
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany
| | - Lara M Waschinger
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany.
| |
Collapse
|
25
|
Kang B, Lee H, Oh S, Kim JY, Ko YJ, Chang IS. Regulatory transcription factor (CooA)-driven carbon monoxide partial pressure sensing whole-cell biosensor. Heliyon 2023; 9:e17391. [PMID: 37408883 PMCID: PMC10318455 DOI: 10.1016/j.heliyon.2023.e17391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 07/07/2023] Open
Abstract
We designed and constructed a whole-cell biosensor capable of detecting the presence and quantity of carbon monoxide (CO) using the CO regulatory transcription factor. This biosensor utilizes CooA, a CO-sensing transcription regulator that activates the expression of carbon monoxide dehydrogenase (CODH), to detect the presence of CO and respond by triggering the expression of a GUS reporter protein (β-glucuronidase). The GUS reporter protein is expressed from a CO-induced CooA-binding promoter (PcooF) by CooA and enables the effective colorimetric detection of CO. An Escherichia coli strain used to validate the biosensor showed growth and GUS activity under anaerobic conditions; this study used the inert gas (Ar) to create anaerobic conditions. The pBRCO biosensor could successfully detect the presence of CO in the headspace. Moreover, the GUS-specific activity of pBRCO according to the CO strength as partial pressure followed Michaelis-Menten kinetics (R2 = 0.98). It was confirmed that the GUS-specific activity of pBRCO increased linearly up to 30.39 kPa (R2 = 0.98), and thus, a quantitative analysis of CO concentration (i.e., partial pressure) was possible.
Collapse
Affiliation(s)
- Byeongchan Kang
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Hyeryeong Lee
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
- Research Center for Innovative Energy and Carbon Optimized Synthesis for Chemicals (inn-ECOSysChem), Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Soyoung Oh
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Ji-Yeon Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
- Research Center for Innovative Energy and Carbon Optimized Synthesis for Chemicals (inn-ECOSysChem), Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Young-Joon Ko
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - In Seop Chang
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
- Research Center for Innovative Energy and Carbon Optimized Synthesis for Chemicals (inn-ECOSysChem), Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| |
Collapse
|
26
|
Dent MR, Weaver BR, Roberts MG, Burstyn JN. Carbon Monoxide-Sensing Transcription Factors: Regulators of Microbial Carbon Monoxide Oxidation Pathway Gene Expression. J Bacteriol 2023; 205:e0033222. [PMID: 37154694 PMCID: PMC10210986 DOI: 10.1128/jb.00332-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Carbon monoxide (CO) serves as a source of energy and carbon for a diverse set of microbes found in anaerobic and aerobic environments. The enzymes that bacteria and archaea use to oxidize CO depend upon complex metallocofactors that require accessory proteins for assembly and proper function. This complexity comes at a high energetic cost and necessitates strict regulation of CO metabolic pathways in facultative CO metabolizers to ensure that gene expression occurs only when CO concentrations and redox conditions are appropriate. In this review, we examine two known heme-dependent transcription factors, CooA and RcoM, that regulate inducible CO metabolism pathways in anaerobic and aerobic microorganisms. We provide an analysis of the known physiological and genomic contexts of these sensors and employ this analysis to contextualize known biochemical properties. In addition, we describe a growing list of putative transcription factors associated with CO metabolism that potentially use cofactors other than heme to sense CO.
Collapse
Affiliation(s)
- Matthew R. Dent
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brian R. Weaver
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Madeleine G. Roberts
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Judith N. Burstyn
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| |
Collapse
|
27
|
Vazquez-Mendoza OV, Andrade-Yucailla V, Elghandour MMMY, Masaquiza-Moposita DA, Cayetano-De-Jesús JA, Alvarado-Ramírez ER, Adegbeye MJ, Barros-Rodríguez M, Salem AZM. Effect of Dietary Guanidinoacetic Acid Levels on the Mitigation of Greenhouse Gas Production and the Rumen Fermentation Profile of Alfalfa-Based Diets. Animals (Basel) 2023; 13:1719. [PMID: 37889628 PMCID: PMC10252124 DOI: 10.3390/ani13111719] [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: 04/10/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 10/29/2023] Open
Abstract
The objective of this study was to evaluate the effect of different percentages of alfalfa (Medicago sativa L.) hay (AH) and doses of guanidinoacetic acid (GAA) in the diet on the mitigation of greenhouse gas production, the in vitro rumen fermentation profile and methane (CH4) conversion efficiency. AH percentages were defined for the diets of beef and dairy cattle, as well as under grazing conditions (10 (AH10), 25 (AH25) and 100% (AH100)), while the GAA doses were 0 (control), 0.0005, 0.0010, 0.0015, 0.0020, 0.0025 and 0.0030 g g-1 DM diet. With an increased dose of GAA, the total gas production (GP) and methane (CH4) increased (p = 0.0439) in the AH10 diet, while in AH25 diet, no effect was observed (p = 0.1311), and in AH100, GP and CH4 levels decreased (p = 0.0113). In addition, the increase in GAA decreased (p = 0.0042) the proportion of CH4 in the AH25 diet, with no influence (p = 0.1050) on CH4 in the AH10 and AH100 diet groups. Carbon monoxide production decreased (p = 0.0227) in the AH100 diet with most GAA doses, and the other diets did not show an effect (p = 0.0617) on carbon monoxide, while the production of hydrogen sulfide decreased (p = 0.0441) in the AH10 and AH100 diets with the addition of GAA, with no effect observed in association with the AH25 diet (p = 0.3162). The pH level increased (p < 0.0001) and dry matter degradation (DMD) decreased (p < 0.0001) when AH was increased from 10 to 25%, while 25 to 100% AH contents had the opposite effect. In addition, with an increased GAA dose, only the pH in the AH100 diet increased (p = 0.0142 and p = 0.0023) the DMD in the AH10 diet group. Similarly, GAA influenced (p = 0.0002) SCFA, ME and CH4 conversion efficiency but only in the AH10 diet group. In this diet group, it was observed that with an increased dose of GAA, SCFA and ME increased (p = 0.0002), while CH4 per unit of OM decreased (p = 0.0002) only with doses of 0.0010, 0.0015 and 0.0020 g, with no effect on CH4 per unit of SCFA and ME (p = 0.1790 and p = 0.1343). In conclusion, the positive effects of GAA depend on the percentage of AH, and diets with 25 and 100% AH showed very little improvement with the addition of GAA, while the diet with 10% AH presented the best results.
Collapse
Affiliation(s)
- Oscar Vicente Vazquez-Mendoza
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Toluca 50295, Mexico; (O.V.V.-M.); (M.M.M.Y.E.); (J.A.C.-D.-J.)
| | - Veronica Andrade-Yucailla
- Centro de Investigaciones Agropecuarias, Facultad de Ciencias Agrarias, Universidad Estatal Península de Santa Elena, La Libertad 240204, Ecuador;
| | | | | | - Jorge Adalberto Cayetano-De-Jesús
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Toluca 50295, Mexico; (O.V.V.-M.); (M.M.M.Y.E.); (J.A.C.-D.-J.)
| | | | - Moyosore Joseph Adegbeye
- Department of Animal Production and Health, Federal University of Technology, Akure 340110, Nigeria;
| | - Marcos Barros-Rodríguez
- Facultad de Ciencias Agropecuarias, Universidad Técnica de Ambato, Cevallos 1801334, Ecuador;
| | - Abdelfattah Zeidan Mohamed Salem
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Toluca 50295, Mexico; (O.V.V.-M.); (M.M.M.Y.E.); (J.A.C.-D.-J.)
| |
Collapse
|
28
|
Nwaokorie UJ, Reinmets K, de Lima LA, Pawar PR, Shaikh KM, Harris A, Köpke M, Valgepea K. Deletion of genes linked to the C 1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum. Front Bioeng Biotechnol 2023; 11:1167892. [PMID: 37265994 PMCID: PMC10230548 DOI: 10.3389/fbioe.2023.1167892] [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: 02/16/2023] [Accepted: 05/03/2023] [Indexed: 06/03/2023] Open
Abstract
Gas fermentation has emerged as a sustainable route to produce fuels and chemicals by recycling inexpensive one-carbon (C1) feedstocks from gaseous and solid waste using gas-fermenting microbes. Currently, acetogens that utilise the Wood-Ljungdahl pathway to convert carbon oxides (CO and CO2) into valuable products are the most advanced biocatalysts for gas fermentation. However, our understanding of the functionalities of the genes involved in the C1-fixing gene cluster and its closely-linked genes is incomplete. Here, we investigate the role of two genes with unclear functions-hypothetical protein (hp; LABRINI_07945) and CooT nickel binding protein (nbp; LABRINI_07950)-directly adjacent and expressed at similar levels to the C1-fixing gene cluster in the gas-fermenting model-acetogen Clostridium autoethanogenum. Targeted deletion of either the hp or nbp gene using CRISPR/nCas9, and phenotypic characterisation in heterotrophic and autotrophic batch and autotrophic bioreactor continuous cultures revealed significant growth defects and altered by-product profiles for both ∆hp and ∆nbp strains. Variable effects of gene deletion on autotrophic batch growth on rich or minimal media suggest that both genes affect the utilisation of complex nutrients. Autotrophic chemostat cultures showed lower acetate and ethanol production rates and higher carbon flux to CO2 and biomass for both deletion strains. Additionally, proteome analysis revealed that disruption of either gene affects the expression of proteins of the C1-fixing gene cluster and ethanol synthesis pathways. Our work contributes to a better understanding of genotype-phenotype relationships in acetogens and offers engineering targets to improve carbon fixation efficiency in gas fermentation.
Collapse
Affiliation(s)
- Ugochi Jennifer Nwaokorie
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Kristina Reinmets
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Lorena Azevedo de Lima
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Pratik Rajendra Pawar
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | | | | | | | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| |
Collapse
|
29
|
Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
Collapse
Affiliation(s)
- Sarah Bierbaumer
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J. Erb
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K. Winkler
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M. Glueck
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| |
Collapse
|
30
|
Pavao A, Girinathan B, Peltier J, Altamirano Silva P, Dupuy B, Muti IH, Malloy C, Cheng LL, Bry L. Elucidating dynamic anaerobe metabolism with HRMAS 13C NMR and genome-scale modeling. Nat Chem Biol 2023; 19:556-564. [PMID: 36894723 PMCID: PMC10154198 DOI: 10.1038/s41589-023-01275-9] [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: 08/24/2022] [Accepted: 01/30/2023] [Indexed: 03/11/2023]
Abstract
Anaerobic microbial metabolism drives critical functions within global ecosystems, host-microbiota interactions, and industrial applications, yet remains ill-defined. Here we advance a versatile approach to elaborate cellular metabolism in obligate anaerobes using the pathogen Clostridioides difficile, an amino acid and carbohydrate-fermenting Clostridia. High-resolution magic angle spinning nuclear magnetic resonance (NMR) spectroscopy of C. difficile, grown with fermentable 13C substrates, informed dynamic flux balance analysis (dFBA) of the pathogen's genome-scale metabolism. Analyses identified dynamic recruitment of oxidative and supporting reductive pathways, with integration of high-flux amino acid and glycolytic metabolism at alanine's biosynthesis to support efficient energy generation, nitrogen handling and biomass generation. Model predictions informed an approach leveraging the sensitivity of 13C NMR spectroscopy to simultaneously track cellular carbon and nitrogen flow from [U-13C]glucose and [15N]leucine, confirming the formation of [13C,15N]alanine. Findings identify metabolic strategies used by C. difficile to support its rapid colonization and expansion in gut ecosystems.
Collapse
Affiliation(s)
- Aidan Pavao
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brintha Girinathan
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Ginkgo Bioworks, The Innovation and Design Building, Boston, MA, USA
| | - Johann Peltier
- Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Paris, France
- Institute for Integrative Biology of the Cell (I2BC), 91198, University of Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Pamela Altamirano Silva
- Centre for Investigations in Tropical Diseases, Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Paris, France
| | - Isabella H Muti
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Craig Malloy
- Department of Radiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Leo L Cheng
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Clinical Microbiology Laboratory, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
31
|
Allaart MT, Diender M, Sousa DZ, Kleerebezem R. Overflow metabolism at the thermodynamic limit of life: How carboxydotrophic acetogens mitigate carbon monoxide toxicity. Microb Biotechnol 2023; 16:697-705. [PMID: 36632026 PMCID: PMC10034630 DOI: 10.1111/1751-7915.14212] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/29/2022] [Accepted: 01/01/2023] [Indexed: 01/13/2023] Open
Abstract
Carboxydotrophic metabolism is gaining interest due to its applications in gas fermentation technology, enabling the conversion of carbon monoxide to fuels and commodities. Acetogenic carboxydotrophs play a central role in current gas fermentation processes. In contrast to other energy-rich microbial substrates, CO is highly toxic, which makes it a challenging substrate to utilize. Instantaneous scavenging of CO upon entering the cell is required to mitigate its toxicity. Experiments conducted with Clostridium autoethanogenum at different biomass-specific growth rates show that elevated ethanol production occurs at increasing growth rates. The increased allocation of electrons towards ethanol at higher growth rates strongly suggests that C. autoethanogenum employs a form of overflow metabolism to cope with high dissolved CO concentrations. We argue that this overflow branch enables acetogens to efficiently use CO at highly variable substrate influxes by increasing the conversion rate almost instantaneously when required to remove toxic substrate and promote growth. In this perspective, we will address the case study of C. autoethanogenum grown solely on CO and syngas mixtures to assess how it employs acetate reduction to ethanol as a form of overflow metabolism.
Collapse
Affiliation(s)
| | - Martijn Diender
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Robbert Kleerebezem
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| |
Collapse
|
32
|
Al-Mamun A, Ahmed W, Jafary T, Nayak JK, Al-Nuaimi A, Sana A. Recent advances in microbial electrosynthesis system: Metabolic investigation and process optimization. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
|
33
|
Anachad O, Taouil A, Taha W, Bennis F, Chegdani F. The Implication of Short-Chain Fatty Acids in Obesity and Diabetes. Microbiol Insights 2023; 16:11786361231162720. [PMID: 36994236 PMCID: PMC10041598 DOI: 10.1177/11786361231162720] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/21/2023] [Indexed: 03/28/2023] Open
Abstract
Evidence indicates that short-chain fatty acids (SCFAs) generated from the gut microbiota play crucial roles in host metabolism. They contribute to metabolic regulation and energy acquisition of the host by influencing the development of metabolic disorders. This review aims to synthesize recent advances from the literature to investigate the implication of SCFAs in the modulation of obesity and diabetes pathologies. For a better understanding of the relationships between SCFAs and host metabolism, we need to answer some questions: What is the biochemistry of SCFAs, and how they are generated by gut microbiota? What are the bacteria producing of SCFAs and from which routes? How SCFAs are absorbed and transported in the gut by different mechanisms and receptors? How SCFAs involved in obesity and diabetes pathologies?
Collapse
Affiliation(s)
- Oumaima Anachad
- Laboratory of Immunology and biodiversity, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
| | - Amine Taouil
- Laboratory of Immunology and biodiversity, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
| | - Wafaa Taha
- Laboratory of Immunology and biodiversity, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
| | - Faiza Bennis
- Laboratory of Immunology and biodiversity, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
| | - Fatima Chegdani
- Laboratory of Immunology and biodiversity, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
| |
Collapse
|
34
|
Aithal A, Dagar S, Rajamani S. Metals in Prebiotic Catalysis: A Possible Evolutionary Pathway for the Emergence of Metalloproteins. ACS OMEGA 2023; 8:5197-5208. [PMID: 36816708 PMCID: PMC9933472 DOI: 10.1021/acsomega.2c07635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/12/2023] [Indexed: 06/07/2023]
Abstract
Proteinaceous catalysts found in extant biology are products of life that were potentially derived through prolonged periods of evolution. Given their complexity, it is reasonable to assume that they were not accessible to prebiotic chemistry as such. Nevertheless, the dependence of many enzymes on metal ions or metal-ligand cores suggests that catalysis relevant to biology could also be possible with just the metal centers. Given their availability on the Hadean/Archean Earth, it is fair to conjecture that metal ions could have constituted the first forms of catalysts. A slow increase of complexity that was facilitated through the provision of organic ligands and amino acids/peptides possibly allowed for further evolution and diversification, eventually demarcating them into specific functions. Herein, we summarize some key experimental developments and observations that support the possible roles of metal catalysts in shaping the origins of life. Further, we also discuss how they could have evolved into modern-day enzymes, with some suggestions for what could be the imminent next steps that researchers can pursue, to delineate the putative sequence of catalyst evolution during the early stages of life.
Collapse
Affiliation(s)
- Anuraag Aithal
- Department
of Biology, Indian Institute of Science
Education and Research, Pune, Maharashtra 411008, India
| | - Shikha Dagar
- Department
of Biology, Indian Institute of Science
Education and Research, Pune, Maharashtra 411008, India
| | - Sudha Rajamani
- Department
of Biology, Indian Institute of Science
Education and Research, Pune, Maharashtra 411008, India
| |
Collapse
|
35
|
Sobieraj K, Stegenta-Dąbrowska S, Luo G, Koziel JA, Białowiec A. Biological treatment of biowaste as an innovative source of CO-The role of composting process. Front Bioeng Biotechnol 2023; 11:1126737. [PMID: 36845185 PMCID: PMC9947533 DOI: 10.3389/fbioe.2023.1126737] [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: 12/18/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Carbon monoxide (CO) is an essential "building block" for producing everyday chemicals on industrial scale. Carbon monoxide can also be generated though a lesser-known and sometimes forgotten biorenewable pathways that could be explored to advance biobased production from large and more sustainable sources such as bio-waste treatment. Organic matter decomposition can generate carbon monoxide both under aerobic and anaerobic conditions. While anaerobic carbon monoxide generation is relatively well understood, the aerobic is not. Yet many industrial-scale bioprocesses involve both conditions. This review summarizes the necessary basic biochemistry knowledge needed for realization of initial steps towards biobased carbon monoxide production. We analyzed for the first time, the complex information about carbon monoxide production during aerobic, anaerobic bio-waste treatment and storage, carbon monoxide-metabolizing microorganisms, pathways, and enzymes with bibliometric analysis of trends. The future directions recognizing limitations of combined composting and carbon monoxide production have been discussed in greater detail.
Collapse
Affiliation(s)
- Karolina Sobieraj
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Sylwia Stegenta-Dąbrowska
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, China,Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai, China,Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | - Jacek A. Koziel
- USDA-ARS Conservation and Production Research Laboratory, Bushland, TX, United States,Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Andrzej Białowiec
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, Wrocław, Poland,Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States,*Correspondence: Andrzej Białowiec,
| |
Collapse
|
36
|
Beyazay T, Belthle KS, Farès C, Preiner M, Moran J, Martin WF, Tüysüz H. Ambient temperature CO 2 fixation to pyruvate and subsequently to citramalate over iron and nickel nanoparticles. Nat Commun 2023; 14:570. [PMID: 36732515 PMCID: PMC9894855 DOI: 10.1038/s41467-023-36088-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
The chemical reactions that formed the building blocks of life at origins required catalysts, whereby the nature of those catalysts influenced the type of products that accumulated. Recent investigations have shown that at 100 °C awaruite, a Ni3Fe alloy that naturally occurs in serpentinizing systems, is an efficient catalyst for CO2 conversion to formate, acetate, and pyruvate. These products are identical with the intermediates and products of the acetyl-CoA pathway, the most ancient CO2 fixation pathway and the backbone of carbon metabolism in H2-dependent autotrophic microbes. Here, we show that Ni3Fe nanoparticles prepared via the hard-templating method catalyze the conversion of H2 and CO2 to formate, acetate and pyruvate at 25 °C under 25 bar. Furthermore, the 13C-labeled pyruvate can be further converted to acetate, parapyruvate, and citramalate over Ni, Fe, and Ni3Fe nanoparticles at room temperature within one hour. These findings strongly suggest that awaruite can catalyze both the formation of citramalate, the C5 product of pyruvate condensation with acetyl-CoA in microbial carbon metabolism, from pyruvate and the formation of pyruvate from CO2 at very moderate reaction conditions without organic catalysts. These results align well with theories for an autotrophic origin of microbial metabolism under hydrothermal vent conditions.
Collapse
Affiliation(s)
- Tuğçe Beyazay
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Kendra S Belthle
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Christophe Farès
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Martina Preiner
- Faculty of Geosciences, Utrecht University, Department of Ocean Systems, Royal Netherlands Institute for Sea Research (NIOZ), Yerseke, The Netherlands
| | - Joseph Moran
- Université de Strasbourg, CNRS, ISIS UMR 7006, Strasbourg, France
| | - William F Martin
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany.
| | - Harun Tüysüz
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany.
| |
Collapse
|
37
|
Kropochev AI, Lashin SA, Matushkin YG, Klimenko AI. Trait-Based Method of Quantitative Assessment of Ecological Functional Groups in the Human Intestinal Microbiome. BIOLOGY 2023; 12:biology12010115. [PMID: 36671807 PMCID: PMC9855786 DOI: 10.3390/biology12010115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/15/2022] [Accepted: 12/30/2022] [Indexed: 01/15/2023]
Abstract
We propose the trait-based method for quantifying the activity of functional groups in the human gut microbiome based on metatranscriptomic data. It allows one to assess structural changes in the microbial community comprised of the following functional groups: butyrate-producers, acetogens, sulfate-reducers, and mucin-decomposing bacteria. It is another way to perform a functional analysis of metatranscriptomic data by focusing on the ecological level of the community under study. To develop the method, we used published data obtained in a carefully controlled environment and from a synthetic microbial community, where the problem of ambiguity between functionality and taxonomy is absent. The developed method was validated using RNA-seq data and sequencing data of the 16S rRNA amplicon on a simplified community. Consequently, the successful verification provides prospects for the application of this method for analyzing natural communities of the human intestinal microbiota.
Collapse
Affiliation(s)
- Andrew I. Kropochev
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk 630090, Russia
- Correspondence:
| | - Sergey A. Lashin
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Yury G. Matushkin
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexandra I. Klimenko
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk 630090, Russia
| |
Collapse
|
38
|
Abstract
Covering: up to 2022The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD+) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways.
Collapse
Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
| |
Collapse
|
39
|
Annie Modestra J, Matsakas L, Rova U, Christakopoulos P. Prospects and trends in bioelectrochemical systems: Transitioning from CO 2 towards a low-carbon circular bioeconomy. BIORESOURCE TECHNOLOGY 2022; 364:128040. [PMID: 36182019 DOI: 10.1016/j.biortech.2022.128040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Resource scarcity and climate change are the most quested topics in view of environmental sustainability. CO2 sequestration through bioelectrochemical systems is an attractive option for fostering bioeconomy development upon several value-added products generation. This review details the state-of-the-art of bioelectrochemical systems for resource recovery from CO2 along with various biocatalysts capable of utilizing CO2. Two bioprocesses (photo-electrosynthesis and chemolithoelectrosynthesis) were discussed projecting their potential for biobased economy development from CO2. Significance of adopting circular strategies for efficient resource recycling, intensifying product value, integrations/interlinking of multiple process chains for the development of circular bioeconomy were discussed. Existing constrains as well as outlook for near establishment of circular bioeconomy from CO2 is presented by weighing fore-sighted plans with current actions. Need for developing CO2-based circular bioeconomy via innovative business models by analyzing social, technical, environmental and product related aspects are also discussed providing a roadmap of gaps to pursue for attaining practicality.
Collapse
Affiliation(s)
- J Annie Modestra
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, 971‑87, Luleå, Sweden
| | - Leonidas Matsakas
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, 971‑87, Luleå, Sweden.
| | - Ulrika Rova
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, 971‑87, Luleå, Sweden
| | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, 971‑87, Luleå, Sweden
| |
Collapse
|
40
|
Berben T, Forlano Bó F, In 't Zandt MH, Yang S, Liebner S, Welte CU. The Polar Fox Lagoon in Siberia harbours a community of Bathyarchaeota possessing the potential for peptide fermentation and acetogenesis. Antonie Van Leeuwenhoek 2022; 115:1229-1244. [PMID: 35947314 PMCID: PMC9534799 DOI: 10.1007/s10482-022-01767-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/18/2022] [Indexed: 11/05/2022]
Abstract
Archaea belonging to the phylum Bathyarchaeota are the predominant archaeal species in cold, anoxic marine sediments and additionally occur in a variety of habitats, both natural and man-made. Metagenomic and single-cell sequencing studies suggest that Bathyarchaeota may have a significant impact on the emissions of greenhouse gases into the atmosphere, either through direct production of methane or through the degradation of complex organic matter that can subsequently be converted into methane. This is especially relevant in permafrost regions where climate change leads to thawing of permafrost, making high amounts of stored carbon bioavailable. Here we present the analysis of nineteen draft genomes recovered from a sediment core metagenome of the Polar Fox Lagoon, a thermokarst lake located on the Bykovsky Peninsula in Siberia, Russia, which is connected to the brackish Tiksi Bay. We show that the Bathyarchaeota in this lake are predominantly peptide degraders, producing reduced ferredoxin from the fermentation of peptides, while degradation pathways for plant-derived polymers were found to be incomplete. Several genomes encoded the potential for acetogenesis through the Wood-Ljungdahl pathway, but methanogenesis was determined to be unlikely due to the lack of genes encoding the key enzyme in methanogenesis, methyl-CoM reductase. Many genomes lacked a clear pathway for recycling reduced ferredoxin. Hydrogen metabolism was also hardly found: one type 4e [NiFe] hydrogenase was annotated in a single MAG and no [FeFe] hydrogenases were detected. Little evidence was found for syntrophy through formate or direct interspecies electron transfer, leaving a significant gap in our understanding of the metabolism of these organisms.
Collapse
Affiliation(s)
- Tom Berben
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Franco Forlano Bó
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Michiel H In 't Zandt
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
- Netherlands Earth System Science Centre, Utrecht University, Utrecht, The Netherlands
| | - Sizhong Yang
- Section Geomicrobiology, GFZ German Research Centre for Geosciences, Potsdam, Germany
- Cryosphere Research Station On the Qinghai-Tibet Plateau, State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Susanne Liebner
- Section Geomicrobiology, GFZ German Research Centre for Geosciences, Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands.
| |
Collapse
|
41
|
Wang Y, Zhang M, Li L, Yi J, Liang J, Wang S, Xu P. Biosynthesis of L-5-methyltetrahydrofolate by genetically engineered Escherichia coli. Microb Biotechnol 2022; 15:2758-2772. [PMID: 36070350 DOI: 10.1111/1751-7915.14139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 08/17/2022] [Accepted: 08/24/2022] [Indexed: 11/26/2022] Open
Abstract
L-5-Methyltetrahydrofolate (L-5-MTHF) is the only biologically active form of folate in the human body. Production of L-5-MTHF by using microbes is an emerging consideration for green synthesis. However, microbes naturally produce only a small amount of L-5-MTHF. Here, Escherichia coli BL21(DE3) was engineered to increase the production of L-5-MTHF by overexpressing the intrinsic genes of dihydrofolate reductase and methylenetetrahydrofolate (methylene-THF) reductase, introducing the genes encoding formate-THF ligase, formyl-THF cyclohydrolase and methylene-THF dehydrogenase from the one-carbon metabolic pathway of Methylobacterium extorquens or Clostridium autoethanogenum and disrupting the gene of methionine synthase involved in the consumption and synthesis inhibition of the target product. Thus, upon its native pathway, an additional pathway for L-5-MTHF synthesis was developed in E. coli, which was further analysed and confirmed by qRT-PCR, enzyme assays and metabolite determination. After optimizing the conditions of induction time, temperature, cell density and concentration of IPTG and supplementing exogenous substances (folic acid, sodium formate and glucose) to the culture, the highest yield of 527.84 μg g-1 of dry cell weight for L-5-MTHF was obtained, which was about 11.8 folds of that of the original strain. This study paves the way for further metabolic engineering to improve the biosynthesis of L-5-MTHF in E. coli.
Collapse
Affiliation(s)
- Yubo Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Meng Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Lexin Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Jihong Yi
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Jiyu Liang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Shuning Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
42
|
Meier AB, Oppermann S, Drake HL, Schmidt O. The root zone of graminoids: A niche for H2-consuming acetogens in a minerotrophic peatland. Front Microbiol 2022; 13:978296. [PMID: 35992704 PMCID: PMC9391049 DOI: 10.3389/fmicb.2022.978296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
The importance of acetogens for H2 turnover and overall anaerobic degradation in peatlands remains elusive. In the well-studied minerotrophic peatland fen Schlöppnerbrunnen, H2-consuming acetogens are conceptualized to be largely outcompeted by iron reducers, sulfate reducers, and hydrogenotrophic methanogens in bulk peat soil. However, in root zones of graminoids, fermenters thriving on rhizodeposits and root litter might temporarily provide sufficient H2 for acetogens. In the present study, root-free peat soils from around the roots of Molinia caerulea and Carex rostrata (i.e., two graminoids common in fen Schlöpnnerbrunnen) were anoxically incubated with or without supplemental H2 to simulate conditions of high and low H2 availability in the fen. In unsupplemented soil treatments, H2 concentrations were largely below the detection limit (∼10 ppmV) and possibly too low for acetogens and methanogens, an assumption supported by the finding that neither acetate nor methane substantially accumulated. In the presence of supplemental H2, acetate accumulation exceeded CH4 accumulation in Molinia soil whereas acetate and methane accumulated equally in Carex soil. However, reductant recoveries indicated that initially, additional unknown processes were involved either in H2 consumption or the consumption of acetate produced by H2-consuming acetogens. 16S rRNA and 16S rRNA gene analyses revealed that potential acetogens (Clostridium, Holophagaceae), methanogens (Methanocellales, Methanobacterium), iron reducers (Geobacter), and physiologically uncharacterized phylotypes (Acidobacteria, Actinobacteria, Bacteroidetes) were stimulated by supplemental H2 in soil treatments. Phylotypes closely related to clostridial acetogens were also active in soil-free Molinia and Carex root treatments with or without supplemental H2. Due to pronounced fermentation activities, H2 consumption was less obvious in root treatments, and acetogens likely thrived on root organic carbon and fermentation products (e.g., ethanol) in addition to H2. Collectively, the data highlighted that in fen Schlöppnerbrunnen, acetogens are associated to graminoid roots and inhabit the peat soil around the roots, where they have to compete for H2 with methanogens and iron reducers. Furthermore, the study underscored that the metabolically flexible acetogens do not rely on H2, potentially a key advantage over other H2 consumers under the highly dynamic conditions characteristic for the root-zones of graminoids in peatlands.
Collapse
Affiliation(s)
- Anja B. Meier
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Sindy Oppermann
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Harold L. Drake
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
- *Correspondence: Oliver Schmidt,
| |
Collapse
|
43
|
Reconsidering the in vivo functions of Clostridial Stickland amino acid fermentations. Anaerobe 2022; 76:102600. [PMID: 35709938 PMCID: PMC9831356 DOI: 10.1016/j.anaerobe.2022.102600] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/03/2022] [Indexed: 01/13/2023]
Abstract
Stickland amino acid fermentations occur primarily among species of Clostridia. An ancient form of metabolism, Stickland fermentations use amino acids as electron acceptors in the absence of stronger oxidizing agents and provide metabolic capabilities to support growth when other fermentable substrates, such as carbohydrates, are lacking. The reactions were originally described as paired fermentations of amino acid electron donors, such as the branched-chain amino acids, with recipients that include proline and glycine. We present a redox-focused view of Stickland metabolism following electron flow through metabolically diverse oxidative reactions and the defined-substrate reductase systems, including for proline and glycine, and the role of dual redox pathways for substrates such as leucine and ornithine. Genetic studies and Environment and Gene Regulatory Interaction Network (EGRIN) models for the pathogen Clostridioides difficile have improved our understanding of the regulation and metabolic recruitment of these systems, and their functions in modulating inter-species interactions within host-pathogen-commensal systems and uses in industrial and environmental applications.
Collapse
|
44
|
Bell PJL, Paras FE, Mandarakas S, Arcenal P, Robinson-Cast S, Grobler AS, Attfield PV. An Electro-Microbial Process to Uncouple Food Production from Photosynthesis for Application in Space Exploration. LIFE (BASEL, SWITZERLAND) 2022; 12:life12071002. [PMID: 35888090 PMCID: PMC9317029 DOI: 10.3390/life12071002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/10/2022] [Accepted: 07/05/2022] [Indexed: 12/21/2022]
Abstract
Here we propose the concept of an electro–microbial route to uncouple food production from photosynthesis, thereby enabling production of nutritious food in space without the need to grow plant-based crops. In the proposed process, carbon dioxide is fixed into ethanol using either chemical catalysis or microbial carbon fixation, and the ethanol created is used as a carbon source for yeast to synthesize food for human or animal consumption. The process depends upon technologies that can utilize electrical energy to fix carbon into ethanol and uses an optimized strain of the yeast Saccharomyces cerevisiae to produce high-quality, food-grade, single-cell protein using ethanol as the sole carbon source in a minimal medium. Crops performing photosynthesis require months to mature and are challenging to grow under the conditions found in space, whereas the electro–microbial process could generate significant quantities of food on demand with potentially high yields and productivities. In this paper we explore the potential to provide yeast-based protein and other nutrients relevant to human dietary needs using only ethanol, urea, phosphate, and inorganic salts as inputs. It should be noted that as well as having potential to provide nutrition in space, this novel approach to food production has many valuable terrestrial applications too. For example, by enabling food production in climatically challenged environments, the electro–microbial process could potentially turn deserts into food bowls. Similarly, surplus electricity generated from large-scale renewable power sources could be used to supplement the human food chain.
Collapse
|
45
|
A clean in-frame knockout system for gene deletion in Acetobacterium woodii. J Biotechnol 2022; 353:9-18. [PMID: 35659892 DOI: 10.1016/j.jbiotec.2022.05.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 11/24/2022]
Abstract
Acetogenic bacteria produce acetate following the fixation of CO2 via the Wood-Ljungdahl pathway. As such, they represent excellent process organisms for the production of novel chemicals and fuels from this waste greenhouse gas. Acetobacterium woodii is the model acetogen and numerous studies have been conducted investigating its biochemistry, gas consumption and use as a production chassis. However, there are a dearth of available tools for A. woodii gene modification which limits the research options available for genetic studies. Here, the previously proposed Clostridia Roadmap is implemented in A. woodii leading to the derivation of a knockout system for the generation of clean, in-frame deletions. The replicon of the Gram-positive plasmid pCD6 that originated in Clostridioides difficile was identified as being replication-defective in A. woodii, a property that was exploited to construct a pseudo-suicide knockout plasmid which was used to generate an auxotrophic, pyrE mutant. This allowed the subsequent use of a heterologous pyrE gene (from Clostridium acetobutylicum) as a counter selection marker and the deletion of a number of genes by allelic exchange. Specific mutants generated were affected in growth on glucose, fructose and ethanol as a consequence of deletion of fruA, pstG and adhE, respectively.
Collapse
|
46
|
Bourgade B, Humphreys CM, Millard J, Minton NP, Islam MA. Design, Analysis, and Implementation of a Novel Biochemical Pathway for Ethylene Glycol Production in Clostridium autoethanogenum. ACS Synth Biol 2022; 11:1790-1800. [PMID: 35543716 PMCID: PMC9127970 DOI: 10.1021/acssynbio.1c00624] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
![]()
The platform chemical
ethylene glycol (EG) is used to manufacture
various commodity chemicals of industrial importance, but largely
remains synthesized from fossil fuels. Although several novel metabolic
pathways have been reported for its bioproduction in model organisms,
none has been reported for gas-fermenting, non-model acetogenic chassis
organisms. Here, we describe a novel, synthetic biochemical pathway
to convert acetate into EG in the industrially important gas-fermenting
acetogen,Clostridium autoethanogenum. We not only developed a computational workflow to design and analyze
hundreds of novel biochemical pathways for EG production but also
demonstrated a successful pathway construction in the chosen host.
The EG production was achieved using a two-plasmid system to bypass
unfeasible expression levels and potential toxic enzymatic interactions.
Although only a yield of 0.029 g EG/g fructose was achieved and therefore
requiring further strain engineering efforts to optimize the designed
strain, this work demonstrates an important proof-of-concept approach
to computationally design and experimentally implement fully synthetic
metabolic pathways in a metabolically highly specific, non-model host
organism.
Collapse
Affiliation(s)
- Barbara Bourgade
- Department of Chemical Engineering, Loughborough University, Loughborough LE11 3TU, U.K
| | - Christopher M. Humphreys
- BBSRC/EPSRC Synthetic Biology Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, U.K
| | - James Millard
- BBSRC/EPSRC Synthetic Biology Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Nigel P. Minton
- BBSRC/EPSRC Synthetic Biology Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, U.K
| | - M. Ahsanul Islam
- Department of Chemical Engineering, Loughborough University, Loughborough LE11 3TU, U.K
| |
Collapse
|
47
|
He Y, Wang S, Han X, Shen J, Lu Y, Zhao J, Shen C, Qiao L. Photosynthesis of Acetate by Sporomusa ovata-CdS Biohybrid System. ACS APPLIED MATERIALS & INTERFACES 2022; 14:23364-23374. [PMID: 35576621 DOI: 10.1021/acsami.2c01918] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Sporomusa ovata, a typical electroautotrophic microorganism, has been utilized in bioelectrosynthesis for carbon dioxide fixation to multicarbon organic chemicals. However, additional photovoltaic devices are normally needed to convert photo energy to electric energy to power the carbon dioxide fixation, which restricts the overall energy conversion efficiency. Herein, we report Sporomusa ovata-CdS biohybrids for artificial photosynthesis driven by light without any other power source. The quantum yield can reach 16.8 ± 9%, and the active duration time of the system can last for 5 days. During the artificial photosynthesis, carbon dioxide is first reduced to formate and finally converted to acetate via the Wood-Ljungdahl pathway. The carbon dioxide fixation, electron transfer, energy metabolism, and reactive oxygen species damage repair processes in the biohybrid system were characterized by proteomic analysis. Key enzymes, e.g., flavoprotein, ferredoxin, formate-tetrahydrofolate ligase, 5-methyltetrahydrofolate:corrinoid iron-sulfur protein methyltransferase, thioredoxin, and rubrerythrin, were found up-regulated in the biohybrid system. The findings are helpful in understanding the mechanism of the artificial photosynthesis and useful for the development of new biohybrid systems using genetically engineered microbes in the future. The study is expected to boost the development of bioabiotic hybrid system in solar energy harvest.
Collapse
Affiliation(s)
- Ying He
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
| | - Shurong Wang
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
| | - Xinyue Han
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
| | - Jiayuan Shen
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
| | - Yanwei Lu
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
| | - Jinzhi Zhao
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
| | - Chengpin Shen
- Shanghai Omicsolution Co., Ltd., Shanghai 200000, China
| | - Liang Qiao
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
| |
Collapse
|
48
|
Trischler R, Roth J, Sorbara MT, Schlegel X, Müller V. A functional Wood-Ljungdahl pathway devoid of a formate dehydrogenase in the gut acetogens Blautia wexlerae, Blautia luti and beyond. Environ Microbiol 2022; 24:3111-3123. [PMID: 35466558 DOI: 10.1111/1462-2920.16029] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/14/2022] [Accepted: 04/22/2022] [Indexed: 11/30/2022]
Abstract
Species of the genus Blautia are typical inhabitants of the human gut and considered as beneficial gut microbes. However, their role in the gut microbiome and their metabolic features are poorly understood. Blautia schinkii was described as an acetogenic bacterium, characterized by a functional Wood-Ljungdahl pathway (WLP) of acetogenesis from H2 + CO2 . Here we report that two relatives, Blautia luti and Blautia wexlerae do not grow on H2 + CO2 . Inspection of the genome sequence revealed all genes of the WLP except genes encoding a formate dehydrogenase and an electron-bifurcating hydrogenase. Enzyme assays confirmed this prediction. Accordingly, resting cells neither converted H2 + CO2 nor H2 + HCOOH + CO2 to acetate. Carbon monoxide is an intermediate of the WLP and substrate for many acetogens. B. luti and B. wexlerae had an active CO dehydrogenase and resting cells performed acetogenesis from HCOOH + CO2 + CO, demonstrating a functional WLP. Bioinformatic analyses revealed that many Blautia strains as well as other gut acetogens lack formate dehydrogenases and hydrogenases. Thus, the use of formate instead of H2 + CO2 as an interspecies hydrogen and electron carrier seems to be more common in the gut microbiome. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Raphael Trischler
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Jennifer Roth
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Matthew T Sorbara
- Department Molecular and Cellular Biology, University of Guelph, Ontario, N1G 2W1, Canada
| | - Xenia Schlegel
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| |
Collapse
|
49
|
Marcel M, Darina E, Patrick K, Aline H, Gabriele P, Stefan J, Jochen B. Impact of different trace elements on metabolic routes during heterotrophic growth of C. ljungdahlii investigated through online measurement of the carbon dioxide transfer rate. Biotechnol Prog 2022; 38:e3263. [PMID: 35434968 DOI: 10.1002/btpr.3263] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/30/2022] [Accepted: 04/15/2022] [Indexed: 11/09/2022]
Abstract
Synthesis gas fermentation using acetogenic clostridia is a rapidly increasing research area. It offers the possibility to produce platform chemicals from sustainable C1 carbon sources. The Wood-Ljungdahl pathway (WLP), which allows acetogens to grow autotrophically, is also active during heterotrophic growth. It acts as an electron sink and allows for the utilization of a wide variety of soluble substrates and increases ATP yields during heterotrophic growth. While glycolysis leads to CO2 evolution, WLP activity results in CO2 fixation. Thus, a reduction of net CO2 emissions during growth with sugars is an indicator of WLP activity. To study the effect of trace elements and ventilation rates on the interaction between glycolysis and the WLP, the model acetogen Clostridium ljungdahlii was cultivated in YTF medium, a complex medium generally employed for heterotrophic growth, with fructose as growth substrate. The recently reported anaRAMOS device was used for online measurement of metabolic activity, in form of CO2 evolution. The addition of multiple trace elements (iron, cobalt, manganese, zinc, nickel, copper, selenium, and tungsten) was tested, to study the interaction between glycolysis and the Wood ljungdahl pathway. While the addition of iron(II) increased growth rates and ethanol production, added nickel(II) increased WLP activity and acetate formation, reducing net CO2 production by 28%. Also, higher CO2 availability through reduced volumetric gas flow resulted in 25% reduction of CO2 evolution. These online metabolic data demonstrate that the anaRAMOS is a valuable tool in the investigation of metabolic responses i.e. to determine nutrient requirements that results in reduced CO2 production. Thereby the media composition can be optimized depending on the specific goal. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Mann Marcel
- RWTH Aachen University, AVT - Biochemical Engineering, Aachen, Germany
| | - Effert Darina
- RWTH Aachen University, AVT - Biochemical Engineering, Aachen, Germany
| | - Kottenhahn Patrick
- RWTH Aachen University, AVT - Biochemical Engineering, Aachen, Germany.,Department for Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, Aachen, Germany
| | - Hüser Aline
- RWTH Aachen University, AVT - Biochemical Engineering, Aachen, Germany
| | - Philipps Gabriele
- Department for Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, Aachen, Germany
| | - Jennewein Stefan
- Department for Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, Aachen, Germany
| | - Büchs Jochen
- RWTH Aachen University, AVT - Biochemical Engineering, Aachen, Germany
| |
Collapse
|
50
|
Abstract
Microbes that can recycle one-carbon (C1) greenhouse gases into fuels and chemicals are vital for the biosustainability of future industries. Acetogens are the most efficient known microbes for fixing carbon oxides CO2 and CO. Understanding proteome allocation is important for metabolic engineering as it dictates metabolic fitness. Here, we use absolute proteomics to quantify intracellular concentrations for >1,000 proteins in the model acetogen Clostridium autoethanogenum grown autotrophically on three gas mixtures (CO, CO+H2, or CO+CO2+H2). We detect the prioritization of proteome allocation for C1 fixation and the significant expression of proteins involved in the production of acetate and ethanol as well as proteins with unclear functions. The data also revealed which isoenzymes are likely relevant in vivo for CO oxidation, H2 metabolism, and ethanol production. The integration of proteomic and metabolic flux data demonstrated that enzymes catalyze high fluxes with high concentrations and high in vivo catalytic rates. We show that flux adjustments were dominantly accompanied by changing enzyme catalytic rates rather than concentrations. IMPORTANCE Acetogen bacteria are important for maintaining biosustainability as they can recycle gaseous C1 waste feedstocks (e.g., industrial waste gases and syngas from gasified biomass or municipal solid waste) into fuels and chemicals. Notably, the acetogen Clostridium autoethanogenum is being used as a cell factory in industrial-scale gas fermentation. Here, we perform reliable absolute proteome quantification for the first time in an acetogen. This is important as our work advances both rational metabolic engineering of acetogen cell factories and accurate in silico reconstruction of their phenotypes. Furthermore, this absolute proteomics data set serves as a reference toward a better systems-level understanding of the ancient metabolism of acetogens.
Collapse
|