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Rao A, Driessen AJM. Unraveling the multiplicity of geranylgeranyl reductases in Archaea: potential roles in saturation of terpenoids. Extremophiles 2024; 28:14. [PMID: 38280122 PMCID: PMC10821996 DOI: 10.1007/s00792-023-01330-2] [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: 07/17/2023] [Accepted: 12/15/2023] [Indexed: 01/29/2024]
Abstract
The enzymology of the key steps in the archaeal phospholipid biosynthetic pathway has been elucidated in recent years. In contrast, the complete biosynthetic pathways for proposed membrane regulators consisting of polyterpenes, such as carotenoids, respiratory quinones, and polyprenols remain unknown. Notably, the multiplicity of geranylgeranyl reductases (GGRs) in archaeal genomes has been correlated with the saturation of polyterpenes. Although GGRs, which are responsible for saturation of the isoprene chains of phospholipids, have been identified and studied in detail, there is little information regarding the structure and function of the paralogs. Here, we discuss the diversity of archaeal membrane-associated polyterpenes which is correlated with the genomic loci, structural and sequence-based analyses of GGR paralogs.
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Affiliation(s)
- Alka Rao
- Department of Molecular Microbiology, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands.
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2
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Lipidomics and Comparative Metabolite Excretion Analysis of Methanogenic Archaea Reveal Organism-Specific Adaptations to Varying Temperatures and Substrate Concentrations. mSystems 2023; 8:e0115922. [PMID: 36880756 PMCID: PMC10134847 DOI: 10.1128/msystems.01159-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Methanogenic archaea possess diverse metabolic characteristics and are an ecologically and biotechnologically important group of anaerobic microorganisms. Although the scientific and biotechnological value of methanogens is evident with regard to their methane-producing physiology, little is known about their amino acid excretion, and virtually nothing is known about the lipidome at different substrate concentrations and temperatures on a quantitative comparative basis. Here, we present the lipidome and a comprehensive quantitative analysis of proteinogenic amino acid excretion as well as methane, water, and biomass production of the three autotrophic, hydrogenotrophic methanogens Methanothermobacter marburgensis, Methanothermococcus okinawensis, and Methanocaldococcus villosus under varying temperatures and nutrient supplies. The patterns and rates of production of excreted amino acids and the lipidome are unique for each tested methanogen and can be modulated by varying the incubation temperature and substrate concentration, respectively. Furthermore, the temperature had a significant influence on the lipidomes of the different archaea. The water production rate was much higher, as anticipated from the rate of methane production for all studied methanogens. Our results demonstrate the need for quantitative comparative physiological studies connecting intracellular and extracellular constraints of organisms to holistically investigate microbial responses to environmental conditions. IMPORTANCE Biological methane production by methanogenic archaea has been well studied for biotechnological purposes. This study reveals that methanogenic archaea actively modulate their lipid inventory and proteinogenic amino acid excretion pattern in response to environmental changes and the possible utilization of methanogenic archaea as microbial cell factories for the targeted production of lipids and amino acids.
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Baumann LMF, Taubner RS, Oláh K, Rohrweber AC, Schuster B, Birgel D, Rittmann SKMR. Quantitative Analysis of Core Lipid Production in Methanothermobacter marburgensis at Different Scales. Bioengineering (Basel) 2022; 9:169. [PMID: 35447729 PMCID: PMC9027985 DOI: 10.3390/bioengineering9040169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/06/2022] [Indexed: 11/17/2022] Open
Abstract
Archaeal lipids have a high biotechnological potential, caused by their high resistance to oxidative stress, extreme pH values and temperatures, as well as their ability to withstand phospholipases. Further, methanogens, a specific group of archaea, are already well-established in the field of biotechnology because of their ability to use carbon dioxide and molecular hydrogen or organic substrates. In this study, we show the potential of the model organism Methanothermobacter marburgensis to act both as a carbon dioxide based biological methane producer and as a potential supplier of archaeal lipids. Different cultivation settings were tested to gain an insight into the optimal conditions to produce specific core lipids. The study shows that up-scaling at a constant particle number (n/n = const.) seems to be a promising approach. Further optimizations regarding the length and number of the incubation periods and the ratio of the interaction area to the total liquid volume are necessary for scaling these settings for industrial purposes.
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Affiliation(s)
- Lydia M. F. Baumann
- Institute for Geology, Center for Earth System Research and Sustainability, Universität Hamburg, Bundesstraße 55, 20146 Hamburg, Germany; (L.M.F.B.); (A.-C.R.); (D.B.)
| | - Ruth-Sophie Taubner
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Djerassiplatz 1, 1030 Wien, Austria;
- Institute for Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria; (K.O.); (B.S.)
- Institute for Chemical Technology of Organic Materials, Johannes Kepler Universität Linz, Altenbergerstraße 69, 4040 Linz, Austria
| | - Kinga Oláh
- Institute for Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria; (K.O.); (B.S.)
| | - Ann-Cathrin Rohrweber
- Institute for Geology, Center for Earth System Research and Sustainability, Universität Hamburg, Bundesstraße 55, 20146 Hamburg, Germany; (L.M.F.B.); (A.-C.R.); (D.B.)
| | - Bernhard Schuster
- Institute for Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria; (K.O.); (B.S.)
| | - Daniel Birgel
- Institute for Geology, Center for Earth System Research and Sustainability, Universität Hamburg, Bundesstraße 55, 20146 Hamburg, Germany; (L.M.F.B.); (A.-C.R.); (D.B.)
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Djerassiplatz 1, 1030 Wien, Austria;
- Arkeon GmbH, Technopark 1, 3430 Tulln an der Donau, Austria
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Haloarchaea as emerging big players in future polyhydroxyalkanoate bioproduction: Review of trends and perspectives. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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5
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Mauerhofer LM, Zwirtmayr S, Pappenreiter P, Bernacchi S, Seifert AH, Reischl B, Schmider T, Taubner RS, Paulik C, Rittmann SKMR. Hyperthermophilic methanogenic archaea act as high-pressure CH 4 cell factories. Commun Biol 2021; 4:289. [PMID: 33674723 PMCID: PMC7935968 DOI: 10.1038/s42003-021-01828-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 02/10/2021] [Indexed: 01/31/2023] Open
Abstract
Bioprocesses converting carbon dioxide with molecular hydrogen to methane (CH4) are currently being developed to enable a transition to a renewable energy production system. In this study, we present a comprehensive physiological and biotechnological examination of 80 methanogenic archaea (methanogens) quantifying growth and CH4 production kinetics at hyperbaric pressures up to 50 bar with regard to media, macro-, and micro-nutrient supply, specific genomic features, and cell envelope architecture. Our analysis aimed to systematically prioritize high-pressure and high-performance methanogens. We found that the hyperthermophilic methanococci Methanotorris igneus and Methanocaldococcoccus jannaschii are high-pressure CH4 cell factories. Furthermore, our analysis revealed that high-performance methanogens are covered with an S-layer, and that they harbour the amino acid motif Tyrα444 Glyα445 Tyrα446 in the alpha subunit of the methyl-coenzyme M reductase. Thus, high-pressure biological CH4 production in pure culture could provide a purposeful route for the transition to a carbon-neutral bioenergy sector.
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Affiliation(s)
- Lisa-Maria Mauerhofer
- grid.10420.370000 0001 2286 1424Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria
| | - Sara Zwirtmayr
- grid.9970.70000 0001 1941 5140Institute for Chemical Technology of Organic Materials, Johannes Kepler Universität Linz, Linz, Austria
| | - Patricia Pappenreiter
- grid.9970.70000 0001 1941 5140Institute for Chemical Technology of Organic Materials, Johannes Kepler Universität Linz, Linz, Austria
| | | | | | - Barbara Reischl
- grid.10420.370000 0001 2286 1424Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria ,Krajete GmbH, Linz, Austria
| | - Tilman Schmider
- grid.10420.370000 0001 2286 1424Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria
| | - Ruth-Sophie Taubner
- grid.10420.370000 0001 2286 1424Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria ,grid.9970.70000 0001 1941 5140Institute for Chemical Technology of Organic Materials, Johannes Kepler Universität Linz, Linz, Austria
| | - Christian Paulik
- grid.9970.70000 0001 1941 5140Institute for Chemical Technology of Organic Materials, Johannes Kepler Universität Linz, Linz, Austria
| | - Simon K.-M. R. Rittmann
- grid.10420.370000 0001 2286 1424Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria
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Pfeifer K, Ergal İ, Koller M, Basen M, Schuster B, Rittmann SKMR. Archaea Biotechnology. Biotechnol Adv 2020; 47:107668. [PMID: 33271237 DOI: 10.1016/j.biotechadv.2020.107668] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 12/13/2022]
Abstract
Archaea are a domain of prokaryotic organisms with intriguing physiological characteristics and ecological importance. In Microbial Biotechnology, archaea are historically overshadowed by bacteria and eukaryotes in terms of public awareness, industrial application, and scientific studies, although their biochemical and physiological properties show a vast potential for a wide range of biotechnological applications. Today, the majority of microbial cell factories utilized for the production of value-added and high value compounds on an industrial scale are bacterial, fungal or algae based. Nevertheless, archaea are becoming ever more relevant for biotechnology as their cultivation and genetic systems improve. Some of the main advantages of archaeal cell factories are the ability to cultivate many of these often extremophilic organisms under non-sterile conditions, and to utilize inexpensive feedstocks often toxic to other microorganisms, thus drastically reducing cultivation costs. Currently, the only commercially available products of archaeal cell factories are bacterioruberin, squalene, bacteriorhodopsin and diether-/tetraether-lipids, all of which are produced utilizing halophiles. Other archaeal products, such as carotenoids and biohydrogen, as well as polyhydroxyalkanoates and methane are in early to advanced development stages, respectively. The aim of this review is to provide an overview of the current state of Archaea Biotechnology by describing the actual state of research and development as well as the industrial utilization of archaeal cell factories, their role and their potential in the future of sustainable bioprocessing, and to illustrate their physiological and biotechnological potential.
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Affiliation(s)
- Kevin Pfeifer
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Wien, Austria; Institute of Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Wien, Austria
| | - İpek Ergal
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Wien, Austria
| | - Martin Koller
- Office of Research Management and Service, c/o Institute of Chemistry, University of Graz, Austria
| | - Mirko Basen
- Microbial Physiology Group, Division of Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Bernhard Schuster
- Institute of Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Wien, Austria
| | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Wien, Austria.
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Bywaters K, Stoker CR, Batista Do Nascimento N, Lemke L. Towards Determining Biosignature Retention in Icy World Plumes. Life (Basel) 2020; 10:life10040040. [PMID: 32316157 PMCID: PMC7235855 DOI: 10.3390/life10040040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/11/2020] [Accepted: 04/14/2020] [Indexed: 02/07/2023] Open
Abstract
With the discovery of the persistent jets of water being ejected to space from Enceladus, an understanding of the effect of the space environment on potential organisms and biosignatures in them is necessary for planning life detection missions. We experimentally determine the survivability of microbial cells in liquid medium when ejected into vacuum. Epifluorescence microscopy, using a lipid stain, and SEM imaging were used to interrogate the cellular integrity of E. coli after ejected through a pressurized nozzle into a vacuum chamber. The experimental samples showed a 94% decrease in visible intact E. coli cells but showed a fluorescence residue in the shape of the sublimated droplets that indicated the presence of lipids. The differences in the experimental conditions versus those expected on Enceladus should not change the analog value because the process a sample would undergo when ejected into space was representative. E. coli was selected for testing although other cell types could vary physiologically which would affect their response to a vacuum environment. More testing is needed to determine the dynamic range in concentration of cells expected to survive the plume environment. However, these results suggest that lipids may be directly detectable evidence of life in icy world plumes.
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Affiliation(s)
- Kathryn Bywaters
- SETI Institute, Moffett Field, CA 94043, USA
- Correspondence: (K.B.); (C.R.S.); Tel.: +1-650-604-2295 (K.B.); +1-650-604-6490 (C.R.S.)
| | - Carol R. Stoker
- NASA Ames Research Center, Space Science Division, Moffett Field, CA 94035, USA; (N.B.D.N.J.); (L.L.)
- Correspondence: (K.B.); (C.R.S.); Tel.: +1-650-604-2295 (K.B.); +1-650-604-6490 (C.R.S.)
| | | | - Lawrence Lemke
- NASA Ames Research Center, Space Science Division, Moffett Field, CA 94035, USA; (N.B.D.N.J.); (L.L.)
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Taubner RS, Olsson-Francis K, Vance SD, Ramkissoon NK, Postberg F, de Vera JP, Antunes A, Camprubi Casas E, Sekine Y, Noack L, Barge L, Goodman J, Jebbar M, Journaux B, Karatekin Ö, Klenner F, Rabbow E, Rettberg P, Rückriemen-Bez T, Saur J, Shibuya T, Soderlund KM. Experimental and Simulation Efforts in the Astrobiological Exploration of Exooceans. SPACE SCIENCE REVIEWS 2020; 216:9. [PMID: 32025060 PMCID: PMC6977147 DOI: 10.1007/s11214-020-0635-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/06/2020] [Indexed: 05/05/2023]
Abstract
The icy satellites of Jupiter and Saturn are perhaps the most promising places in the Solar System regarding habitability. However, the potential habitable environments are hidden underneath km-thick ice shells. The discovery of Enceladus' plume by the Cassini mission has provided vital clues in our understanding of the processes occurring within the interior of exooceans. To interpret these data and to help configure instruments for future missions, controlled laboratory experiments and simulations are needed. This review aims to bring together studies and experimental designs from various scientific fields currently investigating the icy moons, including planetary sciences, chemistry, (micro-)biology, geology, glaciology, etc. This chapter provides an overview of successful in situ, in silico, and in vitro experiments, which explore different regions of interest on icy moons, i.e. a potential plume, surface, icy shell, water and brines, hydrothermal vents, and the rocky core.
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Affiliation(s)
- Ruth-Sophie Taubner
- Archaea Biology and Ecogenomics Division, University of Vienna, Vienna, Austria
| | | | | | | | | | | | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Macau SAR, China
| | | | | | - Lena Noack
- Freie Universität Berlin, Berlin, Germany
| | | | | | | | | | | | | | - Elke Rabbow
- German Aerospace Center (DLR), Cologne, Germany
| | | | | | | | - Takazo Shibuya
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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