1
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Sedlmayr VL, Luger M, Pittenauer E, Marchetti-Deschmann M, Kronlachner L, Limbeck A, Raunjak P, Quehenberger J, Spadiut O. Development of a defined medium for the heterotrophic cultivation of Metallosphaera sedula. Extremophiles 2024; 28:36. [PMID: 39060419 PMCID: PMC11282131 DOI: 10.1007/s00792-024-01348-0] [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: 03/25/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024]
Abstract
The heterotrophic cultivation of extremophilic archaea still heavily relies on complex media. However, complex media are associated with unknown composition, high batch-to-batch variability, potential inhibiting and interfering components, as well as regulatory challenges, hampering advancements of extremophilic archaea in genetic engineering and bioprocessing. For Metallosphaera sedula, a widely studied organism for biomining and bioremediation and a potential production host for archaeal ether lipids, efforts to find defined cultivation conditions have still been unsuccessful. This study describes the development of a novel chemically defined growth medium for M. sedula. Initial experiments with commonly used complex casein-derived media sources deciphered Casamino Acids as the most suitable foundation for further development. The imitation of the amino acid composition of Casamino Acids in basal Brock medium delivered the first chemically defined medium. We could further simplify the medium to 5 amino acids based on the respective specific substrate uptake rates. This first defined cultivation medium for M. sedula allows advanced genetic engineering and more controlled bioprocess development approaches for this highly interesting archaeon.
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Affiliation(s)
- Viktor Laurin Sedlmayr
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, 1060, Vienna, Austria
| | - Maximilian Luger
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, 1060, Vienna, Austria
| | - Ernst Pittenauer
- TU Wien, Institute of Chemical Technologies and Analytics, 1060, Vienna, Austria
| | | | - Laura Kronlachner
- TU Wien, Institute of Chemical Technologies and Analytics, 1060, Vienna, Austria
| | - Andreas Limbeck
- TU Wien, Institute of Chemical Technologies and Analytics, 1060, Vienna, Austria
| | - Philipp Raunjak
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, 1060, Vienna, Austria
| | - Julian Quehenberger
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, 1060, Vienna, Austria
| | - Oliver Spadiut
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, 1060, Vienna, Austria.
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2
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Zhong W, Li H, Wang Y. Design and Construction of Artificial Biological Systems for One-Carbon Utilization. BIODESIGN RESEARCH 2023; 5:0021. [PMID: 37915992 PMCID: PMC10616972 DOI: 10.34133/bdr.0021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/05/2023] [Indexed: 11/03/2023] Open
Abstract
The third-generation (3G) biorefinery aims to use microbial cell factories or enzymatic systems to synthesize value-added chemicals from one-carbon (C1) sources, such as CO2, formate, and methanol, fueled by renewable energies like light and electricity. This promising technology represents an important step toward sustainable development, which can help address some of the most pressing environmental challenges faced by modern society. However, to establish processes competitive with the petroleum industry, it is crucial to determine the most viable pathways for C1 utilization and productivity and yield of the target products. In this review, we discuss the progresses that have been made in constructing artificial biological systems for 3G biorefineries in the last 10 years. Specifically, we highlight the representative works on the engineering of artificial autotrophic microorganisms, tandem enzymatic systems, and chemo-bio hybrid systems for C1 utilization. We also prospect the revolutionary impact of these developments on biotechnology. By harnessing the power of 3G biorefinery, scientists are establishing a new frontier that could potentially revolutionize our approach to industrial production and pave the way for a more sustainable future.
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Affiliation(s)
- Wei Zhong
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering,
Westlake University, Hangzhou 310000, PR China
| | - Hailong Li
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering,
Westlake University, Hangzhou 310000, PR China
- School of Materials Science and Engineering,
Zhejiang University, Zhejiang Province, Hangzhou 310000, PR China
| | - Yajie Wang
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering,
Westlake University, Hangzhou 310000, PR China
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3
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Leles SG, Levine NM. Mechanistic constraints on the trade-off between photosynthesis and respiration in response to warming. SCIENCE ADVANCES 2023; 9:eadh8043. [PMID: 37656790 PMCID: PMC10796116 DOI: 10.1126/sciadv.adh8043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
Abstract
Phytoplankton are responsible for half of all oxygen production and drive the ocean carbon cycle. Metabolic theory predicts that increasing global temperatures will cause phytoplankton to become more heterotrophic and smaller. Here, we uncover the metabolic trade-offs between cellular space, energy, and stress management driving phytoplankton thermal acclimation and how these might be overcome through evolutionary adaptation. We show that the observed relationships between traits such as chlorophyll, lipid content, C:N, and size can be predicted on the basis of the metabolic demands of the cell, the thermal dependency of transporters, and changes in membrane lipids. We suggest that many of the observed relationships are not fixed physiological constraints but rather can be altered through adaptation. For example, the evolution of lipid metabolism can favor larger cells with higher lipid content to mitigate oxidative stress. These results have implications for rates of carbon sequestration and export in a warmer ocean.
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Affiliation(s)
- Suzana G. Leles
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, USA
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4
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Xu J, Wang J, Ma C, Wei Z, Zhai Y, Tian N, Zhu Z, Xue M, Li D. Embracing a low-carbon future by the production and marketing of C1 gas protein. Biotechnol Adv 2023; 63:108096. [PMID: 36621726 DOI: 10.1016/j.biotechadv.2023.108096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/14/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
Food scarcity and environmental deterioration are two major problems that human populations currently face. Fortunately, the disruptive innovation of raw food materials has been stimulated by the rapid evolution of biomanufacturing. Therefore, it is expected that the new trends in technology will not only alter the natural resource-dependent food production systems and the traditional way of life but also reduce and assimilate the greenhouse gases released into the atmosphere. This review article summarizes the metabolic pathways associated with C1 gas conversion and the production of single-cell protein for animal feed. Moreover, the protein function, worldwide authorization, market access, and methods to overcome challenges in C1 gas assimilation microbial cell factory construction are also provided. With widespread attention and increasing policy support, the production of C1 gas protein will bring more opportunities and make tremendous contributions to our sustainable future.
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Affiliation(s)
- Jian Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Jie Wang
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunling Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Haihe Laboratory of Synthetic Biology, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Zuoxi Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Yida Zhai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Na Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China.
| | - Min Xue
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Demao Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China.
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5
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Liu L, Schubert DM, Könneke M, Berg IA. ( S)-3-Hydroxybutyryl-CoA Dehydrogenase From the Autotrophic 3-Hydroxypropionate/4-Hydroxybutyrate Cycle in Nitrosopumilus maritimus. Front Microbiol 2021; 12:712030. [PMID: 34290692 PMCID: PMC8287830 DOI: 10.3389/fmicb.2021.712030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/11/2021] [Indexed: 11/18/2022] Open
Abstract
Ammonia-oxidizing archaea of the phylum Thaumarchaeota are among the most abundant organisms that exert primary control of oceanic and soil nitrification and are responsible for a large part of dark ocean primary production. They assimilate inorganic carbon via an energetically efficient version of the 3-hydroxypropionate/4-hydroxybutyrate cycle. In this cycle, acetyl-CoA is carboxylated to succinyl-CoA, which is then converted to two acetyl-CoA molecules with 4-hydroxybutyrate as the key intermediate. This conversion includes the (S)-3-hydroxybutyryl-CoA dehydrogenase reaction. Here, we heterologously produced the protein Nmar_1028 catalyzing this reaction in thaumarchaeon Nitrosopumilus maritimus, characterized it biochemically and performed its phylogenetic analysis. This NAD-dependent dehydrogenase is highly active with its substrate, (S)-3-hydroxybutyryl-CoA, and its low Km value suggests that the protein is adapted to the functioning in the 3-hydroxypropionate/4-hydroxybutyrate cycle. Nmar_1028 is homologous to the dehydrogenase domain of crotonyl-CoA hydratase/(S)-3-hydroxybutyryl-CoA dehydrogenase that is present in many Archaea. Apparently, the loss of the dehydratase domain of the fusion protein in the course of evolution was accompanied by lateral gene transfer of 3-hydroxypropionyl-CoA dehydratase/crotonyl-CoA hydratase from Bacteria. Although (S)-3-hydroxybutyryl-CoA dehydrogenase studied here is neither unique nor characteristic for the HP/HB cycle, Nmar_1028 appears to be the only (S)-3-hydroxybutyryl-CoA dehydrogenase in N. maritimus and is thus essential for the functioning of the 3-hydroxypropionate/4-hydroxybutyrate cycle and for the biology of this important marine archaeon.
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Affiliation(s)
- Li Liu
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Daniel M Schubert
- Department of Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Martin Könneke
- Marine Archaea Group, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Benthic Microbiology, Institute for Chemistry and Biology of the Marine Environments, University of Oldenburg, Oldenburg, Germany
| | - Ivan A Berg
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
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6
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Convergent Evolution of a Promiscuous 3-Hydroxypropionyl-CoA Dehydratase/Crotonyl-CoA Hydratase in Crenarchaeota and Thaumarchaeota. mSphere 2021; 6:6/1/e01079-20. [PMID: 33472982 PMCID: PMC7845616 DOI: 10.1128/msphere.01079-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Inorganic carbon fixation is the most important biosynthetic process on Earth and the oldest type of metabolism. The autotrophic HP/HB cycle functions in Crenarchaea of the order Sulfolobales and in ammonia-oxidizing Archaea of the phylum Thaumarchaeota that are highly abundant in marine, terrestrial, and geothermal environments. The autotrophic 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) cycle functions in thermoacidophilic, (micro)aerobic, hydrogen-oxidizing Crenarchaeota of the order Sulfolobales as well as in mesophilic, aerobic, ammonia-oxidizing Thaumarchaeota. Notably, the HP/HB cycle evolved independently in these two archaeal lineages, and crenarchaeal and thaumarchaeal versions differ regarding their enzyme properties and phylogeny. These differences result in altered energetic efficiencies between the variants. Compared to the crenarchaeal HP/HB cycle, the thaumarchaeal variant saves two ATP equivalents per turn, rendering it the most energy-efficient aerobic pathway for carbon fixation. Characteristically, the HP/HB cycle includes two enoyl coenzyme A (CoA) hydratase reactions: the 3-hydroxypropionyl-CoA dehydratase reaction and the crotonyl-CoA hydratase reaction. In this study, we show that both reactions are catalyzed in the aforementioned archaeal groups by a promiscuous 3-hydroxypropionyl-CoA dehydratase/crotonyl-CoA hydratase (Msed_2001 in crenarchaeon Metallosphaera sedula and Nmar_1308 in thaumarchaeon Nitrosopumilus maritimus). Although these two enzymes are homologous, they are closely related to bacterial enoyl-CoA hydratases and were retrieved independently from the same enzyme pool by the ancestors of Crenarchaeota and Thaumarchaeota, despite the existence of multiple alternatives. This striking similarity in the emergence of enzymes involved in inorganic carbon fixation from two independently evolved pathways highlights that convergent evolution of autotrophy could be much more widespread than anticipated. IMPORTANCE Inorganic carbon fixation is the most important biosynthetic process on Earth and the oldest type of metabolism. The autotrophic HP/HB cycle functions in Crenarchaeota of the order Sulfolobales and in ammonia-oxidizing Archaea of the phylum Thaumarchaeota that are highly abundant in marine, terrestrial, and geothermal environments. Bioinformatic prediction of the autotrophic potential of microorganisms or microbial communities requires identification of enzymes involved in autotrophy. However, many microorganisms possess several isoenzymes that may potentially catalyze the reactions of the cycle. Here, we studied the enzymes catalyzing 3-hydroxypropionyl-CoA dehydration and crotonyl-CoA hydration in Nitrosopumilus maritimus (Thaumarchaeota) as well as in Metallosphaera sedula (Crenarchaeota). We showed that both reactions were catalyzed by homologous promiscuous enzymes, which evolved independently from each other from their bacterial homologs. Furthermore, the HP/HB cycle is of applied value, and knowledge of its enzymes is necessary to transfer them to a heterologous host for synthesis of various value-added products.
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7
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Liu Z, Wang K, Chen Y, Tan T, Nielsen J. Third-generation biorefineries as the means to produce fuels and chemicals from CO2. Nat Catal 2020. [DOI: 10.1038/s41929-019-0421-5] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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8
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Liu L, Huber H, Berg IA. Enzymes Catalyzing Crotonyl-CoA Conversion to Acetoacetyl-CoA During the Autotrophic CO 2 Fixation in Metallosphaera sedula. Front Microbiol 2020; 11:354. [PMID: 32218776 PMCID: PMC7078158 DOI: 10.3389/fmicb.2020.00354] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/18/2020] [Indexed: 12/13/2022] Open
Abstract
Autotrophic Crenarchaeota use two different cycles for carbon dioxide fixation. Members of the Sulfolobales use the 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) cycle, whereas Desulfurococcales and Thermoproteales use the dicarboxylate/4-hydroxybutyrate cycle. While these two cycles differ in the carboxylation reactions resulting in the conversion of acetyl-CoA + 2 CO2 to succinyl-CoA, they have a common regeneration part in which succinyl-CoA is reconverted to two acetyl-CoA molecules. This common part includes crotonyl-CoA conversion to acetoacetyl-CoA, which has unequivocally been shown in Ignicoccus hospitalis (Desulfurococcales) and Pyrobaculum neutrophilus (Thermoproteales) to be catalyzed by a bifunctional crotonase/3-hydroxybutyryl-CoA dehydrogenase. It is a fusion protein consisting of an enoyl-CoA hydratase and a dehydrogenase domain. As the homologous bifunctional protein is present in Sulfolobales as well, its common functioning in the conversion of crotonyl-CoA to acetoacetyl-CoA was proposed. Here we show that a model autotrophic member of Sulfolobales, Metallosphaera sedula, possesses in addition to the bifunctional protein (Msed_0399) several separate genes coding for crotonyl-CoA hydratase and (S)-3-hydroxybutyryl-CoA dehydrogenase. Their genes were previously shown to be transcribed under autotrophic and mixotrophic conditions. The dehydrogenase Msed_1423 (and not the bifunctional protein Msed_0399) appears to be the main enzyme catalyzing the (S)-3-hydroxybutyryl-CoA dehydrogenase reaction. Homologs of this dehydrogenase are the only (S)-3-hydroxybutyryl-CoA dehydrogenases present in all autotrophic Sulfolobales, strengthening this conclusion. Two uncharacterized crotonase homologs present in M. sedula genome (Msed_0336 and Msed_0384) were heterologously produced and characterized. Both proteins were highly efficient crotonyl-CoA hydratases and may contribute (or be responsible) for the corresponding reaction in the HP/HB cycle in vivo.
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Affiliation(s)
- Li Liu
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Harald Huber
- Institute for Microbiology and Archaeal Center, University of Regensburg, Regensburg, Germany
| | - Ivan A Berg
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
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9
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Lelièvre CM, Balandras M, Petit J, Vergne‐Vaxelaire C, Zaparucha A. ATP Regeneration System in Chemoenzymatic Amide Bond Formation with Thermophilic CoA Ligase. ChemCatChem 2020. [DOI: 10.1002/cctc.201901870] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Chloé M. Lelièvre
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 2 rue Gaston Crémieux 91057 Evry France
| | - Mélanie Balandras
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 2 rue Gaston Crémieux 91057 Evry France
| | - Jean‐Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 2 rue Gaston Crémieux 91057 Evry France
| | - Carine Vergne‐Vaxelaire
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 2 rue Gaston Crémieux 91057 Evry France
| | - Anne Zaparucha
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 2 rue Gaston Crémieux 91057 Evry France
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10
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Hackley RK, Schmid AK. Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response. J Mol Biol 2019; 431:4147-4166. [PMID: 31437442 PMCID: PMC7419163 DOI: 10.1016/j.jmb.2019.07.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 01/06/2023]
Abstract
The environmental stress response (ESR), a global transcriptional program originally identified in yeast, is characterized by a rapid and transient transcriptional response composed of large, oppositely regulated gene clusters. Genes induced during the ESR encode core components of stress tolerance, macromolecular repair, and maintenance of homeostasis. In this review, we investigate the possibility for conservation of the ESR across the eukaryotic and archaeal domains of life. We first re-analyze existing transcriptomics data sets to illustrate that a similar transcriptional response is identifiable in Halobacterium salinarum, an archaeal model organism. To substantiate the archaeal ESR, we calculated gene-by-gene correlations, gene function enrichment, and comparison of temporal dynamics. We note reported examples of variation in the ESR across fungi, then synthesize high-level trends present in expression data of other archaeal species. In particular, we emphasize the need for additional high-throughput time series expression data to further characterize stress-responsive transcriptional programs in the Archaea. Together, this review explores an open question regarding features of global transcriptional stress response programs shared across domains of life.
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Affiliation(s)
- Rylee K Hackley
- Department of Biology, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
| | - Amy K Schmid
- Department of Biology, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA.
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11
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Zeldes BM, Loder AJ, Counts JA, Haque M, Widney KA, Keller LM, Albers S, Kelly RM. Determinants of sulphur chemolithoautotrophy in the extremely thermoacidophilicSulfolobales. Environ Microbiol 2019; 21:3696-3710. [DOI: 10.1111/1462-2920.14712] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/04/2019] [Accepted: 06/09/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin M. Zeldes
- Department of Chemical and Biomolecular EngineeringNorth Carolina State University Raleigh NC 27695‐7905 USA
| | - Andrew J. Loder
- Department of Chemical and Biomolecular EngineeringNorth Carolina State University Raleigh NC 27695‐7905 USA
| | - James A. Counts
- Department of Chemical and Biomolecular EngineeringNorth Carolina State University Raleigh NC 27695‐7905 USA
| | - Mashkurul Haque
- Department of Chemical and Biomolecular EngineeringNorth Carolina State University Raleigh NC 27695‐7905 USA
| | - Karl A. Widney
- Department of Chemical and Biomolecular EngineeringNorth Carolina State University Raleigh NC 27695‐7905 USA
| | - Lisa M. Keller
- Department of Chemical and Biomolecular EngineeringNorth Carolina State University Raleigh NC 27695‐7905 USA
| | - Sonja‐Verena Albers
- Institute of Biology II – MicrobiologyUniversity of Freiburg Freiburg Germany
| | - Robert M. Kelly
- Department of Chemical and Biomolecular EngineeringNorth Carolina State University Raleigh NC 27695‐7905 USA
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12
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Lee SH, Son HF, Kim KJ. Structural insights into the inhibition properties of archaeon citrate synthase from Metallosphaera sedula. PLoS One 2019; 14:e0212807. [PMID: 30794680 PMCID: PMC6386500 DOI: 10.1371/journal.pone.0212807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/08/2019] [Indexed: 11/19/2022] Open
Abstract
Metallosphaera sedula is a thermoacidophilic archaeon and has an incomplete TCA/glyoxylate cycle that is used for production of biosynthetic precursors of essential metabolites. Citrate synthase from M. sedula (MsCS) is an enzyme involved in the first step of the incomplete TCA/glyoxylate cycle by converting oxaloacetate and acetyl-CoA into citrate and coenzyme A. To elucidate the inhibition properties of MsCS, we determined its crystal structure at 1.7 Å resolution. Like other Type-I CS, MsCS functions as a dimer and each monomer consists of two distinct domains, a large domain and a small domain. The oxaloacetate binding site locates at the cleft between the two domains, and the active site was more closed upon binding of the oxaloacetate substrate than binding of the citrate product. Interestingly, the inhibition kinetic analysis showed that, unlike other Type-I CSs, MsCS is non-competitively inhibited by NADH. Finally, amino acids and structural comparison of MsCS with other Type-II CSs, which were reported to be non-competitively inhibited by NADH, revealed that MsCS has quite unique NADH binding mode for non-competitive inhibition.
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Affiliation(s)
- Seul Hoo Lee
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, Republic of Korea
| | - Hyeoncheol Francis Son
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, Republic of Korea
- * E-mail:
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13
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Crystal structure and biochemical characterization of malate dehydrogenase from Metallosphaera sedula. Biochem Biophys Res Commun 2019; 509:833-838. [DOI: 10.1016/j.bbrc.2019.01.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 01/04/2019] [Indexed: 11/22/2022]
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14
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Lee SH, Kim KJ. Crystal structure and biochemical properties of msed_0281, the citrate synthase from Metallosphaera sedula. Biochem Biophys Res Commun 2019; 509:722-727. [PMID: 30611567 DOI: 10.1016/j.bbrc.2018.12.172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 12/27/2018] [Indexed: 11/25/2022]
Abstract
Metallosphaera sedula is a thermoacidophilic archaeon that has carbon fixation ability using the 3-hydroxypropionate/4-hydroxybutyrate(3-HP/4-HB) cycle, and has an incomplete TCA cycle to produce necessary biosynthetic precursors. The citrate synthase from M. sedula (MsCS) is an enzyme involved in the first step of the incomplete TCA cycle, catalyzing the conversion of oxaloacetate and acetyl-CoA into citrate and coenzyme A. To investigate the molecular mechanism of MsCS, we determined its crystal structure at 1.8 Å resolution. As other known CSs, MsCS functions as a dimer, and each monomer consists of two domains, a large domain and a small domain. We also determined the structure of the complex with acetyl-CoA and revealed the acetyl-CoA binding mode of MsCS. Structural comparison of MsCS with another CS in complex with oxaloacetate enabled us to predict the oxaloacetate binding site. Moreover, we performed inhibitory kinetic analyses of MsCS, and showed that the protein is inhibited by citrate and ATP by competitive and non-competitive inhibition modes, respectively, but not by NADH. Based on these results, we suggest that MsCS belongs to the type-I CS with structural and biochemical properties similar to those of CSs involved in the conventional TCA cycle.
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Affiliation(s)
- Seul Hoo Lee
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.
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15
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Reaction kinetic analysis of the 3-hydroxypropionate/4-hydroxybutyrate CO 2 fixation cycle in extremely thermoacidophilic archaea. Metab Eng 2016; 38:446-463. [PMID: 27771364 DOI: 10.1016/j.ymben.2016.10.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/07/2016] [Accepted: 10/17/2016] [Indexed: 12/21/2022]
Abstract
The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle fixes CO2 in extremely thermoacidophilic archaea and holds promise for metabolic engineering because of its thermostability and potentially rapid pathway kinetics. A reaction kinetics model was developed to examine the biological and biotechnological attributes of the 3HP/4HB cycle as it operates in Metallosphaera sedula, based on previous information as well as on kinetic parameters determined here for recombinant versions of five of the cycle enzymes (malonyl-CoA/succinyl-CoA reductase, 3-hydroxypropionyl-CoA synthetase, 3-hydroxypropionyl-CoA dehydratase, acryloyl-CoA reductase, and succinic semialdehyde reductase). The model correctly predicted previously observed features of the cycle: the 35-65% split of carbon flux through the acetyl-CoA and succinate branches, the high abundance and relative ratio of acetyl-CoA/propionyl-CoA carboxylase (ACC) and MCR, and the significance of ACC and hydroxybutyryl-CoA synthetase (HBCS) as regulated control points for the cycle. The model was then used to assess metabolic engineering strategies for incorporating CO2 into chemical intermediates and products of biotechnological importance: acetyl-CoA, succinate, and 3-hydroxypropionate.
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Ye Z, Li X, Cheng Y, Liu Z, Tan G, Zhu F, Fu S, Deng Z, Liu T. Evaluation of 3-hydroxypropionate biosynthesis in vitro by partial introduction of the 3-hydroxypropionate/4-hydroxybutyrate cycle from Metallosphaera sedula. J Ind Microbiol Biotechnol 2016; 43:1313-21. [PMID: 27300329 PMCID: PMC4983293 DOI: 10.1007/s10295-016-1793-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 05/31/2016] [Indexed: 01/03/2023]
Abstract
The chemical 3-hydroxypropionate (3HP) is an important starting reagent for the commercial synthesis of specialty chemicals. In this study, a part of the 3-hydroxypropionate/4-hydroxybutyrate cycle from Metallosphaera sedula was utilized for 3HP production. To study the basic biochemistry of this pathway, an in vitro-reconstituted system was established using acetyl-CoA as the substrate for the kinetic analysis of this system. The results indicated that 3HP formation was sensitive to acetyl-CoA carboxylase and malonyl-CoA reductase, but not malonate semialdehyde reductase. Also, the competition between 3HP formation and fatty acid production was analyzed both in vitro and in vivo. This study has highlighted how metabolic flux is controlled by different catalytic components. We believe that this reconstituted system would be valuable for understanding 3HP biosynthesis pathway and for future engineering studies to enhance 3HP production.
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Affiliation(s)
- Ziling Ye
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, People's Republic of China
| | - Xiaowei Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, People's Republic of China
| | - Yongbo Cheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, People's Republic of China
| | - Zhijie Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, People's Republic of China
| | - Gaoyi Tan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, People's Republic of China
| | - Fayin Zhu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, People's Republic of China
| | - Shuai Fu
- J1 Biotech, Co., Ltd, Wuhan, 430075, People's Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, People's Republic of China.,Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, 430075, People's Republic of China.,The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, People's Republic of China. .,Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, 430075, People's Republic of China. .,Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan, 430068, People's Republic of China.
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Hawkins AB, Lian H, Zeldes BM, Loder AJ, Lipscomb GL, Schut GJ, Keller MW, Adams MWW, Kelly RM. Bioprocessing analysis of Pyrococcus furiosus strains engineered for CO₂-based 3-hydroxypropionate production. Biotechnol Bioeng 2015; 112:1533-43. [PMID: 25753826 PMCID: PMC4664069 DOI: 10.1002/bit.25584] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 02/23/2015] [Indexed: 01/29/2023]
Abstract
Metabolically engineered strains of the hyperthermophile Pyrococcus furiosus (T(opt) 95-100°C), designed to produce 3-hydroxypropionate (3HP) from maltose and CO2 using enzymes from the Metallosphaera sedula (T(opt) 73°C) carbon fixation cycle, were examined with respect to the impact of heterologous gene expression on metabolic activity, fitness at optimal and sub-optimal temperatures, gas-liquid mass transfer in gas-intensive bioreactors, and potential bottlenecks arising from product formation. Transcriptomic comparisons of wild-type P. furiosus, a genetically-tractable, naturally-competent mutant (COM1), and COM1-based strains engineered for 3HP production revealed numerous differences after being shifted from 95°C to 72°C, where product formation catalyzed by the heterologously-produced M. sedula enzymes occurred. At 72°C, significantly higher levels of metabolic activity and a stress response were evident in 3HP-forming strains compared to the non-producing parent strain (COM1). Gas-liquid mass transfer limitations were apparent, given that 3HP titers and volumetric productivity in stirred bioreactors could be increased over 10-fold by increased agitation and higher CO2 sparging rates, from 18 mg/L to 276 mg/L and from 0.7 mg/L/h to 11 mg/L/h, respectively. 3HP formation triggered transcription of genes for protein stabilization and turnover, RNA degradation, and reactive oxygen species detoxification. The results here support the prospects of using thermally diverse sources of pathways and enzymes in metabolically engineered strains designed for product formation at sub-optimal growth temperatures.
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Affiliation(s)
- Aaron B Hawkins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27695-7905
| | - Hong Lian
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27695-7905
| | - Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27695-7905
| | - Andrew J Loder
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27695-7905
| | - Gina L Lipscomb
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602
| | - Matthew W Keller
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27695-7905.
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Leyn SA, Rodionova IA, Li X, Rodionov DA. Novel Transcriptional Regulons for Autotrophic Cycle Genes in Crenarchaeota. J Bacteriol 2015; 197:2383-91. [PMID: 25939834 PMCID: PMC4524184 DOI: 10.1128/jb.00249-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 04/29/2015] [Indexed: 12/18/2022] Open
Abstract
UNLABELLED Autotrophic microorganisms are able to utilize carbon dioxide as their only carbon source, or, alternatively, many of them can grow heterotrophically on organics. Different variants of autotrophic pathways have been identified in various lineages of the phylum Crenarchaeota. Aerobic members of the order Sulfolobales utilize the hydroxypropionate-hydroxybutyrate cycle (HHC) to fix inorganic carbon, whereas anaerobic Thermoproteales use the dicarboxylate-hydroxybutyrate cycle (DHC). Knowledge of transcriptional regulation of autotrophic pathways in Archaea is limited. We applied a comparative genomics approach to predict novel autotrophic regulons in the Crenarchaeota. We report identification of two novel DNA motifs associated with the autotrophic pathway genes in the Sulfolobales (HHC box) and Thermoproteales (DHC box). Based on genome context evidence, the HHC box regulon was attributed to a novel transcription factor from the TrmB family named HhcR. Orthologs of HhcR are present in all Sulfolobales genomes but were not found in other lineages. A predicted HHC box regulatory motif was confirmed by in vitro binding assays with the recombinant HhcR protein from Metallosphaera yellowstonensis. For the DHC box regulon, we assigned a different potential regulator, named DhcR, which is restricted to the order Thermoproteales. DhcR in Thermoproteus neutrophilus (Tneu_0751) was previously identified as a DNA-binding protein with high affinity for the promoter regions of two autotrophic operons. The global HhcR and DhcR regulons reconstructed by comparative genomics were reconciled with available omics data in Metallosphaera and Thermoproteus spp. The identified regulons constitute two novel mechanisms for transcriptional control of autotrophic pathways in the Crenarchaeota. IMPORTANCE Little is known about transcriptional regulation of carbon dioxide fixation pathways in Archaea. We previously applied the comparative genomics approach for reconstruction of DtxR family regulons in diverse lineages of Archaea. Here, we utilize similar computational approaches to identify novel regulatory motifs for genes that are autotrophically induced in microorganisms from two lineages of Crenarchaeota and to reconstruct the respective regulons. The predicted novel regulons in archaeal genomes control the majority of autotrophic pathway genes and also other carbon and energy metabolism genes. The HhcR regulon was experimentally validated by DNA-binding assays in Metallosphaera spp. Novel regulons described for the first time in this work provide a basis for understanding the mechanisms of transcriptional regulation of autotrophic pathways in Archaea.
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Affiliation(s)
- Semen A Leyn
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Irina A Rodionova
- Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - Xiaoqing Li
- Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - Dmitry A Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia Sanford-Burnham Medical Research Institute, La Jolla, California, USA
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Malonic semialdehyde reductase from the archaeon Nitrosopumilus maritimus is involved in the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle. Appl Environ Microbiol 2014; 81:1700-7. [PMID: 25548047 DOI: 10.1128/aem.03390-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The recently described ammonia-oxidizing archaea of the phylum Thaumarchaeota are highly abundant in marine, geothermal, and terrestrial environments. All characterized representatives of this phylum are aerobic chemolithoautotrophic ammonia oxidizers assimilating inorganic carbon via a recently described thaumarchaeal version of the 3-hydroxypropionate/4-hydroxybutyrate cycle. Although some genes coding for the enzymes of this cycle have been identified in the genomes of Thaumarchaeota, many other genes of the cycle are not homologous to the characterized enzymes from other species and can therefore not be identified bioinformatically. Here we report the identification and characterization of malonic semialdehyde reductase Nmar_1110 in the cultured marine thaumarchaeon Nitrosopumilus maritimus. This enzyme, which catalyzes the reduction of malonic semialdehyde with NAD(P)H to 3-hydroxypropionate, belongs to the family of iron-containing alcohol dehydrogenases and is not homologous to malonic semialdehyde reductases from Chloroflexus aurantiacus and Metallosphaera sedula. It is highly specific to malonic semialdehyde (Km, 0.11 mM; Vmax, 86.9 μmol min(-1) mg(-1) of protein) and exhibits only low activity with succinic semialdehyde (Km, 4.26 mM; Vmax, 18.5 μmol min(-1) mg(-1) of protein). Homologues of N. maritimus malonic semialdehyde reductase can be found in the genomes of all Thaumarchaeota sequenced so far and form a well-defined cluster in the phylogenetic tree of iron-containing alcohol dehydrogenases. We conclude that malonic semialdehyde reductase can be regarded as a characteristic enzyme for the thaumarchaeal version of the 3-hydroxypropionate/4-hydroxybutyrate cycle.
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Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation. Proc Natl Acad Sci U S A 2014; 111:8239-44. [PMID: 24843170 DOI: 10.1073/pnas.1402028111] [Citation(s) in RCA: 244] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Archaea of the phylum Thaumarchaeota are among the most abundant prokaryotes on Earth and are widely distributed in marine, terrestrial, and geothermal environments. All studied Thaumarchaeota couple the oxidation of ammonia at extremely low concentrations with carbon fixation. As the predominant nitrifiers in the ocean and in various soils, ammonia-oxidizing archaea contribute significantly to the global nitrogen and carbon cycles. Here we provide biochemical evidence that thaumarchaeal ammonia oxidizers assimilate inorganic carbon via a modified version of the autotrophic hydroxypropionate/hydroxybutyrate cycle of Crenarchaeota that is far more energy efficient than any other aerobic autotrophic pathway. The identified genes of this cycle were found in the genomes of all sequenced representatives of the phylum Thaumarchaeota, indicating the environmental significance of this efficient CO2-fixation pathway. Comparative phylogenetic analysis of proteins of this pathway suggests that the hydroxypropionate/hydroxybutyrate cycle emerged independently in Crenarchaeota and Thaumarchaeota, thus supporting the hypothesis of an early evolutionary separation of both archaeal phyla. We conclude that high efficiency of anabolism exemplified by this autotrophic cycle perfectly suits the lifestyle of ammonia-oxidizing archaea, which thrive at a constantly low energy supply, thus offering a biochemical explanation for their ecological success in nutrient-limited environments.
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