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Fang J, Chen W, Hou P, Liu Z, Zuo M, Liu S, Feng C, Han Y, Li P, Shi Y, Shao C. NAD + metabolism-based immunoregulation and therapeutic potential. Cell Biosci 2023; 13:81. [PMID: 37165408 PMCID: PMC10171153 DOI: 10.1186/s13578-023-01031-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/14/2023] [Indexed: 05/12/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) is a critical metabolite that acts as a cofactor in energy metabolism, and serves as a cosubstrate for non-redox NAD+-dependent enzymes, including sirtuins, CD38 and poly(ADP-ribose) polymerases. NAD+ metabolism can regulate functionality attributes of innate and adaptive immune cells and contribute to inflammatory responses. Thus, the manipulation of NAD+ bioavailability can reshape the courses of immunological diseases. Here, we review the basics of NAD+ biochemistry and its roles in the immune response, and discuss current challenges and the future translational potential of NAD+ research in the development of therapeutics for inflammatory diseases, such as COVID-19.
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Affiliation(s)
- Jiankai Fang
- Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, The First Affiliated Hospital of Soochow University, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, China
| | - Wangwang Chen
- Laboratory Animal Center, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, China
| | - Pengbo Hou
- Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, The First Affiliated Hospital of Soochow University, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, China
- Department of Experimental Medicine and Biochemical Sciences, TOR, University of Rome Tor Vergata, Rome, Italy
| | - Zhanhong Liu
- Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, The First Affiliated Hospital of Soochow University, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, China
- Department of Experimental Medicine and Biochemical Sciences, TOR, University of Rome Tor Vergata, Rome, Italy
| | - Muqiu Zuo
- Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, The First Affiliated Hospital of Soochow University, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, China
| | - Shisong Liu
- Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, The First Affiliated Hospital of Soochow University, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, China
| | - Chao Feng
- Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, The First Affiliated Hospital of Soochow University, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, China
- Department of Experimental Medicine and Biochemical Sciences, TOR, University of Rome Tor Vergata, Rome, Italy
| | - Yuyi Han
- Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, The First Affiliated Hospital of Soochow University, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, China
- Department of Experimental Medicine and Biochemical Sciences, TOR, University of Rome Tor Vergata, Rome, Italy
| | - Peishan Li
- Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, The First Affiliated Hospital of Soochow University, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, China.
| | - Yufang Shi
- Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, The First Affiliated Hospital of Soochow University, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, China.
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Changshun Shao
- Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, The First Affiliated Hospital of Soochow University, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, China.
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2
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V. K P, Sinha S. A systems level approach to study metabolic networks in prokaryotes with the aromatic amino acid biosynthesis pathway. Front Genet 2023; 13:1084727. [PMID: 36726720 PMCID: PMC9885046 DOI: 10.3389/fgene.2022.1084727] [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: 10/30/2022] [Accepted: 12/30/2022] [Indexed: 01/18/2023] Open
Abstract
Metabolism of an organism underlies its phenotype, which depends on many factors, such as the genetic makeup, habitat, and stresses to which it is exposed. This is particularly important for the prokaryotes, which undergo significant vertical and horizontal gene transfers. In this study we have used the energy-intensive Aromatic Amino Acid (Tryptophan, Tyrosine and Phenylalanine, TTP) biosynthesis pathway, in a large number of prokaryotes, as a model system to query the different levels of organization of metabolism in the whole intracellular biochemical network, and to understand how perturbations, such as mutations, affects the metabolic flux through the pathway - in isolation and in the context of other pathways connected to it. Using an agglomerative approach involving complex network analysis and Flux Balance Analyses (FBA), of the Tryptophan, Tyrosine and Phenylalanine and other pathways connected to it, we identify several novel results. Using the reaction network analysis and Flux Balance Analyses of the Tryptophan, Tyrosine and Phenylalanine and the genome-scale reconstructed metabolic pathways, many common hubs between the connected networks and the whole genome network are identified. The results show that the connected pathway network can act as a proxy for the whole genome network in Prokaryotes. This systems level analysis also points towards designing functional smaller synthetic pathways based on the reaction network and Flux Balance Analyses analysis.
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Affiliation(s)
- Priya V. K
- National Institute of Technology Calicut, Kattangal, Kerala, India,*Correspondence: Priya V. K, ; Somdatta Sinha,
| | - Somdatta Sinha
- Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India,*Correspondence: Priya V. K, ; Somdatta Sinha,
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3
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Shi N, Yan X, Adeleye AS, Zhang X, Zhou D, Zhao L. Effects of WS 2 Nanosheets on N 2-fixing Cyanobacteria: ROS overproduction, cell membrane damage, and cell metabolic reprogramming. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157706. [PMID: 35908696 DOI: 10.1016/j.scitotenv.2022.157706] [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: 05/29/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
The ecotoxicity of tungsten disulfide (WS2) nanomaterials remains unclear so far. Here, the toxicity of WS2 nanosheets on N2-fixing cyanobacteria (Nostoc sphaeroides) was evaluated. Specifically, Nostoc were cultivated in media spiked with different concentrations of WS2 nanosheets (0, 0.05, 0.1 and 0.5 mg/L) for 96 h. Relative to unexposed cells, WS2 nanosheets at 0.5 mg/L significantly decreased cell density, content of total sugar and protein by 10.9 %, 0.43 %, and 6.1 %, respectively. Gas chromatography-mass spectrometry (GC-MS)-based metabolomics revealed that WS2 nanosheets exposure altered the metabolite profile of Nostoc in a dose-dependent manner. Energy metabolism related pathways, including the Calvin-Benson-Bassham (CBB) cycle and tricarboxylic acid (TCA) cycle, were significantly inhibited. In addition, WS2 nanosheets exposure resulted in downregulation (20-40 %) of S-containing amino acids (cystine, methionine, and cysteine) and sulfuric acid. Additionally, fatty acids and antioxidant-related compounds (formononetin, catechin, epigallocatechin, dehydroascorbic acid, and alpha-tocopherol) in Nostoc were drastically decreased by 4-50 % upon exposure to WS2 nanosheets, which implies oxidative stress induced by the nanomaterials. Biochemical assays for reactive oxygen species (ROS) and malondialdehyde (MDA) confirmed that WS2 nanosheets triggered ROS overproduction and induced lipid peroxidation. Taken together, WS2 exposure perturbed carbon (C), nitrogen (N), and sulfate (S) metabolism of Nostoc, which may influence C, N, and S cycling, given the important roles of cyanobacteria in these processes. These results highlight the need for caution in the application and environmental release of WS2 nanomaterials to prevent unintended environmental impacts due to their potential ecotoxicity.
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Affiliation(s)
- Nibin Shi
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Xin Yan
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Adeyemi S Adeleye
- Department of Civil and Environmental Engineering, University of California, Irvine, CA 92697-2175, USA
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Dongmei Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Lijuan Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China.
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Sato T, Utashima S(H, Yoshii Y, Hirata K, Kanda S, Onoda Y, Jin JQ, Xiao S, Minami R, Fukushima H, Noguchi A, Manabe Y, Fukase K, Atomi H. A non-carboxylating pentose bisphosphate pathway in halophilic archaea. Commun Biol 2022; 5:1290. [PMID: 36434094 PMCID: PMC9700705 DOI: 10.1038/s42003-022-04247-2] [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: 07/28/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022] Open
Abstract
Bacteria and Eucarya utilize the non-oxidative pentose phosphate pathway to direct the ribose moieties of nucleosides to central carbon metabolism. Many archaea do not possess this pathway, and instead, Thermococcales utilize a pentose bisphosphate pathway involving ribose-1,5-bisphosphate (R15P) isomerase and ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco). Intriguingly, multiple genomes from halophilic archaea seem only to harbor R15P isomerase, and do not harbor Rubisco. In this study, we identify a previously unrecognized nucleoside degradation pathway in halophilic archaea, composed of guanosine phosphorylase, ATP-dependent ribose-1-phosphate kinase, R15P isomerase, RuBP phosphatase, ribulose-1-phosphate aldolase, and glycolaldehyde reductase. The pathway converts the ribose moiety of guanosine to dihydroxyacetone phosphate and ethylene glycol. Although the metabolic route from guanosine to RuBP via R15P is similar to that of the pentose bisphosphate pathway in Thermococcales, the downstream route does not utilize Rubisco and is unique to halophilic archaea.
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Affiliation(s)
- Takaaki Sato
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan ,grid.258799.80000 0004 0372 2033Integrated Research Center for Carbon Negative Science, Kyoto University, Kyoto, Japan
| | - Sanae (Hodo) Utashima
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Yuta Yoshii
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kosuke Hirata
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Shuichiro Kanda
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Yushi Onoda
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Jian-qiang Jin
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Suyi Xiao
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Ryoko Minami
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Hikaru Fukushima
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Ayako Noguchi
- grid.136593.b0000 0004 0373 3971Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Yoshiyuki Manabe
- grid.136593.b0000 0004 0373 3971Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan ,grid.136593.b0000 0004 0373 3971Forefront Research Center, Osaka University, Osaka, Japan
| | - Koichi Fukase
- grid.136593.b0000 0004 0373 3971Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan ,grid.136593.b0000 0004 0373 3971Forefront Research Center, Osaka University, Osaka, Japan
| | - Haruyuki Atomi
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan ,grid.258799.80000 0004 0372 2033Integrated Research Center for Carbon Negative Science, Kyoto University, Kyoto, Japan
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5
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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.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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6
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Abstract
α-Amino acids are essential molecular constituents of life, twenty of which are privileged because they are encoded by the ribosomal machinery. The question remains open as to why this number and why this 20 in particular, an almost philosophical question that cannot be conclusively resolved. They are closely related to the evolution of the genetic code and whether nucleic acids, amino acids, and peptides appeared simultaneously and were available under prebiotic conditions when the first self-sufficient complex molecular system emerged on Earth. This report focuses on prebiotic and metabolic aspects of amino acids and proteins starting with meteorites, followed by their formation, including peptides, under plausible prebiotic conditions, and the major biosynthetic pathways in the various kingdoms of life. Coenzymes play a key role in the present analysis in that amino acid metabolism is linked to glycolysis and different variants of the tricarboxylic acid cycle (TCA, rTCA, and the incomplete horseshoe version) as well as the biosynthesis of the most important coenzymes. Thus, the report opens additional perspectives and facets on the molecular evolution of primary metabolism.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic ChemistryLeibniz University HannoverSchneiderberg 1B30167HannoverGermany
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7
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di Masi A, Sessa RL, Cerrato Y, Pastore G, Guantario B, Ambra R, Di Gioacchino M, Sodo A, Verri M, Crucitti P, Longo F, Naciu AM, Palermo A, Taffon C, Acconcia F, Bianchi F, Ascenzi P, Ricci MA, Crescenzi A. Unraveling the Effects of Carotenoids Accumulation in Human Papillary Thyroid Carcinoma. Antioxidants (Basel) 2022; 11:antiox11081463. [PMID: 36009182 PMCID: PMC9405418 DOI: 10.3390/antiox11081463] [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: 06/18/2022] [Revised: 07/12/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
Among the thyroid cancers, papillary thyroid cancer (PTC) accounts for 90% of the cases. In addition to the necessity to identify new targets for PTC treatment, early diagnosis and management are highly demanded. Previous data indicated that the multivariate statistical analysis of the Raman spectra allows the discrimination of healthy tissues from PTC ones; this is characterized by bands typical of carotenoids. Here, we dissected the molecular effects of carotenoid accumulation in PTC patients by analyzing whether they were required to provide increased retinoic acid (RA) synthesis and signaling and/or to sustain antioxidant functions. HPLC analysis revealed the lack of a significant difference in the overall content of carotenoids. For this reason, we wondered whether the carotenoid accumulation in PTC patients could be related to vitamin A derivative retinoic acid (RA) biosynthesis and, consequently, the RA-related pathway activation. The transcriptomic analysis performed using a dedicated PCR array revealed a significant downregulation of RA-related pathways in PTCs, suggesting that the carotenoid accumulation in PTC could be related to a lower metabolic conversion into RA compared to that of healthy tissues. In addition, the gene expression profile of 474 PTC cases previously published in the framework of the Cancer Genome Atlas (TGCA) project was examined by hierarchical clustering and heatmap analyses. This metanalysis study indicated that the RA-related pathways resulted in being significantly downregulated in PTCs and being associated with the follicular variant of PTC (FV-PTC). To assess whether the possible fate of the carotenoids accumulated in PTCs is associated with the oxidative stress response, the expression of enzymes involved in ROS scavenging was checked. An increased oxidative stress status and a reduced antioxidant defense response were observed in PTCs compared to matched healthy thyroids; this was possibly associated with the prooxidant effects of high levels of carotenoids. Finally, the DepMap datasets were used to profile the levels of 225 metabolites in 12 thyroid cancer cell lines. The results obtained suggested that the high carotenoid content in PTCs correlates with tryptophan metabolism. This pilot provided novel possible markers and possible therapeutic targets for PTC diagnosis and therapy. For the future, a larger study including a higher number of PTC patients will be necessary to further validate the molecular data reported here.
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Affiliation(s)
- Alessandra di Masi
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (R.L.S.); (Y.C.); (M.D.G.); (A.S.); (F.A.); (P.A.); (M.A.R.)
- Correspondence: ; Tel.: +39-06-57336363
| | - Rosario Luigi Sessa
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (R.L.S.); (Y.C.); (M.D.G.); (A.S.); (F.A.); (P.A.); (M.A.R.)
| | - Ylenia Cerrato
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (R.L.S.); (Y.C.); (M.D.G.); (A.S.); (F.A.); (P.A.); (M.A.R.)
| | - Gianni Pastore
- CREA (Council for Agricultural Research and Economics), Research Centre for Food and Nutrition, 00178 Rome, Italy; (G.P.); (B.G.); (R.A.)
| | - Barbara Guantario
- CREA (Council for Agricultural Research and Economics), Research Centre for Food and Nutrition, 00178 Rome, Italy; (G.P.); (B.G.); (R.A.)
| | - Roberto Ambra
- CREA (Council for Agricultural Research and Economics), Research Centre for Food and Nutrition, 00178 Rome, Italy; (G.P.); (B.G.); (R.A.)
| | - Michael Di Gioacchino
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (R.L.S.); (Y.C.); (M.D.G.); (A.S.); (F.A.); (P.A.); (M.A.R.)
| | - Armida Sodo
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (R.L.S.); (Y.C.); (M.D.G.); (A.S.); (F.A.); (P.A.); (M.A.R.)
| | - Martina Verri
- Pathology Unit, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy; (M.V.); (C.T.); (A.C.)
| | - Pierfilippo Crucitti
- Unit of Thoracic Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy; (P.C.); (F.L.)
| | - Filippo Longo
- Unit of Thoracic Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy; (P.C.); (F.L.)
| | - Anda Mihaela Naciu
- Unit of Metabolic Bone and Thyroid Disorders, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy; (A.M.N.); (A.P.)
| | - Andrea Palermo
- Unit of Metabolic Bone and Thyroid Disorders, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy; (A.M.N.); (A.P.)
| | - Chiara Taffon
- Pathology Unit, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy; (M.V.); (C.T.); (A.C.)
| | - Filippo Acconcia
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (R.L.S.); (Y.C.); (M.D.G.); (A.S.); (F.A.); (P.A.); (M.A.R.)
| | - Fabrizio Bianchi
- Cancer Biomarkers Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, FG, Italy;
| | - Paolo Ascenzi
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (R.L.S.); (Y.C.); (M.D.G.); (A.S.); (F.A.); (P.A.); (M.A.R.)
| | - Maria Antonietta Ricci
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (R.L.S.); (Y.C.); (M.D.G.); (A.S.); (F.A.); (P.A.); (M.A.R.)
| | - Anna Crescenzi
- Pathology Unit, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy; (M.V.); (C.T.); (A.C.)
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Fuentes-Ugarte N, Herrera SM, Maturana P, Castro-Fernandez V, Guixé V. Structural and Kinetic Insights Into the Molecular Basis of Salt Tolerance of the Short-Chain Glucose-6-Phosphate Dehydrogenase From Haloferax volcanii. Front Microbiol 2021; 12:730429. [PMID: 34650535 PMCID: PMC8506132 DOI: 10.3389/fmicb.2021.730429] [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: 06/24/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
Halophilic enzymes need high salt concentrations for activity and stability and are considered a promising source for biotechnological applications. The model study for haloadaptation has been proteins from the Halobacteria class of Archaea, where common structural characteristics have been found. However, the effect of salt on enzyme function and conformational dynamics has been much less explored. Here we report the structural and kinetic characteristics of glucose-6-phosphate dehydrogenase from Haloferax volcanii (HvG6PDH) belonging to the short-chain dehydrogenases/reductases (SDR) superfamily. The enzyme was expressed in Escherichia coli and successfully solubilized and refolded from inclusion bodies. The enzyme is active in the presence of several salts, though the maximum activity is achieved in the presence of KCl, mainly by an increment in the kcat value, that correlates with a diminution of its flexibility according to molecular dynamics simulations. The high KM for glucose-6-phosphate and its promiscuous activity for glucose restrict the use of HvG6PDH as an auxiliary enzyme for the determination of halophilic glucokinase activity. Phylogenetic analysis indicates that SDR-G6PDH enzymes are exclusively present in Halobacteria, with HvG6PDH being the only enzyme characterized. Homology modeling and molecular dynamics simulations of HvG6PDH identified a conserved NLTX2H motif involved in glucose-6-phosphate interaction at high salt concentrations, whose residues could be crucial for substrate specificity. Structural differences in its conformational dynamics, potentially related to the haloadaptation strategy, were also determined.
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Affiliation(s)
- Nicolás Fuentes-Ugarte
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Sixto M Herrera
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Pablo Maturana
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Victor Castro-Fernandez
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Victoria Guixé
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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9
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Abstract
DPANN is known as highly diverse, globally widespread, and mostly ectosymbiotic archaeal superphylum. However, this group of archaea was overlooked for a long time, and there were limited in-depth studies reported. In this investigation, 41 metagenome-assembled genomes (MAGs) belonging to the DPANN superphylum were recovered (18 MAGs had average nucleotide identity [ANI] values of <95% and a percentage of conserved proteins [POCP] of >50%, while 14 MAGs showed a POCP of <50%), which were analyzed comparatively with 515 other published DPANN genomes. Mismatches to known 16S rRNA gene primers were identified among 16S rRNA genes of DPANN archaea. Numbers of gene families lost (mostly related to energy and amino acid metabolism) were over three times greater than those gained in the evolution of DPANN archaea. Lateral gene transfer (LGT; ∼45.5% was cross-domain) had facilitated niche adaption of the DPANN archaea, ensuring a delicate equilibrium of streamlined genomes with efficient niche-adaptive strategies. For instance, LGT-derived cytochrome bd ubiquinol oxidase and arginine deiminase in the genomes of “Candidatus Micrarchaeota” could help them better adapt to aerobic acidic mine drainage habitats. In addition, most DPANN archaea acquired enzymes for biosynthesis of extracellular polymeric substances (EPS) and transketolase/transaldolase for the pentose phosphate pathway from Bacteria. IMPORTANCE The domain Archaea is a key research model for gaining insights into the origin and evolution of life, as well as the relevant biogeochemical processes. The discovery of nanosized DPANN archaea has overthrown many aspects of microbiology. However, the DPANN superphylum still contains a vast genetic novelty and diversity that need to be explored. Comprehensively comparative genomic analysis on the DPANN superphylum was performed in this study, with an attempt to illuminate its metabolic potential, ecological distribution and evolutionary history. Many interphylum differences within the DPANN superphylum were found. For example, Altiarchaeota had the biggest genome among DPANN phyla, possessing many pathways missing in other phyla, such as formaldehyde assimilation and the Wood-Ljungdahl pathway. In addition, LGT acted as an important force to provide DPANN archaeal genetic flexibility that permitted the occupation of diverse niches. This study has advanced our understanding of the diversity and genome evolution of archaea.
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The Pentose Phosphate Pathway in Yeasts-More Than a Poor Cousin of Glycolysis. Biomolecules 2021; 11:biom11050725. [PMID: 34065948 PMCID: PMC8151747 DOI: 10.3390/biom11050725] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 01/14/2023] Open
Abstract
The pentose phosphate pathway (PPP) is a route that can work in parallel to glycolysis in glucose degradation in most living cells. It has a unidirectional oxidative part with glucose-6-phosphate dehydrogenase as a key enzyme generating NADPH, and a non-oxidative part involving the reversible transketolase and transaldolase reactions, which interchange PPP metabolites with glycolysis. While the oxidative branch is vital to cope with oxidative stress, the non-oxidative branch provides precursors for the synthesis of nucleic, fatty and aromatic amino acids. For glucose catabolism in the baker’s yeast Saccharomyces cerevisiae, where its components were first discovered and extensively studied, the PPP plays only a minor role. In contrast, PPP and glycolysis contribute almost equally to glucose degradation in other yeasts. We here summarize the data available for the PPP enzymes focusing on S. cerevisiae and Kluyveromyces lactis, and describe the phenotypes of gene deletions and the benefits of their overproduction and modification. Reference to other yeasts and to the importance of the PPP in their biotechnological and medical applications is briefly being included. We propose future studies on the PPP in K. lactis to be of special interest for basic science and as a host for the expression of human disease genes.
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11
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The pentose phosphate pathway in industrially relevant fungi: crucial insights for bioprocessing. Appl Microbiol Biotechnol 2021; 105:4017-4031. [PMID: 33950280 PMCID: PMC8140973 DOI: 10.1007/s00253-021-11314-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/04/2021] [Accepted: 04/20/2021] [Indexed: 11/12/2022]
Abstract
Abstract The pentose phosphate pathway (PPP) is one of the most targeted pathways in metabolic engineering. This pathway is the primary source of NADPH, and it contributes in fungi to the production of many compounds of interest such as polyols, biofuels, carotenoids, or antibiotics. However, the regulatory mechanisms of the PPP are still not fully known. This review provides an insight into the current comprehension of the PPP in fungi and the limitations of this current understanding. It highlights how this knowledge contributes to targeted engineering of the PPP and thus to better performance of industrially used fungal strains. Key points • Type of carbon and nitrogen source as well as oxidative stress influence the PPP. • A complex network of transcription factors regulates the PPP. • Improved understanding of the PPP will allow to increase yields of bioprocesses.
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Maturana P, Tobar-Calfucoy E, Fuentealba M, Roversi P, Garratt R, Cabrera R. Crystal structure of the 6-phosphogluconate dehydrogenase from Gluconobacter oxydans reveals tetrameric 6PGDHs as the crucial intermediate in the evolution of structure and cofactor preference in the 6PGDH family. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.16572.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: The enzyme 6-phosphogluconate dehydrogenase (6PGDH) is the central enzyme of the oxidative pentose phosphate pathway. Members of the 6PGDH family belong to different classes: either homodimeric enzymes assembled from long-chain subunits or homotetrameric ones assembled from short-chain subunits. Dimeric 6PGDHs bear an internal duplication absent in tetrameric 6PGDHs and distant homologues of the β-hydroxyacid dehydrogenase (βHADH) superfamily. Methods: We use X-ray crystallography to determine the structure of the apo form of the 6PGDH from Gluconobacter oxydans (Go6PGDH). We carried out a structural and phylogenetic analysis of short and long-chain 6PGDHs. We put forward an evolutionary hypothesis explaining the differences seen in oligomeric state vs. dinucleotide preference of the 6PGDH family. We determined the cofactor preference of Go6PGDH at different 6-phosphogluconate concentrations, characterizing the wild-type enzyme and three-point mutants of residues in the cofactor binding site of Go6PGDH. Results: The structural comparison suggests that the 6PG binding site initially evolved by exchanging C-terminal α-helices between subunits. An internal duplication event changed the quaternary structure of the enzyme from a tetrameric to a dimeric arrangement. The phylogenetic analysis suggests that 6PGDHs have spread from Bacteria to Archaea and Eukarya on multiple occasions by lateral gene transfer. Sequence motifs consistent with NAD+- and NADP+-specificity are found in the β2-α2 loop of dimeric and tetrameric 6PGDHs. Site-directed mutagenesis of Go6PGDH inspired by this analysis fully reverses dinucleotide preference. One of the mutants we engineered has the highest efficiency and specificity for NAD+ so far described for a 6PGDH. Conclusions: The family 6PGDH comprises dimeric and tetrameric members whose active sites are conformed by a C-terminal α-helix contributed from adjacent subunits. Dimeric 6PGDHs have evolved from the duplication-fusion of the tetrameric C-terminal domain before independent transitions of cofactor specificity. Changes in the conserved β2-α2 loop are crucial to modulate the cofactor specificity in Go6PGDH.
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Gao X, Jing X, Liu X, Lindblad P. Biotechnological Production of the Sunscreen Pigment Scytonemin in Cyanobacteria: Progress and Strategy. Mar Drugs 2021; 19:129. [PMID: 33673485 PMCID: PMC7997468 DOI: 10.3390/md19030129] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/22/2022] Open
Abstract
Scytonemin is a promising UV-screen and antioxidant small molecule with commercial value in cosmetics and medicine. It is solely biosynthesized in some cyanobacteria. Recently, its biosynthesis mechanism has been elucidated in the model cyanobacterium Nostoc punctiforme PCC 73102. The direct precursors for scytonemin biosynthesis are tryptophan and p-hydroxyphenylpyruvate, which are generated through the shikimate and aromatic amino acid biosynthesis pathway. More upstream substrates are the central carbon metabolism intermediates phosphoenolpyruvate and erythrose-4-phosphate. Thus, it is a long route to synthesize scytonemin from the fixed atmospheric CO2 in cyanobacteria. Metabolic engineering has risen as an important biotechnological means for achieving sustainable high-efficiency and high-yield target metabolites. In this review, we summarized the biochemical properties of this molecule, its biosynthetic gene clusters and transcriptional regulations, the associated carbon flux-driving progresses, and the host selection and biosynthetic strategies, with the aim to expand our understanding on engineering suitable cyanobacteria for cost-effective production of scytonemin in future practices.
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Affiliation(s)
- Xiang Gao
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi’an 710021, China;
| | - Xin Jing
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi’an 710021, China;
| | - Xufeng Liu
- Microbial Chemistry, Department of Chemistry-Ångstrom, Uppsala University, Box 523, 751 20 Uppsala, Sweden;
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångstrom, Uppsala University, Box 523, 751 20 Uppsala, Sweden;
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14
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Bedaquiline reprograms central metabolism to reveal glycolytic vulnerability in Mycobacterium tuberculosis. Nat Commun 2020; 11:6092. [PMID: 33257709 PMCID: PMC7705017 DOI: 10.1038/s41467-020-19959-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/04/2020] [Indexed: 02/06/2023] Open
Abstract
The approval of bedaquiline (BDQ) for the treatment of tuberculosis has generated substantial interest in inhibiting energy metabolism as a therapeutic paradigm. However, it is not known precisely how BDQ triggers cell death in Mycobacterium tuberculosis (Mtb). Using 13C isotopomer analysis, we show that BDQ-treated Mtb redirects central carbon metabolism to induce a metabolically vulnerable state susceptible to genetic disruption of glycolysis and gluconeogenesis. Metabolic flux profiles indicate that BDQ-treated Mtb is dependent on glycolysis for ATP production, operates a bifurcated TCA cycle by increasing flux through the glyoxylate shunt, and requires enzymes of the anaplerotic node and methylcitrate cycle. Targeting oxidative phosphorylation (OXPHOS) with BDQ and simultaneously inhibiting substrate level phosphorylation via genetic disruption of glycolysis leads to rapid sterilization. Our findings provide insight into the metabolic mechanism of BDQ-induced cell death and establish a paradigm for the development of combination therapies that target OXPHOS and glycolysis.
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James P, Isupov MN, De Rose SA, Sayer C, Cole IS, Littlechild JA. A 'Split-Gene' Transketolase From the Hyper-Thermophilic Bacterium Carboxydothermus hydrogenoformans: Structure and Biochemical Characterization. Front Microbiol 2020; 11:592353. [PMID: 33193259 PMCID: PMC7661550 DOI: 10.3389/fmicb.2020.592353] [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: 08/06/2020] [Accepted: 10/12/2020] [Indexed: 11/26/2022] Open
Abstract
A novel transketolase has been reconstituted from two separate polypeptide chains encoded by a ‘split-gene’ identified in the genome of the hyperthermophilic bacterium, Carboxydothermus hydrogenoformans. The reconstituted active α2β2 tetrameric enzyme has been biochemically characterized and its activity has been determined using a range of aldehydes including glycolaldehyde, phenylacetaldehyde and cyclohexanecarboxaldehyde as the ketol acceptor and hydroxypyruvate as the donor. This reaction proceeds to near 100% completion due to the release of the product carbon dioxide and can be used for the synthesis of a range of sugars of interest to the pharmaceutical industry. This novel reconstituted transketolase is thermally stable with no loss of activity after incubation for 1 h at 70°C and is stable after 1 h incubation with 50% of the organic solvents methanol, ethanol, isopropanol, DMSO, acetonitrile and acetone. The X-ray structure of the holo reconstituted α2β2 tetrameric transketolase has been determined to 1.4 Å resolution. In addition, the structure of an inactive tetrameric β4 protein has been determined to 1.9 Å resolution. The structure of the active reconstituted α2β2 enzyme has been compared to the structures of related enzymes; the E1 component of the pyruvate dehydrogenase complex and D-xylulose-5-phosphate synthase, in an attempt to rationalize differences in structure and substrate specificity between these enzymes. This is the first example of a reconstituted ‘split-gene’ transketolase to be biochemically and structurally characterized allowing its potential for industrial biocatalysis to be evaluated.
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Affiliation(s)
- Paul James
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Simone Antonio De Rose
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Isobel S Cole
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
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Chien HJ, Xue YT, Chen HC, Wu KY, Lai CC. Proteomic analysis of rat kidney under maleic acid treatment by SWATH-MS technology. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34 Suppl 1:e8633. [PMID: 31677360 DOI: 10.1002/rcm.8633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/03/2019] [Accepted: 10/09/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE Maleic acid is an industrial-grade chemical that is often used in adhesives, stabilizers, and preservatives. It is unknown whether long-term consumption of maleic acid modified starch is harmful to humans. However, many studies have indicated that maleic acid causes renal tubular damage in animal models, even as the associated pathways remain unclear. Sequential window acquisition of all theoretical fragment ion spectra (SWATH) is the most innovative of the label-free quantitative technologies which have better quantification performance. Therefore, SWATH technology was used to investigate the effect of maleic acid on the rat kidney proteome in this study. METHODS Sprague-Dawley(SD) rats were treated with 0 mg/kg (control), 6 mg/kg (low-dose), 10 mg/kg (medium-dose), and 60 mg/kg (high-dose) of maleic acid. After kidney protein extraction, 28% SDS-PAGE was used, followed by in-gel digestion and desalting. Next, the samples were analyzed with ultra-performance liquid chromatography (UPLC) coupled with quadrupole time-of-flight mass spectrometry (Q-TOF MS), and data-dependent acquisition (DDA) and SWATH technology were also used. The gene ontology and pathway analysis were accomplished. Ultimately, these protein biomarkers were validated by using scheduled high-resolution multiple reaction monitoring (sMRMHR ). RESULTS Comparisons of the control group with the other three groups revealed that 95, 130, and 103 proteins were expressed at significantly different levels in the control group and in the low-dose, medium-dose, and high-dose groups, respectively. According to the gene ontology analysis, the major processes that these proteins were involved in were metabolic processes, biological regulation, cellular processes, and responses to stimuli; the major functions that these proteins were involved in were binding, hydrolase activity, catalytic activity, and oxidoreductase activity; and the major cellular components hat they were involved in were the cytoplasm, extracellular region, membrane, and mitochondria. According to the KEGG pathway analysis, these proteins were involved in 35 pathways, five of which, the carbohydrate metabolism, folate biosynthesis, renal tubular resorption, amino acid metabolism, and Ras signaling pathways, are discussed in this study. Ultimately, 19 proteins involved in 12 important pathways were validated by sMRMHR . CONCLUSIONS It was demonstrated that maleic acid caused insufficient energy production, which might lead to a decrease in the activity of the sodium-potassium ATP pump and hydrogen ion ATP pump, which could in turn have caused renal tubular resorption and hydrogen ion regulation to be blocked, thus leading to the accumulation of hydrogen ions in the renal tubules, which would then result in renal tubular acidification followed finally by Fanconi syndrome.
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Affiliation(s)
- Han-Ju Chien
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Yu-Ting Xue
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hsin-Chang Chen
- Institute of Occupational Medicine and Industrial Hygiene, College of Public Health, National Taiwan University, No. 17, ShiuJou Road, Taipei, 10055, Taiwan
| | - Kuen-Yuh Wu
- Institute of Occupational Medicine and Industrial Hygiene, College of Public Health, National Taiwan University, No. 17, ShiuJou Road, Taipei, 10055, Taiwan
| | - Chien-Chen Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40227, Taiwan
- Graduate Institute of Chinese Medical Science, China Medical University, Taichung, 40447, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, 40402, Taiwan
- Department of Pharmacology, National Defense Medical Center, Taipei City, 11490, Taiwan
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Abstract
The mammalian kidney relies on abundant mitochondria in the renal tubule to generate sufficient ATP to provide the energy required for constant reclamation of solutes from crude blood filtrate. The highly metabolically active cells of the renal tubule also pair their energetic needs to the regulation of diverse cellular processes, including energy generation, antioxidant responses, autophagy and mitochondrial quality control. Nicotinamide adenine dinucleotide (NAD+) is essential not only for the harvesting of energy from substrates but also for an array of regulatory reactions that determine cellular health. In acute kidney injury (AKI), substantial decreases in the levels of NAD+ impair energy generation and, ultimately, the core kidney function of selective solute transport. Conversely, augmentation of NAD+ may protect the kidney tubule against diverse acute stressors. For example, NAD+ augmentation can ameliorate experimental AKI triggered by ischaemia–reperfusion, toxic injury and systemic inflammation. NAD+-dependent maintenance of renal tubular metabolic health may also attenuate long-term profibrotic responses that could lead to chronic kidney disease. Further understanding of the genetic, environmental and nutritional factors that influence NAD+ biosynthesis and renal resilience may lead to novel approaches for the prevention and treatment of kidney disease. Here, the authors discuss evidence for a role of NAD+ imbalance in the pathogenesis of acute kidney injury (AKI) and chronic kidney disease (CKD). They suggest that disruption of NAD+ metabolism may contribute to mechanistic links among AKI, CKD and ageing. NAD+ has critical roles in the generation of ATP from fuel substrates and as a substrate for important enzymes that regulate cellular health and stress responses. The renal tubule is highly metabolically active and requires a constant supply of ATP to provide the energy required to pump solutes across unfavourable gradients. Experimental acute kidney injury (AKI) induced by various insults rapidly leads to a decrease in NAD+ levels that probably results from a combination of reduced NAD+ biosynthesis and increased NAD+ consumption. Renal NAD+ levels can be augmented using vitamin B3 analogues and related nutritional precursors. NAD+ augmentation can prevent and/or treat various aetiologies of experimental AKI and might also attenuate long-term profibrotic responses following AKI, suggesting a potential role in the treatment of chronic kidney disease.
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18
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Yin X, Wu W, Maeke M, Richter-Heitmann T, Kulkarni AC, Oni OE, Wendt J, Elvert M, Friedrich MW. CO 2 conversion to methane and biomass in obligate methylotrophic methanogens in marine sediments. ISME JOURNAL 2019; 13:2107-2119. [PMID: 31040382 PMCID: PMC6775961 DOI: 10.1038/s41396-019-0425-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/04/2019] [Accepted: 04/13/2019] [Indexed: 11/24/2022]
Abstract
Methyl substrates are important compounds for methanogenesis in marine sediments but diversity and carbon utilization by methylotrophic methanogenic archaea have not been clarified. Here, we demonstrate that RNA-stable isotope probing (SIP) requires 13C-labeled bicarbonate as co-substrate for identification of methylotrophic methanogens in sediment samples of the Helgoland mud area, North Sea. Using lipid-SIP, we found that methylotrophic methanogens incorporate 60–86% of dissolved inorganic carbon (DIC) into lipids, and thus considerably more than what can be predicted from known metabolic pathways (~40% contribution). In slurry experiments amended with the marine methylotroph Methanococcoides methylutens, up to 12% of methane was produced from CO2, indicating that CO2-dependent methanogenesis is an alternative methanogenic pathway and suggesting that obligate methylotrophic methanogens grow in fact mixotrophically on methyl compounds and DIC. Although methane formation from methanol is the primary pathway of methanogenesis, the observed high DIC incorporation into lipids is likely linked to CO2-dependent methanogenesis, which was triggered when methane production rates were low. Since methylotrophic methanogenesis rates are much lower in marine sediments than under optimal conditions in pure culture, CO2 conversion to methane is an important but previously overlooked methanogenic process in sediments for methylotrophic methanogens.
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Affiliation(s)
- Xiuran Yin
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM - Center for Marine Environmental Sciences, Bremen, Germany.,International Max-Planck Research School for Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Weichao Wu
- MARUM - Center for Marine Environmental Sciences, Bremen, Germany.,Department of Geosciences, University of Bremen, Bremen, Germany.,Department of Biogeochemistry of Agroecosystems, University of Goettingen, Goettingen, Germany
| | - Mara Maeke
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,International Max-Planck Research School for Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Ajinkya C Kulkarni
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM - Center for Marine Environmental Sciences, Bremen, Germany.,International Max-Planck Research School for Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Oluwatobi E Oni
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM - Center for Marine Environmental Sciences, Bremen, Germany
| | - Jenny Wendt
- MARUM - Center for Marine Environmental Sciences, Bremen, Germany.,Department of Geosciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, Bremen, Germany.,Department of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany. .,MARUM - Center for Marine Environmental Sciences, Bremen, Germany.
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Gogoi P, Kanaujia SP. Role of Structural Features in Oligomerization, Active-Site Integrity and Ligand Binding of Ribose-1,5-Bisphosphate Isomerase. Comput Struct Biotechnol J 2019; 17:333-344. [PMID: 30923607 PMCID: PMC6423476 DOI: 10.1016/j.csbj.2019.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/18/2019] [Accepted: 02/23/2019] [Indexed: 11/18/2022] Open
Abstract
Pentose bisphosphate pathway, exclusively found in archaea, is similar to the pentose phosphate pathway present in bacteria and eukarya. In pentose bisphosphate pathway, the conversion of ribose moieties of nucleosides into 3-phosphoglycerate (3-PGA) involves multiple steps; one of them being the conversion of ribose-1,5-bisphosphate (R15P) to ribulose-1,5-bisphosphate (RuBP) catalyzed by an enzyme ribose-1,5-bisphosphate isomerase (R15Pi). The availability of the three-dimensional structure of R15Pi had facilitated the understanding of various structural and functional aspects of the enzyme. Nevertheless, the structure of R15Pi also left several significant questions unanswered that would aid in understanding the structure-function relationship of the enzyme. Thus, we have taken up a computational approach to further understand the role of various structural features of the enzyme R15Pi. Results obtained from molecular dynamics (MD) simulations aided in understanding the obligation of the enzyme R15Pi to oligomerize and also in deciphering the role of catalytic residue(s) in structural stability. Identification of invariant water molecules of the enzyme R15Pi helped in discerning their significance at the active-site pocket and structurally important regions. Further, molecular docking studies allowed the identification of the amino acid residues essential for holding the substrate (R15P) or product (RuBP) in the vicinity of the active site of the enzyme R15Pi. Interestingly, results of the molecular docking studies assisted in the identification of an “alternate binding site” for the substrate, R15P. Finally, based on these results, we propose a mechanism of “substrate sliding” for the enzyme R15Pi. Hexameric state is obligatory for the functionality of R15Pi. Cysteine is more important catalytic residue than aspartate. Invariant water molecules are conserved at the active site and structurally important areas. The substrate does not directly bind to the active site. The substrate slides from the “initial binding site” to the active site.
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Key Words
- 3-PGA, 3-phosphoglycerate
- ADP-R1P, ADP-dependentribose-1-phosphate
- ASU, asymmetric unit
- EFBE, estimated free energy of binding
- Invariant water molecule
- LGA, Lamarckian genetic algorithm
- MD, molecular dynamics
- Molecular docking
- Molecular dynamics simulation
- NMP, nucleoside 5′-monophosphate
- Nucleoside 5′-monophosphate degradation pathway
- R15P, ribose-1,5-bisphosphate
- R15Pi, ribose-1,5-bisphosphate isomerase
- R1P, ribose-1-phosphate
- RMSD, root mean square deviation
- RMSF, root mean square fluctuation
- Ribose-1,5-bisphosphate
- Ribulose-1,5-bisphosphate
- RuBP, ribulose-1,5-bisphosphate
- RuBisCO, ribulose-1,5-bisphosphate carboxylase/oxygenase
- SASA, solvent accessible surface area
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The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism. Microbiol Mol Biol Rev 2018; 83:83/1/e00040-18. [PMID: 30567937 DOI: 10.1128/mmbr.00040-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ribosyl 1,5-bisphosphate (PRibP) was discovered 65 years ago and was believed to be an important intermediate in ribonucleotide metabolism, a role immediately taken over by its "big brother" phosphoribosyldiphosphate. Only recently has PRibP come back into focus as an important player in the metabolism of ribonucleotides with the discovery of the pentose bisphosphate pathway that comprises, among others, the intermediates PRibP and ribulose 1,5-bisphosphate (cf. ribose 5-phosphate and ribulose 5-phosphate of the pentose phosphate pathway). Enzymes of several pathways produce and utilize PRibP not only in ribonucleotide metabolism but also in the catabolism of phosphonates, i.e., compounds containing a carbon-phosphorus bond. Pathways for PRibP metabolism are found in all three domains of life, most prominently among organisms of the archaeal domain, where they have been identified either experimentally or by bioinformatic analysis within all of the four main taxonomic groups, Euryarchaeota, TACK, DPANN, and Asgard. Advances in molecular genetics of archaea have greatly improved the understanding of the physiology of PRibP metabolism, and reconciliation of molecular enzymology and three-dimensional structure analysis of enzymes producing or utilizing PRibP emphasize the versatility of the compound. Finally, PRibP is also an effector of several metabolic activities in many organisms, including higher organisms such as mammals. In the present review, we describe all aspects of PRibP metabolism, with emphasis on the biochemical, genetic, and physiological aspects of the enzymes that produce or utilize PRibP. The inclusion of high-resolution structures of relevant enzymes that bind PRibP provides evidence for the flexibility and importance of the compound in metabolism.
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Hunt KA, Jennings RM, Inskeep WP, Carlson RP. Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community. PLoS Comput Biol 2018; 14:e1006431. [PMID: 30260956 PMCID: PMC6177205 DOI: 10.1371/journal.pcbi.1006431] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 10/09/2018] [Accepted: 08/13/2018] [Indexed: 11/18/2022] Open
Abstract
Interactions among microbial community members can lead to emergent properties, such as enhanced productivity, stability, and robustness. Iron-oxide mats in acidic (pH 2-4), high-temperature (> 65 °C) springs of Yellowstone National Park contain relatively simple microbial communities and are well-characterized geochemically. Consequently, these communities are excellent model systems for studying the metabolic activity of individual populations and key microbial interactions. The primary goals of the current study were to integrate data collected in situ with in silico calculations across process-scales encompassing enzymatic activity, cellular metabolism, community interactions, and ecosystem biogeochemistry, as well as to predict and quantify the functional limits of autotroph-heterotroph interactions. Metagenomic and transcriptomic data were used to reconstruct carbon and energy metabolisms of an important autotroph (Metallosphaera yellowstonensis) and heterotroph (Geoarchaeum sp. OSPB) from the studied Fe(III)-oxide mat communities. Standard and hybrid elementary flux mode and flux balance analyses of metabolic models predicted cellular- and community-level metabolic acclimations to simulated environmental stresses, respectively. In situ geochemical analyses, including oxygen depth-profiles, Fe(III)-oxide deposition rates, stable carbon isotopes and mat biomass concentrations, were combined with cellular models to explore autotroph-heterotroph interactions important to community structure-function. Integration of metabolic modeling with in situ measurements, including the relative population abundance of autotrophs to heterotrophs, demonstrated that Fe(III)-oxide mat communities operate at their maximum total community growth rate (i.e. sum of autotroph and heterotroph growth rates), as opposed to net community growth rate (i.e. total community growth rate subtracting autotroph consumed by heterotroph), as predicted from the maximum power principle. Integration of multiscale data with ecological theory provides a basis for predicting autotroph-heterotroph interactions and community-level cellular organization.
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Affiliation(s)
- Kristopher A. Hunt
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, United States of America
| | - Ryan M. Jennings
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | - William P. Inskeep
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
- * E-mail: (WPI); (RPC)
| | - Ross P. Carlson
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, United States of America
- * E-mail: (WPI); (RPC)
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Quehenberger J, Shen L, Albers SV, Siebers B, Spadiut O. Sulfolobus - A Potential Key Organism in Future Biotechnology. Front Microbiol 2017; 8:2474. [PMID: 29312184 PMCID: PMC5733018 DOI: 10.3389/fmicb.2017.02474] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/28/2017] [Indexed: 11/13/2022] Open
Abstract
Extremophilic organisms represent a potentially valuable resource for the development of novel bioprocesses. They can act as a source for stable enzymes and unique biomaterials. Extremophiles are capable of carrying out microbial processes and biotransformations under extremely hostile conditions. Extreme thermoacidophilic members of the well-characterized genus Sulfolobus are outstanding in their ability to thrive at both high temperatures and low pH. This review gives an overview of the biological system Sulfolobus including its central carbon metabolism and the development of tools for its genetic manipulation. We highlight findings of commercial relevance and focus on potential industrial applications. Finally, the current state of bioreactor cultivations is summarized and we discuss the use of Sulfolobus species in biorefinery applications.
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Affiliation(s)
- Julian Quehenberger
- Research Division Biochemical Engineering, Faculty of Technical Chemistry, Institute of Chemical, Environmental and Biological Engineering, Vienna University of Technology, Vienna, Austria
| | - Lu Shen
- Department of Molecular Enzyme Technology and Biochemistry, Faculty of Chemistry – Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II-Microbiology, Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Faculty of Chemistry – Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Oliver Spadiut
- Research Division Biochemical Engineering, Faculty of Technical Chemistry, Institute of Chemical, Environmental and Biological Engineering, Vienna University of Technology, Vienna, Austria
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Straub CT, Zeldes BM, Schut GJ, Adams MWW, Kelly RM. Extremely thermophilic energy metabolisms: biotechnological prospects. Curr Opin Biotechnol 2017; 45:104-112. [DOI: 10.1016/j.copbio.2017.02.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/14/2017] [Accepted: 02/24/2017] [Indexed: 12/16/2022]
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24
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Le SB, Heggeset TMB, Haugen T, Nærdal I, Brautaset T. 6-Phosphofructokinase and ribulose-5-phosphate 3-epimerase in methylotrophic Bacillus methanolicus ribulose monophosphate cycle. Appl Microbiol Biotechnol 2017; 101:4185-4200. [DOI: 10.1007/s00253-017-8173-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/26/2017] [Accepted: 01/31/2017] [Indexed: 11/29/2022]
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A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea. Nat Commun 2017; 8:14007. [PMID: 28082747 PMCID: PMC5241800 DOI: 10.1038/ncomms14007] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 11/18/2016] [Indexed: 11/08/2022] Open
Abstract
Two enzymes are considered to be unique to the photosynthetic Calvin–Benson cycle: ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for CO2 fixation, and phosphoribulokinase (PRK). Some archaea possess bona fide RuBisCOs, despite not being photosynthetic organisms, but are thought to lack PRK. Here we demonstrate the existence in methanogenic archaea of a carbon metabolic pathway involving RuBisCO and PRK, which we term ‘reductive hexulose-phosphate' (RHP) pathway. These archaea possess both RuBisCO and a catalytically active PRK whose crystal structure resembles that of photosynthetic bacterial PRK. Capillary electrophoresis-mass spectrometric analysis of metabolites reveals that the RHP pathway, which differs from the Calvin–Benson cycle only in a few steps, is active in vivo. Our work highlights evolutionary and functional links between RuBisCO-mediated carbon metabolic pathways in methanogenic archaea and photosynthetic organisms. Whether the RHP pathway allows for autotrophy (that is, growth exclusively with CO2 as carbon source) remains unknown. Although not photosynthetic, some archaea possess RuBisCO, one of the enzymes characteristic of the photosynthetic Calvin-Benson cycle, but apparently lack another one, phosphoribulokinase (PRK). Here the authors describe a carbon metabolic pathway in methanogenic archaea, involving RuBisCO and PRK.
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26
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An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism. Nat Commun 2016; 7:13446. [PMID: 27857065 PMCID: PMC5120207 DOI: 10.1038/ncomms13446] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 10/05/2016] [Indexed: 01/14/2023] Open
Abstract
Routes for cysteine biosynthesis are still unknown in many archaea. Here we find that the hyperthermophilic archaeon Thermococcus kodakarensis generates cysteine from serine via O-phosphoserine, in addition to the classical route from 3-phosphoglycerate. The protein responsible for serine phosphorylation is encoded by TK0378, annotated as a chromosome partitioning protein ParB. The TK0378 protein utilizes ADP as the phosphate donor, but in contrast to previously reported ADP-dependent kinases, recognizes a non-sugar substrate. Activity is specific towards free serine, and not observed with threonine, homoserine and serine residues within a peptide. Genetic analyses suggest that TK0378 is involved in serine assimilation and clearly responsible for cysteine biosynthesis from serine. TK0378 homologs, present in Thermococcales and Desulfurococcales, are most likely not ParB proteins and constitute a group of kinases involved in serine utilization. Archaea metabolism has unique adaptations to hostile environments. Here Makino et al. describe an unusual ADP-dependent kinase that phosphorylates free serine to O-phosphoserine and participates in an additional cysteine biosynthetic pathway in the archaeon Thermococcus kodakarensis.
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27
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Wolf J, Stark H, Fafenrot K, Albersmeier A, Pham TK, Müller KB, Meyer BH, Hoffmann L, Shen L, Albaum SP, Kouril T, Schmidt-Hohagen K, Neumann-Schaal M, Bräsen C, Kalinowski J, Wright PC, Albers SV, Schomburg D, Siebers B. A systems biology approach reveals major metabolic changes in the thermoacidophilic archaeon Sulfolobus solfataricus in response to the carbon source L-fucose versus D-glucose. Mol Microbiol 2016; 102:882-908. [PMID: 27611014 DOI: 10.1111/mmi.13498] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2016] [Indexed: 12/01/2022]
Abstract
Archaea are characterised by a complex metabolism with many unique enzymes that differ from their bacterial and eukaryotic counterparts. The thermoacidophilic archaeon Sulfolobus solfataricus is known for its metabolic versatility and is able to utilize a great variety of different carbon sources. However, the underlying degradation pathways and their regulation are often unknown. In this work, the growth on different carbon sources was analysed, using an integrated systems biology approach. The comparison of growth on L-fucose and D-glucose allows first insights into the genome-wide changes in response to the two carbon sources and revealed a new pathway for L-fucose degradation in S. solfataricus. During growth on L-fucose major changes in the central carbon metabolic network, as well as an increased activity of the glyoxylate bypass and the 3-hydroxypropionate/4-hydroxybutyrate cycle were observed. Within the newly discovered pathway for L-fucose degradation the following key reactions were identified: (i) L-fucose oxidation to L-fuconate via a dehydrogenase, (ii) dehydration to 2-keto-3-deoxy-L-fuconate via dehydratase, (iii) 2-keto-3-deoxy-L-fuconate cleavage to pyruvate and L-lactaldehyde via aldolase and (iv) L-lactaldehyde conversion to L-lactate via aldehyde dehydrogenase. This pathway as well as L-fucose transport shows interesting overlaps to the D-arabinose pathway, representing another example for pathway promiscuity in Sulfolobus species.
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Affiliation(s)
- Jacqueline Wolf
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Helge Stark
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Katharina Fafenrot
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
| | - Andreas Albersmeier
- Center for Biotechnology - CeBiTec, Universität Bielefeld, Bielefeld, 33615, Germany
| | - Trong K Pham
- Departement of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD, UK
| | - Katrin B Müller
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Benjamin H Meyer
- Molecular Biology of Archaea, Institute for Biology II - Microbiology, Universität Freiburg, Freiburg, 79104, Germany
| | - Lena Hoffmann
- Molecular Biology of Archaea, Institute for Biology II - Microbiology, Universität Freiburg, Freiburg, 79104, Germany
| | - Lu Shen
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
| | - Stefan P Albaum
- Center for Biotechnology - CeBiTec, Universität Bielefeld, Bielefeld, 33615, Germany
| | - Theresa Kouril
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
| | - Kerstin Schmidt-Hohagen
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Meina Neumann-Schaal
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, Universität Bielefeld, Bielefeld, 33615, Germany
| | - Phillip C Wright
- Departement of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD, UK
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute for Biology II - Microbiology, Universität Freiburg, Freiburg, 79104, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
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Nitrogen Assimilation, Abiotic Stress and Glucose 6-Phosphate Dehydrogenase: The Full Circle of Reductants. PLANTS 2016; 5:plants5020024. [PMID: 27187489 PMCID: PMC4931404 DOI: 10.3390/plants5020024] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 04/28/2016] [Accepted: 05/03/2016] [Indexed: 02/06/2023]
Abstract
Glucose 6 phosphate dehydrogenase (G6PDH; EC 1.1.1.49) is well-known as the main regulatory enzyme of the oxidative pentose phosphate pathway (OPPP) in living organisms. Namely, in Planta, different G6PDH isoforms may occur, generally localized in cytosol and plastids/chloroplasts. These enzymes are differently regulated by distinct mechanisms, still far from being defined in detail. In the last decades, a pivotal function for plant G6PDHs during the assimilation of nitrogen, providing reductants for enzymes involved in nitrate reduction and ammonium assimilation, has been described. More recently, several studies have suggested a main role of G6PDH to counteract different stress conditions, among these salinity and drought, with the involvement of an ABA depending signal. In the last few years, this recognized vision has been greatly widened, due to studies clearly showing the non-conventional subcellular localization of the different G6PDHs, and the peculiar regulation of the different isoforms. The whole body of these considerations suggests a central question: how do the plant cells distribute the reductants coming from G6PDH and balance their equilibrium? This review explores the present knowledge about these mechanisms, in order to propose a scheme of distribution of reductants produced by G6PDH during nitrogen assimilation and stress.
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29
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Moran JJ, Whitmore LM, Isern NG, Romine MF, Riha KM, Inskeep WP, Kreuzer HW. Formaldehyde as a carbon and electron shuttle between autotroph and heterotroph populations in acidic hydrothermal vents of Norris Geyser Basin, Yellowstone National Park. Extremophiles 2016; 20:291-9. [PMID: 26995682 DOI: 10.1007/s00792-016-0821-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/01/2016] [Indexed: 11/26/2022]
Abstract
The Norris Geyser Basin in Yellowstone National Park contains a large number of hydrothermal systems, which host microbial populations supported by primary productivity associated with a suite of chemolithotrophic metabolisms. We demonstrate that Metallosphaera yellowstonensis MK1, a facultative autotrophic archaeon isolated from a hyperthermal acidic hydrous ferric oxide (HFO) spring in Norris Geyser Basin, excretes formaldehyde during autotrophic growth. To determine the fate of formaldehyde in this low organic carbon environment, we incubated native microbial mat (containing M. yellowstonensis) from a HFO spring with (13)C-formaldehyde. Isotopic analysis of incubation-derived CO2 and biomass showed that formaldehyde was both oxidized and assimilated by members of the community. Autotrophy, formaldehyde oxidation, and formaldehyde assimilation displayed different sensitivities to chemical inhibitors, suggesting that distinct sub-populations in the mat selectively perform these functions. Our results demonstrate that electrons originally resulting from iron oxidation can energetically fuel autotrophic carbon fixation and associated formaldehyde excretion, and that formaldehyde is both oxidized and assimilated by different organisms within the native microbial community. Thus, formaldehyde can effectively act as a carbon and electron shuttle connecting the autotrophic, iron oxidizing members with associated heterotrophic members in the HFO community.
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Affiliation(s)
- James J Moran
- Chemical and Biological Signature Science Group, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Laura M Whitmore
- Chemical and Biological Signature Science Group, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Marine Science, University of Southern Mississippi, Stennis Space Center, MS, 39529, USA
| | - Nancy G Isern
- Environmental and Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Margaret F Romine
- Microbiology Department, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Krystin M Riha
- Chemical and Biological Signature Science Group, Pacific Northwest National Laboratory, Richland, WA, USA
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Helen W Kreuzer
- Chemical and Biological Signature Science Group, Pacific Northwest National Laboratory, Richland, WA, USA
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Carbone V, Schofield LR, Zhang Y, Sang C, Dey D, Hannus IM, Martin WF, Sutherland-Smith AJ, Ronimus RS. Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn-Glycerol-1-phosphate Dehydrogenase. J Biol Chem 2015; 290:21690-704. [PMID: 26175150 DOI: 10.1074/jbc.m115.647461] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Indexed: 01/23/2023] Open
Abstract
One of the most critical events in the origins of cellular life was the development of lipid membranes. Archaea use isoprenoid chains linked via ether bonds to sn-glycerol 1-phosphate (G1P), whereas bacteria and eukaryotes use fatty acids attached via ester bonds to enantiomeric sn-glycerol 3-phosphate. NAD(P)H-dependent G1P dehydrogenase (G1PDH) forms G1P and has been proposed to have played a crucial role in the speciation of the Archaea. We present here, to our knowledge, the first structures of archaeal G1PDH from the hyperthermophilic methanogen Methanocaldococcus jannaschii with bound substrate dihydroxyacetone phosphate, product G1P, NADPH, and Zn(2+) cofactor. We also biochemically characterized the enzyme with respect to pH optimum, cation specificity, and kinetic parameters for dihydroxyacetone phosphate and NAD(P)H. The structures provide key evidence for the reaction mechanism in the stereospecific addition for the NAD(P)H-based pro-R hydrogen transfer and the coordination of the Zn(2+) cofactor during catalysis. Structure-based phylogenetic analyses also provide insight into the origins of G1PDH.
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Affiliation(s)
- Vincenzo Carbone
- From AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Linley R Schofield
- From AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Yanli Zhang
- From AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Carrie Sang
- From AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Debjit Dey
- From AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Ingegerd M Hannus
- From AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - William F Martin
- Institute for Molecular Evolution, Heinrich Heine University, University of Düsseldorf, 40225 Düsseldorf, Germany, and
| | | | - Ron S Ronimus
- From AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand,
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Pickl A, Schönheit P. The oxidative pentose phosphate pathway in the haloarchaeon Haloferax volcanii involves a novel type of glucose-6-phosphate dehydrogenase--The archaeal Zwischenferment. FEBS Lett 2015; 589:1105-11. [PMID: 25836736 DOI: 10.1016/j.febslet.2015.03.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 10/23/2022]
Abstract
The oxidative pentose phosphate pathway (OPPP), catalyzing the oxidation of glucose-6-phosphate to ribulose-5-phosphate is ubiquitous in eukarya and bacteria but has not yet been reported in archaea. In haloarchaea a putative 6-phosphogluconate dehydrogenase (6PGDH) is annotated, whereas a gene coding for glucose-6-phosphate dehydrogenase (Glc6PDH) could not be identified. Here we report the purification and characterization of a novel type of Glc6PDH in Haloferax volcanii that is not related to bacterial and eukaryal Glc6PDHs and the encoding gene is designated as azf (archaeal zwischenferment). Further, recombinant H. volcanii 6PGDH was characterized. Deletion mutant analyses indicate that both, Glc6PDH and 6PGDH, are functionally involved in pentose phosphate formation in vivo. This is the first report on the operation of the OPPP in the domain of archaea.
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Affiliation(s)
- Andreas Pickl
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | - Peter Schönheit
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany.
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32
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Aono R, Sato T, Imanaka T, Atomi H. A pentose bisphosphate pathway for nucleoside degradation in Archaea. Nat Chem Biol 2015; 11:355-60. [PMID: 25822915 DOI: 10.1038/nchembio.1786] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 02/27/2015] [Indexed: 01/08/2023]
Abstract
Owing to the absence of the pentose phosphate pathway, the degradation pathway for the ribose moieties of nucleosides is unknown in Archaea. Here, in the archaeon Thermococcus kodakarensis, we identified a metabolic network that links the pentose moieties of nucleosides or nucleotides to central carbon metabolism. The network consists of three nucleoside phosphorylases, an ADP-dependent ribose-1-phosphate kinase and two enzymes of a previously identified NMP degradation pathway, ribose-1,5-bisphosphate isomerase and type III ribulose-1,5-bisphosphate carboxylase/oxygenase. Ribose 1,5-bisphosphate and ribulose 1,5-bisphosphate are intermediates of this pathway, which is thus designated the pentose bisphosphate pathway.
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Affiliation(s)
- Riku Aono
- 1] Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan. [2] Japan Society for the Promotion of Science, Tokyo, Japan
| | - Takaaki Sato
- 1] Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan. [2] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology, Tokyo, Japan
| | - Tadayuki Imanaka
- 1] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology, Tokyo, Japan. [2] Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kyoto, Japan
| | - Haruyuki Atomi
- 1] Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan. [2] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology, Tokyo, Japan
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Abstract
Genomic analysis of H. salinarum indicated that the de novo pathway for aromatic amino acid (AroAA) biosynthesis does not follow the classical pathway but begins from non-classical precursors, as is the case for M. jannaschii. The first two steps in the pathway were predicted to be carried out by genes OE1472F and OE1475F, while the 3rd step follows the canonical pathway involving gene OE1477R. The functions of these genes and their products were tested by biochemical and genetic methods. In this study, we provide evidence that supports the role of proteins OE1472F and OE1475F catalyzing consecutive enzymatic reactions leading to the production of 3-dehydroquinate (DHQ), after which AroAA production proceeds via the canonical pathway starting with the formation of DHS (dehydroshikimate), catalyzed by the product of ORF OE1477R. Nutritional requirements and AroAA uptake studies of the mutants gave results that were consistent with the proposed roles of these ORFs in AroAA biosynthesis. DNA microarray data indicated that the 13 genes of the canonical pathway appear to be utilised for AroAA biosynthesis in H. salinarum, as they are differentially expressed when cells are grown in medium lacking AroAA.
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Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation. Microbiol Mol Biol Rev 2014; 78:89-175. [PMID: 24600042 DOI: 10.1128/mmbr.00041-13] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The metabolism of Archaea, the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya. However, this metabolic complexity in Archaea is accompanied by the absence of many "classical" pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of "new," unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea. In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya. Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.
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Guo X, Yin H, Liang Y, Hu Q, Zhou X, Xiao Y, Ma L, Zhang X, Qiu G, Liu X. Comparative genome analysis reveals metabolic versatility and environmental adaptations of Sulfobacillus thermosulfidooxidans strain ST. PLoS One 2014; 9:e99417. [PMID: 24940621 PMCID: PMC4062416 DOI: 10.1371/journal.pone.0099417] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 05/14/2014] [Indexed: 12/21/2022] Open
Abstract
The genus Sulfobacillus is a cohort of mildly thermophilic or thermotolerant acidophiles within the phylum Firmicutes and requires extremely acidic environments and hypersalinity for optimal growth. However, our understanding of them is still preliminary partly because few genome sequences are available. Here, the draft genome of Sulfobacillus thermosulfidooxidans strain ST was deciphered to obtain a comprehensive insight into the genetic content and to understand the cellular mechanisms necessary for its survival. Furthermore, the expressions of key genes related with iron and sulfur oxidation were verified by semi-quantitative RT-PCR analysis. The draft genome sequence of Sulfobacillus thermosulfidooxidans strain ST, which encodes 3225 predicted coding genes on a total length of 3,333,554 bp and a 48.35% G+C, revealed the high degree of heterogeneity with other Sulfobacillus species. The presence of numerous transposases, genomic islands and complete CRISPR/Cas defence systems testifies to its dynamic evolution consistent with the genome heterogeneity. As expected, S. thermosulfidooxidans encodes a suit of conserved enzymes required for the oxidation of inorganic sulfur compounds (ISCs). The model of sulfur oxidation in S. thermosulfidooxidans was proposed, which showed some different characteristics from the sulfur oxidation of Gram-negative A. ferrooxidans. Sulfur oxygenase reductase and heterodisulfide reductase were suggested to play important roles in the sulfur oxidation. Although the iron oxidation ability was observed, some key proteins cannot be identified in S. thermosulfidooxidans. Unexpectedly, a predicted sulfocyanin is proposed to transfer electrons in the iron oxidation. Furthermore, its carbon metabolism is rather flexible, can perform the transformation of pentose through the oxidative and non-oxidative pentose phosphate pathways and has the ability to take up small organic compounds. It encodes a multitude of heavy metal resistance systems to adapt the heavy metal-containing environments.
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Affiliation(s)
- Xue Guo
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Qi Hu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xishu Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yunhua Xiao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Liyuan Ma
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Guanzhou Qiu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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Zhi XY, Yao JC, Li HW, Huang Y, Li WJ. Genome-wide identification, domain architectures and phylogenetic analysis provide new insights into the early evolution of shikimate pathway in prokaryotes. Mol Phylogenet Evol 2014; 75:154-64. [DOI: 10.1016/j.ympev.2014.02.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/14/2014] [Accepted: 02/17/2014] [Indexed: 11/30/2022]
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38
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Beam JP, Jay ZJ, Kozubal MA, Inskeep WP. Niche specialization of novel Thaumarchaeota to oxic and hypoxic acidic geothermal springs of Yellowstone National Park. ISME JOURNAL 2013; 8:938-51. [PMID: 24196321 DOI: 10.1038/ismej.2013.193] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/06/2013] [Accepted: 09/17/2013] [Indexed: 11/09/2022]
Abstract
Novel lineages of the phylum Thaumarchaeota are endemic to thermal habitats, and may exhibit physiological capabilities that are not yet observed in members of this phylum. The primary goals of this study were to conduct detailed phylogenetic and functional analyses of metagenome sequence assemblies of two different thaumarchaeal populations found in high-temperature (65-72 °C), acidic (pH~3) iron oxide and sulfur sediment environments of Yellowstone National Park (YNP). Metabolic reconstruction was coupled with detailed geochemical measurements of each geothermal habitat and reverse-transcriptase PCR to confirm the in situ activity of these populations. Phylogenetic analyses of ribosomal and housekeeping proteins place these archaea near the root of the thaumarchaeal branch. Metabolic reconstruction suggests that these populations are chemoorganotrophic and couple growth with the reduction of oxygen or nitrate in iron oxide habitats, or sulfur in hypoxic sulfur sediments. The iron oxide population has the potential for growth via the oxidation of sulfide to sulfate using a novel reverse sulfate reduction pathway. Possible carbon sources include aromatic compounds (for example, 4-hydroxyphenylacetate), complex carbohydrates (for example, starch), oligopeptides and amino acids. Both populations contain a type III ribulose bisphosphate carboxylase/oxygenase used for carbon dioxide fixation or adenosine monophosphate salvage. No evidence for the oxidation of ammonia was obtained from de novo sequence assemblies. Our results show that thermoacidophilic Thaumarchaeota from oxic iron mats and hypoxic sulfur sediments exhibit different respiratory machinery depending on the presence of oxygen versus sulfide, represent deeply rooted lineages within the phylum Thaumarchaeota and are endemic to numerous sites in YNP.
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Affiliation(s)
- Jacob P Beam
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Zackary J Jay
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Mark A Kozubal
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - William P Inskeep
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
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Spang A, Poehlein A, Offre P, Zumbrägel S, Haider S, Rychlik N, Nowka B, Schmeisser C, Lebedeva EV, Rattei T, Böhm C, Schmid M, Galushko A, Hatzenpichler R, Weinmaier T, Daniel R, Schleper C, Spieck E, Streit W, Wagner M. The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol 2012; 14:3122-45. [PMID: 23057602 DOI: 10.1111/j.1462-2920.2012.02893.x] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 09/01/2012] [Indexed: 01/21/2023]
Abstract
The cohort of the ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota is a diverse, widespread and functionally important group of microorganisms in many ecosystems. However, our understanding of their biology is still very rudimentary in part because all available genome sequences of this phylum are from members of the Nitrosopumilus cluster. Here we report on the complete genome sequence of Candidatus Nitrososphaera gargensis obtained from an enrichment culture, representing a different evolutionary lineage of AOA frequently found in high numbers in many terrestrial environments. With its 2.83 Mb the genome is much larger than that of other AOA. The presence of a high number of (active) IS elements/transposases, genomic islands, gene duplications and a complete CRISPR/Cas defence system testifies to its dynamic evolution consistent with low degree of synteny with other thaumarchaeal genomes. As expected, the repertoire of conserved enzymes proposed to be required for archaeal ammonia oxidation is encoded by N. gargensis, but it can also use urea and possibly cyanate as alternative ammonia sources. Furthermore, its carbon metabolism is more flexible at the central pyruvate switch point, encompasses the ability to take up small organic compounds and might even include an oxidative pentose phosphate pathway. Furthermore, we show that thaumarchaeota produce cofactor F420 as well as polyhydroxyalkanoates. Lateral gene transfer from bacteria and euryarchaeota has contributed to the metabolic versatility of N. gargensis. This organisms is well adapted to its niche in a heavy metal-containing thermal spring by encoding a multitude of heavy metal resistance genes, chaperones and mannosylglycerate as compatible solute and has the genetic ability to respond to environmental changes by signal transduction via a large number of two-component systems, by chemotaxis and flagella-mediated motility and possibly even by gas vacuole formation. These findings extend our understanding of thaumarchaeal evolution and physiology and offer many testable hypotheses for future experimental research on these nitrifiers.
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Affiliation(s)
- Anja Spang
- Department of Genetics in Ecology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria
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Enzymatic characterization of AMP phosphorylase and ribose-1,5-bisphosphate isomerase functioning in an archaeal AMP metabolic pathway. J Bacteriol 2012; 194:6847-55. [PMID: 23065974 DOI: 10.1128/jb.01335-12] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AMP phosphorylase (AMPpase), ribose-1,5-bisphosphate (R15P) isomerase, and type III ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) have been proposed to constitute a novel pathway involved in AMP metabolism in the Archaea. Here we performed a biochemical examination of AMPpase and R15P isomerase from Thermococcus kodakarensis. R15P isomerase was specific for the α-anomer of R15P and did not recognize other sugar compounds. We observed that activity was extremely low with the substrate R15P alone but was dramatically activated in the presence of AMP. Using AMP-activated R15P isomerase, we reevaluated the substrate specificity of AMPpase. AMPpase exhibited phosphorylase activity toward CMP and UMP in addition to AMP. The [S]-v plot (plot of velocity versus substrate concentration) of the enzyme toward AMP was sigmoidal, with an increase in activity observed at concentrations higher than approximately 3 mM. The behavior of the two enzymes toward AMP indicates that the pathway is intrinsically designed to prevent excess degradation of intracellular AMP. We further examined the formation of 3-phosphoglycerate from AMP, CMP, and UMP in T. kodakarensis cell extracts. 3-Phosphoglycerate generation was observed from AMP alone, and from CMP or UMP in the presence of dAMP, which also activates R15P isomerase. 3-Phosphoglycerate was not formed when 2-carboxyarabinitol 1,5-bisphosphate, a Rubisco inhibitor, was added. The results strongly suggest that these enzymes are actually involved in the conversion of nucleoside monophosphates to 3-phosphoglycerate in T. kodakarensis.
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41
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Fructose degradation in the haloarchaeon Haloferax volcanii involves a bacterial type phosphoenolpyruvate-dependent phosphotransferase system, fructose-1-phosphate kinase, and class II fructose-1,6-bisphosphate aldolase. J Bacteriol 2012; 194:3088-97. [PMID: 22493022 DOI: 10.1128/jb.00200-12] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The halophilic archaeon Haloferax volcanii utilizes fructose as a sole carbon and energy source. Genes and enzymes involved in fructose uptake and degradation were identified by transcriptional analyses, deletion mutant experiments, and enzyme characterization. During growth on fructose, the gene cluster HVO_1495 to HVO_1499, encoding homologs of the five bacterial phosphotransferase system (PTS) components enzyme IIB (EIIB), enzyme I (EI), histidine protein (HPr), EIIA, and EIIC, was highly upregulated as a cotranscript. The in-frame deletion of HVO_1499, designated ptfC (ptf stands for phosphotransferase system for fructose) and encoding the putative fructose-specific membrane component EIIC, resulted in a loss of growth on fructose, which could be recovered by complementation in trans. Transcripts of HVO_1500 (pfkB) and HVO_1494 (fba), encoding putative fructose-1-phosphate kinase (1-PFK) and fructose-1,6-bisphosphate aldolase (FBA), respectively, as well as 1-PFK and FBA activities were specifically upregulated in fructose-grown cells. pfkB and fba knockout mutants did not grow on fructose, whereas growth on glucose was not inhibited, indicating the functional involvement of both enzymes in fructose catabolism. Recombinant 1-PFK and FBA obtained after homologous overexpression were characterized as having kinetic properties indicative of functional 1-PFK and a class II type FBA. From these data, we conclude that fructose uptake in H. volcanii involves a fructose-specific PTS generating fructose-1-phosphate, which is further converted via fructose-1,6-bisphosphate to triose phosphates by 1-PFK and FBA. This is the first report of the functional involvement of a bacterial-like PTS and of class II FBA in the sugar metabolism of archaea.
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Siebers B, Zaparty M, Raddatz G, Tjaden B, Albers SV, Bell SD, Blombach F, Kletzin A, Kyrpides N, Lanz C, Plagens A, Rampp M, Rosinus A, von Jan M, Makarova KS, Klenk HP, Schuster SC, Hensel R. The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota. PLoS One 2011; 6:e24222. [PMID: 22003381 PMCID: PMC3189178 DOI: 10.1371/journal.pone.0024222] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 08/08/2011] [Indexed: 11/18/2022] Open
Abstract
Here, we report on the complete genome sequence of the hyperthermophilic Crenarchaeum Thermoproteus tenax (strain Kra1, DSM 2078T) a type strain of the crenarchaeotal order Thermoproteales. Its circular 1.84-megabase genome harbors no extrachromosomal elements and 2,051 open reading frames are identified, covering 90.6% of the complete sequence, which represents a high coding density. Derived from the gene content, T. tenax is a representative member of the Crenarchaeota. The organism is strictly anaerobic and sulfur-dependent with optimal growth at 86°C and pH 5.6. One particular feature is the great metabolic versatility, which is not accompanied by a distinct increase of genome size or information density as compared to other Crenarchaeota. T. tenax is able to grow chemolithoautotrophically (CO2/H2) as well as chemoorganoheterotrophically in presence of various organic substrates. All pathways for synthesizing the 20 proteinogenic amino acids are present. In addition, two presumably complete gene sets for NADH:quinone oxidoreductase (complex I) were identified in the genome and there is evidence that either NADH or reduced ferredoxin might serve as electron donor. Beside the typical archaeal A0A1-ATP synthase, a membrane-bound pyrophosphatase is found, which might contribute to energy conservation. Surprisingly, all genes required for dissimilatory sulfate reduction are present, which is confirmed by growth experiments. Mentionable is furthermore, the presence of two proteins (ParA family ATPase, actin-like protein) that might be involved in cell division in Thermoproteales, where the ESCRT system is absent, and of genes involved in genetic competence (DprA, ComF) that is so far unique within Archaea.
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Affiliation(s)
- Bettina Siebers
- Faculty of Chemistry, Biofilm Centre, Molecular Enzyme Technology and Biochemistry, University of Duisburg-Essen, Essen, Germany
- * E-mail: (BS); (MZ)
| | - Melanie Zaparty
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Regensburg, Germany
- * E-mail: (BS); (MZ)
| | - Guenter Raddatz
- Max-Planck-Institute for Biological Cybernetics, Tübingen, Germany
| | - Britta Tjaden
- Prokaryotic RNA Biology, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Steve D. Bell
- Sir William Dunn School of Pathology, Oxford University, Oxford, United Kingdom
| | - Fabian Blombach
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Arnulf Kletzin
- Institute of Microbiology and Genetics, Technical University Darmstadt, Darmstadt, Germany
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Christa Lanz
- Genome Centre, Max-Planck-Institute for Developmental Biology, Tuebingen, Germany
| | - André Plagens
- Prokaryotic RNA Biology, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Markus Rampp
- Computer Centre Garching of the Max-Planck-Society (RZG), Max-Planck-Institute for Plasma Physics, München, Germany
| | - Andrea Rosinus
- Genome Centre, Max-Planck-Institute for Developmental Biology, Tuebingen, Germany
| | - Mathias von Jan
- DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hans-Peter Klenk
- DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Stephan C. Schuster
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Reinhard Hensel
- Prokaryotic RNA Biology, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
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Anderson I, Risso C, Holmes D, Lucas S, Copeland A, Lapidus A, Cheng JF, Bruce D, Goodwin L, Pitluck S, Saunders E, Brettin T, Detter JC, Han C, Tapia R, Larimer F, Land M, Hauser L, Woyke T, Lovley D, Kyrpides N, Ivanova N. Complete genome sequence of Ferroglobus placidus AEDII12DO. Stand Genomic Sci 2011; 5:50-60. [PMID: 22180810 PMCID: PMC3236036 DOI: 10.4056/sigs.2225018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ferroglobus placidus belongs to the order Archaeoglobales within the archaeal phylum Euryarchaeota. Strain AEDII12DO is the type strain of the species and was isolated from a shallow marine hydrothermal system at Vulcano, Italy. It is a hyperthermophilic, anaerobic chemolithoautotroph, but it can also use a variety of aromatic compounds as electron donors. Here we describe the features of this organism together with the complete genome sequence and annotation. The 2,196,266 bp genome with its 2,567 protein-coding and 55 RNA genes was sequenced as part of a DOE Joint Genome Institute Laboratory Sequencing Program (LSP) project.
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Affiliation(s)
- Iain Anderson
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Corresponding author:
| | - Carla Risso
- Microbiology Department, University of Massachusetts, Amherst, Massachusetts, USA
| | - Dawn Holmes
- Microbiology Department, University of Massachusetts, Amherst, Massachusetts, USA
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - David Bruce
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Lynne Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Samuel Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Elizabeth Saunders
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Thomas Brettin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - John C. Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Frank Larimer
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Miriam Land
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Loren Hauser
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Derek Lovley
- Microbiology Department, University of Massachusetts, Amherst, Massachusetts, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
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Yun SH, Kwon SO, Park GW, Kim JY, Kang SG, Lee JH, Chung YH, Kim S, Choi JS, Kim SI. Proteome analysis of Thermococcus onnurineus NA1 reveals the expression of hydrogen gene cluster under carboxydotrophic growth. J Proteomics 2011; 74:1926-33. [DOI: 10.1016/j.jprot.2011.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 04/18/2011] [Accepted: 05/06/2011] [Indexed: 10/18/2022]
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Anderson I, Scheuner C, Göker M, Mavromatis K, Hooper SD, Porat I, Klenk HP, Ivanova N, Kyrpides N. Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes. PLoS One 2011; 6:e20237. [PMID: 21633497 PMCID: PMC3102087 DOI: 10.1371/journal.pone.0020237] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 04/15/2011] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The extremely halophilic archaea are present worldwide in saline environments and have important biotechnological applications. Ten complete genomes of haloarchaea are now available, providing an opportunity for comparative analysis. METHODOLOGY/PRINCIPAL FINDINGS We report here the comparative analysis of five newly sequenced haloarchaeal genomes with five previously published ones. Whole genome trees based on protein sequences provide strong support for deep relationships between the ten organisms. Using a soft clustering approach, we identified 887 protein clusters present in all halophiles. Of these core clusters, 112 are not found in any other archaea and therefore constitute the haloarchaeal signature. Four of the halophiles were isolated from water, and four were isolated from soil or sediment. Although there are few habitat-specific clusters, the soil/sediment halophiles tend to have greater capacity for polysaccharide degradation, siderophore synthesis, and cell wall modification. Halorhabdus utahensis and Haloterrigena turkmenica encode over forty glycosyl hydrolases each, and may be capable of breaking down naturally occurring complex carbohydrates. H. utahensis is specialized for growth on carbohydrates and has few amino acid degradation pathways. It uses the non-oxidative pentose phosphate pathway instead of the oxidative pathway, giving it more flexibility in the metabolism of pentoses. CONCLUSIONS These new genomes expand our understanding of haloarchaeal catabolic pathways, providing a basis for further experimental analysis, especially with regard to carbohydrate metabolism. Halophilic glycosyl hydrolases for use in biofuel production are more likely to be found in halophiles isolated from soil or sediment.
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Affiliation(s)
- Iain Anderson
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
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Berg IA, Kockelkorn D, Ramos-Vera WH, Say RF, Zarzycki J, Hügler M, Alber BE, Fuchs G. Autotrophic carbon fixation in archaea. Nat Rev Microbiol 2010; 8:447-60. [DOI: 10.1038/nrmicro2365] [Citation(s) in RCA: 467] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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47
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Genomic organization and biochemistry of the ribulose monophosphate pathway and its application in biotechnology. Appl Microbiol Biotechnol 2009; 84:407-16. [DOI: 10.1007/s00253-009-2120-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 06/30/2009] [Accepted: 06/30/2009] [Indexed: 10/20/2022]
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Abstract
In spite of their common hypersaline environment, halophilic archaea are surprisingly different in their nutritional demands and metabolic pathways. The metabolic diversity of halophilic archaea was investigated at the genomic level through systematic metabolic reconstruction and comparative analysis of four completely sequenced species: Halobacterium salinarum, Haloarcula marismortui, Haloquadratum walsbyi, and the haloalkaliphile Natronomonas pharaonis. The comparative study reveals different sets of enzyme genes amongst halophilic archaea, e.g. in glycerol degradation, pentose metabolism, and folate synthesis. The carefully assessed metabolic data represent a reliable resource for future system biology approaches as it also links to current experimental data on (halo)archaea from the literature.
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Ohhata N, Yoshida N, Egami H, Katsuragi T, Tani Y, Takagi H. An extremely oligotrophic bacterium, Rhodococcus erythropolis N9T-4, isolated from crude oil. J Bacteriol 2007; 189:6824-31. [PMID: 17675378 PMCID: PMC2045210 DOI: 10.1128/jb.00872-07] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Accepted: 07/25/2007] [Indexed: 11/20/2022] Open
Abstract
Rhodococcus erythropolis N9T-4, which was isolated from crude oil, showed extremely oligotrophic growth and formed its colonies on a minimal salt medium solidified using agar or silica gel without any additional carbon source. N9T-4 did not grow under CO(2)-limiting conditions but could grow on a medium containing NaHCO(3) under the same conditions, suggesting that the oligotrophic growth of N9T-4 depends on CO(2). Proteomic analysis of N9T-4 revealed that two proteins, with molecular masses of 45 and 55 kDa, were highly induced under the oligotrophic conditions. The primary structures of these proteins exhibited striking similarities to those of methanol: N,N'-dimethyl-4-nitrosoaniline oxidoreductase and an aldehyde dehydrogenase from Rhodococcus sp. These enzyme activities were three times higher under oligotrophic conditions than under n-tetradecane-containing heterotrophic conditions, and gene disruption for the aldehyde dehydrogenase caused a lack of growth on the minimal salt medium. Furthermore, 3-hexulose 6-phosphate synthase and phospho-3-hexuloisomerase activities, which are key enzymes in the ribulose monophosphate pathway in methylotrophic bacteria, were detected specifically in the cell extract of oligotrophically grown N9T-4. These results suggest that CO(2) fixation involves methanol (formaldehyde) metabolism in the oligotrophic growth of R. erythropolis N9T-4.
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Affiliation(s)
- Naoko Ohhata
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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Jahn U, Huber H, Eisenreich W, Hügler M, Fuchs G. Insights into the autotrophic CO2 fixation pathway of the archaeon Ignicoccus hospitalis: comprehensive analysis of the central carbon metabolism. J Bacteriol 2007; 189:4108-19. [PMID: 17400748 PMCID: PMC1913412 DOI: 10.1128/jb.00047-07] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Ignicoccus hospitalis is an autotrophic hyperthermophilic archaeon that serves as a host for another parasitic/symbiotic archaeon, Nanoarchaeum equitans. In this study, the biosynthetic pathways of I. hospitalis were investigated by in vitro enzymatic analyses, in vivo (13)C-labeling experiments, and genomic analyses. Our results suggest the operation of a so far unknown pathway of autotrophic CO(2) fixation that starts from acetyl-coenzyme A (CoA). The cyclic regeneration of acetyl-CoA, the primary CO(2) acceptor molecule, has not been clarified yet. In essence, acetyl-CoA is converted into pyruvate via reductive carboxylation by pyruvate-ferredoxin oxidoreductase. Pyruvate-water dikinase converts pyruvate into phosphoenolpyruvate (PEP), which is carboxylated to oxaloacetate by PEP carboxylase. An incomplete citric acid cycle is operating: citrate is synthesized from oxaloacetate and acetyl-CoA by a (re)-specific citrate synthase, whereas a 2-oxoglutarate-oxidizing enzyme is lacking. Further investigations revealed that several special biosynthetic pathways that have recently been described for various archaea are operating. Isoleucine is synthesized via the uncommon citramalate pathway and lysine via the alpha-aminoadipate pathway. Gluconeogenesis is achieved via a reverse Embden-Meyerhof pathway using a novel type of fructose 1,6-bisphosphate aldolase. Pentosephosphates are formed from hexosephosphates via the suggested ribulose-monophosphate pathway, whereby formaldehyde is released from C-1 of hexose. The organism may not contain any sugar-metabolizing pathway. This comprehensive analysis of the central carbon metabolism of I. hospitalis revealed further evidence for the unexpected and unexplored diversity of metabolic pathways within the (hyperthermophilic) archaea.
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Affiliation(s)
- Ulrike Jahn
- Lehrstuhl Mikrobiologie und Archaeenzentrum, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
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