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Padalko A, Nair G, Sousa FL. Fusion/fission protein family identification in Archaea. mSystems 2024; 9:e0094823. [PMID: 38700364 PMCID: PMC11237513 DOI: 10.1128/msystems.00948-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
The majority of newly discovered archaeal lineages remain without a cultivated representative, but scarce experimental data from the cultivated organisms show that they harbor distinct functional repertoires. To unveil the ecological as well as evolutionary impact of Archaea from metagenomics, new computational methods need to be developed, followed by in-depth analysis. Among them is the genome-wide protein fusion screening performed here. Natural fusions and fissions of genes not only contribute to microbial evolution but also complicate the correct identification and functional annotation of sequences. The products of these processes can be defined as fusion (or composite) proteins, the ones consisting of two or more domains originally encoded by different genes and split proteins, and the ones originating from the separation of a gene in two (fission). Fusion identifications are required for proper phylogenetic reconstructions and metabolic pathway completeness assessments, while mappings between fused and unfused proteins can fill some of the existing gaps in metabolic models. In the archaeal genome-wide screening, more than 1,900 fusion/fission protein clusters were identified, belonging to both newly sequenced and well-studied lineages. These protein families are mainly associated with different types of metabolism, genetic, and cellular processes. Moreover, 162 of the identified fusion/fission protein families are archaeal specific, having no identified fused homolog within the bacterial domain. Our approach was validated by the identification of experimentally characterized fusion/fission cases. However, around 25% of the identified fusion/fission families lack functional annotations for both composite and split states, showing the need for experimental characterization in Archaea.IMPORTANCEGenome-wide fusion screening has never been performed in Archaea on a broad taxonomic scale. The overlay of multiple computational techniques allows the detection of a fine-grained set of predicted fusion/fission families, instead of rough estimations based on conserved domain annotations only. The exhaustive mapping of fused proteins to bacterial organisms allows us to capture fusion/fission families that are specific to archaeal biology, as well as to identify links between bacterial and archaeal lineages based on cooccurrence of taxonomically restricted proteins and their sequence features. Furthermore, the identification of poorly characterized lineage-specific fusion proteins opens up possibilities for future experimental and computational investigations. This approach enhances our understanding of Archaea in general and provides potential candidates for in-depth studies in the future.
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Affiliation(s)
- Anastasiia Padalko
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution, University of Vienna, Vienna, Austria
| | - Govind Nair
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Filipa L. Sousa
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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2
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Kirschning A. Why pyridoxal phosphate could be a functional predecessor of thiamine pyrophosphate and speculations on a primordial metabolism. RSC Chem Biol 2024; 5:508-517. [PMID: 38846080 PMCID: PMC11151856 DOI: 10.1039/d4cb00016a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/15/2024] [Indexed: 06/09/2024] Open
Abstract
The account attempts to substantiate the hypothesis that, from an evolutionary perspective, the coenzyme couple pyridoxal phosphate and pyridoxamine phosphate preceded the coenzyme thiamine pyrophosphate and acted as its less efficient chemical analogue in some form of early metabolism. The analysis combines mechanism-based chemical reactivity with biosynthetic arguments and provides evidence that vestiges of "TPP-like reactivity" are still found for PLP today. From these thoughts, conclusions can be drawn about the key elements of a primordial form of metabolism, which includes the citric acid cycle, amino acid biosynthesis and the pentose phosphate pathway.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B 30167 Hannover Germany
- Uppsala Biomedical Center (BMC), University Uppsala, Husargatan 3 752 37 Uppsala Sweden
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3
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Liu WW, Zheng SQ, Li T, Fei YF, Wang C, Zhang S, Wang F, Jiang GM, Wang H. RNA modifications in cellular metabolism: implications for metabolism-targeted therapy and immunotherapy. Signal Transduct Target Ther 2024; 9:70. [PMID: 38531882 DOI: 10.1038/s41392-024-01777-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024] Open
Abstract
Cellular metabolism is an intricate network satisfying bioenergetic and biosynthesis requirements of cells. Relevant studies have been constantly making inroads in our understanding of pathophysiology, and inspiring development of therapeutics. As a crucial component of epigenetics at post-transcription level, RNA modification significantly determines RNA fates, further affecting various biological processes and cellular phenotypes. To be noted, immunometabolism defines the metabolic alterations occur on immune cells in different stages and immunological contexts. In this review, we characterize the distribution features, modifying mechanisms and biological functions of 8 RNA modifications, including N6-methyladenosine (m6A), N6,2'-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N4-acetylcytosine (ac4C), N7-methylguanosine (m7G), Pseudouridine (Ψ), adenosine-to-inosine (A-to-I) editing, which are relatively the most studied types. Then regulatory roles of these RNA modification on metabolism in diverse health and disease contexts are comprehensively described, categorized as glucose, lipid, amino acid, and mitochondrial metabolism. And we highlight the regulation of RNA modifications on immunometabolism, further influencing immune responses. Above all, we provide a thorough discussion about clinical implications of RNA modification in metabolism-targeted therapy and immunotherapy, progression of RNA modification-targeted agents, and its potential in RNA-targeted therapeutics. Eventually, we give legitimate perspectives for future researches in this field from methodological requirements, mechanistic insights, to therapeutic applications.
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Affiliation(s)
- Wei-Wei Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- School of Clinical Medicine, Shandong University, Jinan, China
| | - Si-Qing Zheng
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Tian Li
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Yun-Fei Fei
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Chen Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Shuang Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Fei Wang
- Neurosurgical Department, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Guan-Min Jiang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.
| | - Hao Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China.
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4
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Arya CK, Maurya S, Ramanathan G. Insight into the metabolic pathways of Paracoccus sp. strain DMF: a non-marine halotolerant methylotroph capable of degrading aliphatic amines/amides. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:125947-125964. [PMID: 38010547 DOI: 10.1007/s11356-023-30858-1] [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: 05/29/2023] [Accepted: 10/31/2023] [Indexed: 11/29/2023]
Abstract
Paracoccus sp. strain DMF (P. DMF from henceforth) is a gram-negative heterotroph known to tolerate and utilize high concentrations of N,N-dimethylformamide (DMF). The work presented here elaborates on the metabolic pathways involved in the degradation of C1 compounds, many of which are well-known pollutants and toxic to the environment. Investigations on microbial growth and detection of metabolic intermediates corroborate the outcome of the functional genome analysis. Several classes of C1 compounds, such as methanol, methylated amines, aliphatic amides, and naturally occurring quaternary amines like glycine betaine, were tested as growth substrates. The detailed growth and kinetic parameter analyses reveal that P. DMF can efficiently aerobically degrade trimethylamine (TMA) and grow on quaternary amines such as glycine betaine. The results show that the mechanism for halotolerant adaptation in the presence of glycine betaine is dissimilar from those observed for conventional trehalose-mediated halotolerance in heterotrophic bacteria. In addition, a close genomic survey revealed the presence of a Co(I)-based substrate-specific corrinoid methyltransferase operon, referred to as mtgBC. This demethylation system has been associated with glycine betaine catabolism in anaerobic methanogens and is unknown in denitrifying aerobic heterotrophs. This report on an anoxic-specific demethylation system in an aerobic heterotroph is unique. Our finding exposes the metabolic potential for the degradation of a variety of C1 compounds by P. DMF, making it a novel organism of choice for remediating a wide range of possible environmental contaminants.
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Affiliation(s)
- Chetan Kumar Arya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Shiwangi Maurya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Gurunath Ramanathan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India.
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5
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Qu YN, Rao YZ, Qi YL, Li YX, Li A, Palmer M, Hedlund BP, Shu WS, Evans PN, Nie GX, Hua ZS, Li WJ. Panguiarchaeum symbiosum, a potential hyperthermophilic symbiont in the TACK superphylum. Cell Rep 2023; 42:112158. [PMID: 36827180 DOI: 10.1016/j.celrep.2023.112158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/27/2022] [Accepted: 02/09/2023] [Indexed: 02/24/2023] Open
Abstract
The biology of Korarchaeia remains elusive due to the lack of genome representatives. Here, we reconstruct 10 closely related metagenome-assembled genomes from hot spring habitats and place them into a single species, proposed herein as Panguiarchaeum symbiosum. Functional investigation suggests that Panguiarchaeum symbiosum is strictly anaerobic and grows exclusively in thermal habitats by fermenting peptides coupled with sulfide and hydrogen production to dispose of electrons. Due to its inability to biosynthesize archaeal membranes, amino acids, and purines, this species likely exists in a symbiotic lifestyle similar to DPANN archaea. Population metagenomics and metatranscriptomic analyses demonstrated that genes associated with amino acid/peptide uptake and cell attachment exhibited positive selection and were highly expressed, supporting the proposed proteolytic catabolism and symbiotic lifestyle. Our study sheds light on the metabolism, evolution, and potential symbiotic lifestyle of Panguiarchaeum symbiosum, which may be a unique host-dependent archaeon within the TACK superphylum.
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Affiliation(s)
- Yan-Ni Qu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yang-Zhi Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yan-Ling Qi
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Yu-Xian Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Andrew Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Paul N Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Guo-Xing Nie
- College of Fisheries, Henan Normal University, Xinxiang, China
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China.
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6
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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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Hao S, Meng Q, Sun H, Li Y, Li Y, Gu L, Liu B, Zhang Y, Zhou H, Xu Z, Wang Y. The role of transketolase in human cancer progression and therapy. Biomed Pharmacother 2022; 154:113607. [PMID: 36030587 DOI: 10.1016/j.biopha.2022.113607] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/02/2022] Open
Abstract
Transketolase (TKT) is an enzyme that is ubiquitously expressed in all living organisms and has been identified as an important regulator of cancer. Recent studies have shown that the TKT family includes the TKT gene and two TKT-like (TKTL) genes; TKTL1 and TKTL2. TKT and TKTL1 have been reported to be involved in the regulation of multiple cancer-related events, such as cancer cell proliferation, metastasis, invasion, epithelial-mesenchymal transition, chemoradiotherapy resistance, and patient survival and prognosis. Therefore, TKT may be an ideal target for cancer treatment. More importantly, the levels of TKTL1 were detected using EDIM technology for the early detection of some malignancies, and TKTL1 was more sensitive and specific than traditional tumor markers. Detecting TKTL1 levels before and after surgery could be used to evaluate the surgery's effect. While targeted TKT suppresses cancer in multiple ways, in some cases, it has detrimental effects on the organism. In this review, we discuss the role of TKT in different tumors and the detailed mechanisms while evaluating its value and limitations in clinical applications. Therefore, this review provides a basis for the clinical application of targeted therapy for TKT in the future, and a strategy for subsequent cancer-related research.
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Affiliation(s)
- Shiming Hao
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Qingfei Meng
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Huihui Sun
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Yunkuo Li
- Department of Urology, The First Hospital of Jilin University, Changchun 130021, China
| | - Yao Li
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Liting Gu
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Bin Liu
- Department of Urology, The First Hospital of Jilin University, Changchun 130021, China
| | - Yanghe Zhang
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Honglan Zhou
- Department of Urology, The First Hospital of Jilin University, Changchun 130021, China.
| | - Zhixiang Xu
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China.
| | - Yishu Wang
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China.
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8
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Tian L, Chang J, Shi S, Ji L, Zhang J, Sun Y, Li X, Li X, Xie H, Cai Y, Chen D, Wang J, van Veen JA, Kuramae EE, Tran LSP, Tian C. Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 803:150131. [PMID: 34788940 DOI: 10.1016/j.scitotenv.2021.150131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 06/28/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
Microbial communities from rhizosphere (rhizomicrobiomes) have been significantly impacted by domestication as evidenced by a comparison of the rhizomicrobiomes of wild and related cultivated rice accessions. While there have been many published studies focusing on the structure of the rhizomicrobiome, studies comparing the functional traits of the microbial communities in the rhizospheres of wild rice and cultivated rice accessions are not yet available. In this study, we used metagenomic data from experimental rice plots to analyze the potential functional traits of the microbial communities in the rhizospheres of wild rice accessions originated from Africa and Asia in comparison with their related cultivated rice accessions. The functional potential of rhizosphere microbial communities involved in alanine, aspartate and glutamate metabolism, methane metabolism, carbon fixation pathways, citrate cycle (TCA cycle), pyruvate metabolism and lipopolysaccharide biosynthesis pathways were found to be enriched in the rhizomicrobiomes of wild rice accessions. Notably, methane metabolism in the rhizomicrobiomes of wild and cultivated rice accessions clearly differed. Key enzymes involved in methane production and utilization were overrepresented in the rhizomicrobiome samples obtained from wild rice accessions, suggesting that the rhizomicrobiomes of wild rice maintain a different ecological balance for methane production and utilization compared with those of the related cultivated rice accessions. A novel assessment of the impact of rice domestication on the primary metabolic pathways associated with microbial taxa in the rhizomicrobiomes was performed. Results indicated a strong impact of rice domestication on methane metabolism; a process that represents a critical function of the rhizosphere microbial community of rice. The findings of this study provide important information for future breeding of rice varieties with reduced methane emission during cultivation for sustainable agriculture.
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Affiliation(s)
- Lei Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Jingjing Chang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands
| | - Shaohua Shi
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Li Ji
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianfeng Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yu Sun
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Xiaojie Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Xiujun Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Hongwei Xie
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Yaohui Cai
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Dazhou Chen
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Jilin Wang
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands.
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, Da Nang 550000, Viet Nam; Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, TX 79409, USA.
| | - Chunjie Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China.
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9
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Dadgar T, Ebrahimi N, Gholipour AR, Akbari M, Khani L, Ahmadi A, Hamblin MR. Targeting the metabolism of cancer stem cells by energy disruptor molecules. Crit Rev Oncol Hematol 2021; 169:103545. [PMID: 34838705 DOI: 10.1016/j.critrevonc.2021.103545] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 10/17/2021] [Accepted: 11/01/2021] [Indexed: 02/06/2023] Open
Abstract
Cancer stem cells (CSCs) have been identified in various tumor types. CSCs are believed to contribute to tumor metastasis and resistance to conventional therapy. So targeting these cells could be an effective strategy to eliminate tumors and a promising new type of cancer treatment. Alterations in metabolism play an essential role in CSC biology and their resistance to treatment. The metabolic properties pathways in CSCs are different from normal cells, and to some extent, are different from regular tumor cells. Interestingly, CSCs can use other nutrients for their metabolism and growth. The different metabolism causes increased sensitivity of CSCs to agents that disrupt cellular homeostasis. Compounds that interfere with the central metabolic pathways are known as energy disruptors and can reduce CSC survival. This review highlights the differences between regular cancer cells and CSC metabolism and discusses the action mechanisms of energy disruptors at the cellular and molecular levels.
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Affiliation(s)
- Tahere Dadgar
- Department of Biology, Neyshabur Branch, Islamic Azad University, Neyshabur, Iran
| | - Nasim Ebrahimi
- Division of Genetics, Department of Cell and Molecular & Microbiology, Faculty of Science and Technology, University of Isfahan, Isfahan, Iran
| | - Amir Reza Gholipour
- Department of Medical Biotechnology, Faculty of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Maryam Akbari
- Department of Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Leila Khani
- Department of Immunology, School of Medicine, Iran University of Medical Science, Tehran, Iran
| | - Amirhossein Ahmadi
- Department of Biological Science and Technology, Faculty of Nano and Bio Science and Technology, Persian Gulf University, Bushehr, 75169, Iran.
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa.
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10
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Rapp J, Forchhammer K. 5-Deoxyadenosine Metabolism: More than "Waste Disposal". Microb Physiol 2021; 31:248-259. [PMID: 34126623 DOI: 10.1159/000516105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/19/2021] [Indexed: 11/19/2022]
Abstract
5-Deoxyadenosine (5dAdo) is a by-product of many radical SAM enzyme reactions in all domains of life, and an inhibitor of the radical SAM enzymes themselves. Hence, pathways to recycle or dispose of this toxic by-product must exist but remain largely unexplored. In this review, we discuss the current knowledge about canonical and atypical 5dAdo salvage pathways that have been characterized in the last years. We highlight studies that report on how, in certain organisms, the salvage of 5dAdo via specific pathways can confer a growth advantage by providing either intermediates for the synthesis of secondary metabolites or a carbon source for the synthesis of metabolites of the central carbon metabolism. Yet, an alternative recycling route exists in organisms that use 5dAdo as a substrate to synthesize and excrete 7-deoxysedoheptulose, an allelopathic inhibitor of one enzyme of the shikimate pathway, thereby competing for their own niche. Remarkably, most steps of 5dAdo salvage are the result of the activity of promiscuous enzymes. This strategy enables even organisms with a small genome to synthesize bioactive compounds which they can deploy under certain conditions to gain a competitive growth advantage. We conclude emphasizing that, unexpectedly, 5dAdo salvage pathways seem not to be ubiquitously present, raising questions about the fate of such a toxic by-product in those species. This observation also suggests that additional 5dAdo salvage pathways, possibly relying on the activity of promiscuous enzymes, may exist. The future challenge will be to bring to light these "cryptic" 5dAdo recycling pathways.
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Affiliation(s)
- Johanna Rapp
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Organismic Interactions, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Organismic Interactions, Eberhard Karls Universität Tübingen, Tübingen, Germany
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11
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Qiang W, Xuan H, Yu S, Hailun P, Yueli Z, Zhiguo P, Lei S. Impact of the gut microbiota on heat stroke rat mediated by Xuebijing metabolism. Microb Pathog 2021; 155:104861. [PMID: 33864878 DOI: 10.1016/j.micpath.2021.104861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 12/17/2022]
Abstract
The goal of the present study was to evaluate the fecal microbiome and serum metabolites in Xuebijing (XBJ)-injected rats after heat stroke using 16S rRNA gene sequencing and gas chromatography-mass spectrometry (GC-MS) metabolomics. Eighteen rats were divided into the control group (CON), heat stroke group (HS), and XBJ group. The 16S rRNA gene sequencing results revealed that the abundance of Bacteroidetes was overrepresented in the XBJ group compared to the HS group, while Actinobacteria was underrepresented. Metabolomic profiling showed that the pyrimidine metabolism pathway, pentose phosphate pathway, and glycerophospholipid metabolism pathway were upregulated in the XBJ group compared to the HS group. Taken together, these results demonstrated that heat stroke not only altered the gut microbiome community structure of rats but also greatly affected metabolic functions, leading to gut microbiome toxicity.
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Affiliation(s)
- Wen Qiang
- The First Clinical Medical College, Southern Medical University, Guangzhou, China; Department of Critical Care Medicine, General Hospital of Guangzhou Military Command, Guangzhou, China
| | - He Xuan
- Department of Critical Care Medicine, General Hospital of Guangzhou Military Command, Guangzhou, China
| | - Shao Yu
- Second Department of Internal Medicine for Cadres, General Hospital of Guangzhou Military Command, China
| | - Peng Hailun
- The First Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Zhao Yueli
- Graduate School, Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Pan Zhiguo
- The First Clinical Medical College, Southern Medical University, Guangzhou, China; Department of Critical Care Medicine, General Hospital of Guangzhou Military Command, Guangzhou, China.
| | - Su Lei
- The First Clinical Medical College, Southern Medical University, Guangzhou, China; Department of Critical Care Medicine, General Hospital of Guangzhou Military Command, Guangzhou, China.
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12
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Zhao W, Quansah E, Yuan M, Gou Q, Mengal K, Li P, Wu S, Xu C, Yi C, Cai X. Region-specific gene expression in the epididymis of Yak. Theriogenology 2019; 139:132-146. [DOI: 10.1016/j.theriogenology.2019.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 08/02/2019] [Accepted: 08/02/2019] [Indexed: 12/25/2022]
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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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Ghanbari Movahed Z, Rastegari-Pouyani M, Mohammadi MH, Mansouri K. Cancer cells change their glucose metabolism to overcome increased ROS: One step from cancer cell to cancer stem cell? Biomed Pharmacother 2019; 112:108690. [PMID: 30798124 DOI: 10.1016/j.biopha.2019.108690] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/12/2019] [Accepted: 02/14/2019] [Indexed: 12/11/2022] Open
Abstract
Cancer cells can adapt to low energy sources in the face of ATP depletion as well as to their high levels of ROS by altering their metabolism and energy production networks which might also have a role in determining cell fate and developing drug resistance. Cancer cells are generally characterized by increased glycolysis. This is while; cancer stem cells (CSCs) exhibit an enhanced pentose phosphate pathway (PPP) metabolism. Based on the current literature, we suggest that cancer cells when encountering ROS, first increase the glycolysis rate and then following the continuation of oxidative stress, the metabolic balance is skewed from glycolysis to PPP. Therefore, we hypothesize in this review that in cancer cells this metabolic deviation during persistent oxidative stress might be a sign of cancer cells' shift towards CSCs, an issue that might be pivotal in more effective targeting of cancer cells and CSCs.
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Affiliation(s)
- Zahra Ghanbari Movahed
- Medical Biology Research Center, Kermanshah University of Medical sciences, Kermanshah, Iran
| | - Mohsen Rastegari-Pouyani
- Student Research Committee, Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Hossein Mohammadi
- HSCT research center, Laboratory Hematology and blood Banking Department, School of Allied Medical Sciences, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Kamran Mansouri
- Medical Biology Research Center, Kermanshah University of Medical sciences, Kermanshah, Iran; Department of Molecular Medicine, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Metabolomics analysis of gut barrier dysfunction in a trauma-hemorrhagic shock rat model. Biosci Rep 2019; 39:BSR20181215. [PMID: 30393232 PMCID: PMC6328858 DOI: 10.1042/bsr20181215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 09/30/2018] [Accepted: 10/10/2018] [Indexed: 12/12/2022] Open
Abstract
Intestinal barrier dysfunction has been implicated in the development of multiorgan dysfunction syndrome caused by the trauma-hemorrhagic shock (THS). However, the mechanisms underlying THS-induced gut barrier injury are still poorly understood. In the present study, we used the metabolomics analysis to test the hypothesis that altered metabolites might be related to the development of THS-induced barrier dysfunction in the large intestine. Under the induction of THS, gut barrier failure was characterized by injury of permeability and mucus layer, which were companied by the decreased expression of zonula occludens-1 in the colon and increased levels of inflammatory factors including tumor necrosis factor-α, interferon-γ, interleukin (IL)-6, and IL-1β in the serum. A total of 16 differential metabolites were identified in colonic tissues from THS-treated rats compared with control rats. These altered metabolites included dihydroxy acetone phosphate, ribose-5-phosphate, fructose, glyceric acid, succinic acid, and adenosine, which are critical intermediates or end products that are involved in pentose phosphate pathway, glycolysis, and tricarboxylic acid cycle as well as mitochondrial adenosine triphosphate biosynthesis. These findings may offer important insight into the metabolic alterations in THS-treated gut injury, which will be helpful for developing effective metabolites-based strategies to prevent THS-induced gut barrier dysfunction.
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16
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Hawkins JP, Ordonez PA, Oresnik IJ. Characterization of Mutations That Affect the Nonoxidative Pentose Phosphate Pathway in Sinorhizobium meliloti. J Bacteriol 2018; 200:e00436-17. [PMID: 29084855 PMCID: PMC5738737 DOI: 10.1128/jb.00436-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/21/2017] [Indexed: 12/12/2022] Open
Abstract
Sinorhizobium meliloti is a Gram-negative alphaproteobacterium that can enter into a symbiotic relationship with Medicago sativa and Medicago truncatula Previous work determined that a mutation in the tkt2 gene, which encodes a putative transketolase, could prevent medium acidification associated with a mutant strain unable to metabolize galactose. Since the pentose phosphate pathway in S. meliloti is not well studied, strains carrying mutations in either tkt2 and tal, which encodes a putative transaldolase, were characterized. Carbon metabolism phenotypes revealed that both mutants were impaired in growth on erythritol and ribose. This phenotype was more pronounced for the tkt2 mutant strain, which also displayed auxotrophy for aromatic amino acids. Changes in pentose phosphate pathway metabolite concentrations were also consistent with a mutation in either tkt2 or tal The concentrations of metabolites in central carbon metabolism were also found to shift dramatically in strains carrying a tkt2 mutation. While the concentrations of proteins involved in central carbon metabolism did not change significantly under any conditions, the levels of those associated with iron acquisition increased in the wild-type strain with erythritol induction. These proteins were not detected in either mutant, resulting in less observable rhizobactin production in the tkt2 mutant. While both mutants were impaired in succinoglycan synthesis, only the tkt2 mutant strain was unable to establish symbiosis with alfalfa. These results suggest that tkt2 and tal play central roles in regulating the carbon flow necessary for carbon metabolism and the establishment of symbiosis.IMPORTANCESinorhizobium meliloti is a model organism for the study of plant-microbe interactions and metabolism, especially because it effects nitrogen fixation. The ability to derive the energy necessary for nitrogen fixation is dependent on an organism's ability to metabolize carbon efficiently. The pentose phosphate pathway is central in the interconversion of hexoses and pentoses. This study characterizes the key enzymes of the nonoxidative branch of the pentose phosphate pathway by using defined genetic mutations and shows the effects the mutations have on the metabolite profile and on physiological processes such as the biosynthesis of exopolysaccharide, as well as the ability to regulate iron acquisition.
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Affiliation(s)
- Justin P Hawkins
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Patricia A Ordonez
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ivan J Oresnik
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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17
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Decoding how a soil bacterium extracts building blocks and metabolic energy from ligninolysis provides road map for lignin valorization. Proc Natl Acad Sci U S A 2016; 113:E5802-E5811. [PMID: 27634497 DOI: 10.1073/pnas.1606043113] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Sphingobium sp. SYK-6 is a soil bacterium boasting a well-studied ligninolytic pathway and the potential for development into a microbial chassis for lignin valorization. An improved understanding of its metabolism will help researchers in the engineering of SYK-6 for the production of value-added chemicals through lignin valorization. We used 13C-fingerprinting, 13C metabolic flux analysis (13C-MFA), and RNA-sequencing differential expression analysis to uncover the following metabolic traits: (i) SYK-6 prefers alkaline conditions, making it an efficient host for the consolidated bioprocessing of lignin, and it also lacks the ability to metabolize sugars or organic acids; (ii) the CO2 release (i.e., carbon loss) from the ligninolysis-based metabolism of SYK-6 is significantly greater than the CO2 release from the sugar-based metabolism of Escherichia coli; (iii) the vanillin catabolic pathway (which is the converging point of majority of the lignin catabolic pathways) is coupled with the tetrahydrofolate-dependent C1 pathway that is essential for the biosynthesis of serine, histidine, and methionine; (iv) catabolic end products of lignin (pyruvate and oxaloacetate) must enter the tricarboxylic acid (TCA) cycle first and then use phosphoenolpyruvate carboxykinase to initiate gluconeogenesis; and (v) 13C-MFA together with RNA-sequencing differential expression analysis establishes the vanillin catabolic pathway as the major contributor of NAD(P)H synthesis. Therefore, the vanillin catabolic pathway is essential for SYK-6 to obtain sufficient reducing equivalents for its healthy growth; cosubstrate experiments support this finding. This unique energy feature of SYK-6 is particularly interesting because most heterotrophs rely on the transhydrogenase, the TCA cycle, and the oxidative pentose phosphate pathway to obtain NADPH.
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18
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Schönheit P, Buckel W, Martin WF. On the Origin of Heterotrophy. Trends Microbiol 2016; 24:12-25. [DOI: 10.1016/j.tim.2015.10.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/28/2015] [Accepted: 10/07/2015] [Indexed: 10/22/2022]
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S-Inosyl-L-Homocysteine Hydrolase, a Novel Enzyme Involved in S-Adenosyl-L-Methionine Recycling. J Bacteriol 2015; 197:2284-91. [PMID: 25917907 DOI: 10.1128/jb.00080-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/22/2015] [Indexed: 01/18/2023] Open
Abstract
UNLABELLED S-Adenosyl-L-homocysteine, the product of S-adenosyl-L-methionine (SAM) methyltransferases, is known to be a strong feedback inhibitor of these enzymes. A hydrolase specific for S-adenosyl-L-homocysteine produces L-homocysteine, which is remethylated to methionine and can be used to regenerate SAM. Here, we show that the annotated S-adenosyl-L-homocysteine hydrolase in Methanocaldococcus jannaschii is specific for the hydrolysis and synthesis of S-inosyl-L-homocysteine, not S-adenosyl-L-homocysteine. This is the first report of an enzyme specific for S-inosyl-L-homocysteine. As with S-adenosyl-L-homocysteine hydrolase, which shares greater than 45% sequence identity with the M. jannaschii homologue, the M. jannaschii enzyme was found to copurify with bound NAD(+) and has Km values of 0.64 ± 0.4 mM, 0.0054 ± 0.006 mM, and 0.22 ± 0.11 mM for inosine, L-homocysteine, and S-inosyl-L-homocysteine, respectively. No enzymatic activity was detected with S-adenosyl-L-homocysteine as the substrate in either the synthesis or hydrolysis direction. These results prompted us to redesignate the M. jannaschii enzyme an S-inosyl-L-homocysteine hydrolase (SIHH). Identification of SIHH demonstrates a modified pathway in this methanogen for the regeneration of SAM from S-adenosyl-L-homocysteine that uses the deamination of S-adenosyl-L-homocysteine to form S-inosyl-L-homocysteine. IMPORTANCE In strictly anaerobic methanogenic archaea, such as Methanocaldococcus jannaschii, canonical metabolic pathways are often not present, and instead, unique pathways that are deeply rooted on the phylogenetic tree are utilized by the organisms. Here, we discuss the recycling pathway for S-adenosyl-L-homocysteine, produced from S-adenosyl-L-methionine (SAM)-dependent methylation reactions, which uses a hydrolase specific for S-inosyl-L-homocysteine, an uncommon metabolite. Identification of the pathways and the enzymes involved in the unique pathways in the methanogens will provide insight into the biochemical reactions that were occurring when life originated.
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Gunnigle E, Siggins A, Botting CH, Fuszard M, O'Flaherty V, Abram F. Low-temperature anaerobic digestion is associated with differential methanogenic protein expression. FEMS Microbiol Lett 2015; 362:fnv059. [PMID: 25862577 DOI: 10.1093/femsle/fnv059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2015] [Indexed: 11/14/2022] Open
Abstract
Anaerobic digestion (AD) is an attractive wastewater treatment technology, leading to the generation of recoverable biofuel (methane). Most industrial AD applications, carry excessive heating costs, however, as AD reactors are commonly operated at mesophilic temperatures while handling waste streams discharged at ambient or cold temperatures. Consequently, low-temperature AD represents a cost-effective strategy for wastewater treatment. The comparative investigation of key microbial groups underpinning laboratory-scale AD bioreactors operated at 37, 15 and 7°C was carried out. Community structure was monitored using 16S rRNA clone libraries, while abundance of the most prominent methanogens was investigated using qPCR. In addition, metaproteomics was employed to access the microbial functions carried out in situ. While δ-Proteobacteria were prevalent at 37°C, their abundance decreased dramatically at lower temperatures with inverse trends observed for Bacteroidetes and Firmicutes. Methanobacteriales and Methanosaeta were predominant at all temperatures investigated while Methanomicrobiales abundance increased at 15°C compared to 37 and 7°C. Changes in operating temperature resulted in the differential expression of proteins involved in methanogenesis, which was found to occur in all bioreactors, as corroborated by bioreactors' performance. This study demonstrated the value of employing a polyphasic approach to address microbial community dynamics and highlighted the functional redundancy of AD microbiomes.
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Affiliation(s)
- Eoin Gunnigle
- Microbial Ecology Laboratory, School of Natural Sciences, National University of Ireland, Galway, University Road, Galway, Ireland Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Alma Siggins
- Microbial Ecology Laboratory, School of Natural Sciences, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Catherine H Botting
- BSRC Mass Spectrometry and Proteomics Facility, Biomedical Sciences Research Complex, North Haugh, University of St Andrews, Fife KY16 9ST, Scotland
| | - Matthew Fuszard
- BSRC Mass Spectrometry and Proteomics Facility, Biomedical Sciences Research Complex, North Haugh, University of St Andrews, Fife KY16 9ST, Scotland
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory, School of Natural Sciences, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Florence Abram
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland, Galway, University Road, Galway, Ireland
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21
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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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22
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Stincone A, Prigione A, Cramer T, Wamelink MMC, Campbell K, Cheung E, Olin-Sandoval V, Grüning NM, Krüger A, Tauqeer Alam M, Keller MA, Breitenbach M, Brindle KM, Rabinowitz JD, Ralser M. The return of metabolism: biochemistry and physiology of the pentose phosphate pathway. Biol Rev Camb Philos Soc 2014; 90:927-63. [PMID: 25243985 PMCID: PMC4470864 DOI: 10.1111/brv.12140] [Citation(s) in RCA: 793] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 07/07/2014] [Accepted: 07/16/2014] [Indexed: 12/13/2022]
Abstract
The pentose phosphate pathway (PPP) is a fundamental component of cellular metabolism. The PPP is important to maintain carbon homoeostasis, to provide precursors for nucleotide and amino acid biosynthesis, to provide reducing molecules for anabolism, and to defeat oxidative stress. The PPP shares reactions with the Entner–Doudoroff pathway and Calvin cycle and divides into an oxidative and non-oxidative branch. The oxidative branch is highly active in most eukaryotes and converts glucose 6-phosphate into carbon dioxide, ribulose 5-phosphate and NADPH. The latter function is critical to maintain redox balance under stress situations, when cells proliferate rapidly, in ageing, and for the ‘Warburg effect’ of cancer cells. The non-oxidative branch instead is virtually ubiquitous, and metabolizes the glycolytic intermediates fructose 6-phosphate and glyceraldehyde 3-phosphate as well as sedoheptulose sugars, yielding ribose 5-phosphate for the synthesis of nucleic acids and sugar phosphate precursors for the synthesis of amino acids. Whereas the oxidative PPP is considered unidirectional, the non-oxidative branch can supply glycolysis with intermediates derived from ribose 5-phosphate and vice versa, depending on the biochemical demand. These functions require dynamic regulation of the PPP pathway that is achieved through hierarchical interactions between transcriptome, proteome and metabolome. Consequently, the biochemistry and regulation of this pathway, while still unresolved in many cases, are archetypal for the dynamics of the metabolic network of the cell. In this comprehensive article we review seminal work that led to the discovery and description of the pathway that date back now for 80 years, and address recent results about genetic and metabolic mechanisms that regulate its activity. These biochemical principles are discussed in the context of PPP deficiencies causing metabolic disease and the role of this pathway in biotechnology, bacterial and parasite infections, neurons, stem cell potency and cancer metabolism.
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Affiliation(s)
- Anna Stincone
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Alessandro Prigione
- Max Delbrueck Centre for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Thorsten Cramer
- Department of Gastroenterology and Hepatology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Mirjam M C Wamelink
- Metabolic Unit, Department of Clinical Chemistry, VU University Medical Centre Amsterdam, De Boelelaaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Kate Campbell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Eric Cheung
- Cancer Research UK, Beatson Institute, Switchback Road, Glasgow G61 1BD, U.K
| | - Viridiana Olin-Sandoval
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Nana-Maria Grüning
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Antje Krüger
- Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany
| | - Mohammad Tauqeer Alam
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Markus A Keller
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Michael Breitenbach
- Department of Cell Biology, University of Salzburg, Hellbrunnerstrasse 34, A-5020 Salzburg, Austria
| | - Kevin M Brindle
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cancer Research UK Cambridge Research Institute (CRI), Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, U.K
| | - Joshua D Rabinowitz
- Department of Chemistry, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, 08544 NJ, U.S.A
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Division of Physiology and Metabolism, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7, U.K
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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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Keller MA, Turchyn AV, Ralser M. Non-enzymatic glycolysis and pentose phosphate pathway-like reactions in a plausible Archean ocean. Mol Syst Biol 2014; 10:725. [PMID: 24771084 PMCID: PMC4023395 DOI: 10.1002/msb.20145228] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 03/11/2014] [Accepted: 03/18/2014] [Indexed: 11/30/2022] Open
Abstract
The reaction sequences of central metabolism, glycolysis and the pentose phosphate pathway provide essential precursors for nucleic acids, amino acids and lipids. However, their evolutionary origins are not yet understood. Here, we provide evidence that their structure could have been fundamentally shaped by the general chemical environments in earth's earliest oceans. We reconstructed potential scenarios for oceans of the prebiotic Archean based on the composition of early sediments. We report that the resultant reaction milieu catalyses the interconversion of metabolites that in modern organisms constitute glycolysis and the pentose phosphate pathway. The 29 observed reactions include the formation and/or interconversion of glucose, pyruvate, the nucleic acid precursor ribose-5-phosphate and the amino acid precursor erythrose-4-phosphate, antedating reactions sequences similar to that used by the metabolic pathways. Moreover, the Archean ocean mimetic increased the stability of the phosphorylated intermediates and accelerated the rate of intermediate reactions and pyruvate production. The catalytic capacity of the reconstructed ocean milieu was attributable to its metal content. The reactions were particularly sensitive to ferrous iron Fe(II), which is understood to have had high concentrations in the Archean oceans. These observations reveal that reaction sequences that constitute central carbon metabolism could have been constrained by the iron-rich oceanic environment of the early Archean. The origin of metabolism could thus date back to the prebiotic world.
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Affiliation(s)
- Markus A Keller
- Department of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUK
| | | | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUK
- Division of Physiology and MetabolismMRC National Institute for Medical ResearchMill HillLondonUK
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25
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Identification of a 5'-deoxyadenosine deaminase in Methanocaldococcus jannaschii and its possible role in recycling the radical S-adenosylmethionine enzyme reaction product 5'-deoxyadenosine. J Bacteriol 2013; 196:1064-72. [PMID: 24375099 DOI: 10.1128/jb.01308-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We characterize here the MJ1541 gene product from Methanocaldococcus jannaschii, an enzyme that was annotated as a 5'-methylthioadenosine/S-adenosylhomocysteine deaminase (EC 3.5.4.31/3.5.4.28). The MJ1541 gene product catalyzes the conversion of 5'-deoxyadenosine to 5'-deoxyinosine as its major product but will also deaminate 5'-methylthioadenosine, S-adenosylhomocysteine, and adenosine to a small extent. On the basis of these findings, we are naming this new enzyme 5'-deoxyadenosine deaminase (DadD). The Km for 5'-deoxyadenosine was found to be 14.0 ± 1.2 μM with a kcat/Km of 9.1 × 10(9) M(-1) s(-1). Radical S-adenosylmethionine (SAM) enzymes account for nearly 2% of the M. jannaschii genome, where the major SAM derived products is 5'-deoxyadenosine. Since 5'-dA has been demonstrated to be an inhibitor of radical SAM enzymes; a pathway for removing this product must be present. We propose here that DadD is involved in the recycling of 5'-deoxyadenosine, whereupon the 5'-deoxyribose moiety of 5'-deoxyinosine is further metabolized to deoxyhexoses used for the biosynthesis of aromatic amino acids in methanogens.
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Kanauchi M, Chijimi A, Ohnishi-Kameyama M, Bamforth CW. An investigation of two xylan-degrading enzymes and a novel xylanase inhibitor in malted barley. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/jib.64] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Makoto Kanauchi
- Department of Food Management; Miyagi University; 2-2-1 Hatatate Taihaku-ku; Sendai; Miyagi; 982-0215; Japan
| | - Ayaka Chijimi
- Department of Food Management; Miyagi University; 2-2-1 Hatatate Taihaku-ku; Sendai; Miyagi; 982-0215; Japan
| | | | - Charles W. Bamforth
- Department of Food Science & Technology; University of California; Davis; CA; 95616-8598; USA
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27
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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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Genome-scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A. J Bacteriol 2011; 194:855-65. [PMID: 22139506 DOI: 10.1128/jb.06040-11] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methanosarcina acetivorans strain C2A is a marine methanogenic archaeon notable for its substrate utilization, genetic tractability, and novel energy conservation mechanisms. To help probe the phenotypic implications of this organism's unique metabolism, we have constructed and manually curated a genome-scale metabolic model of M. acetivorans, iMB745, which accounts for 745 of the 4,540 predicted protein-coding genes (16%) in the M. acetivorans genome. The reconstruction effort has identified key knowledge gaps and differences in peripheral and central metabolism between methanogenic species. Using flux balance analysis, the model quantitatively predicts wild-type phenotypes and is 96% accurate in knockout lethality predictions compared to currently available experimental data. The model was used to probe the mechanisms and energetics of by-product formation and growth on carbon monoxide, as well as the nature of the reaction catalyzed by the soluble heterodisulfide reductase HdrABC in M. acetivorans. The genome-scale model provides quantitative and qualitative hypotheses that can be used to help iteratively guide additional experiments to further the state of knowledge about methanogenesis.
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29
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Matsubara K, Yokooji Y, Atomi H, Imanaka T. Biochemical and genetic characterization of the three metabolic routes in Thermococcus kodakarensis linking glyceraldehyde 3-phosphate and 3-phosphoglycerate. Mol Microbiol 2011; 81:1300-12. [PMID: 21736643 DOI: 10.1111/j.1365-2958.2011.07762.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In the classical Embden-Meyerhof (EM) pathway for glycolysis, the conversion between glyceraldehyde 3-phosphate (GAP) and 3-phosphoglycerate (3-PGA) is reversibly catalysed by phosphorylating GAP dehydrogenase (GAPDH) and phosphoglycerate kinase (PGK). In the Euryarchaeota Thermococcus kodakarensis and Pyrococcus furiosus, an additional gene encoding GAP:ferredoxin oxidoreductase (GAPOR) and a gene similar to non-phosphorylating GAP dehydrogenase (GAPN) are present. In order to determine the physiological roles of the three routes that link GAP and 3-PGA, we individually disrupted the GAPOR, GAPN, GAPDH and PGK genes (gor, gapN, gapDH and pgk respectively) of T. kodakarensis. The Δgor strain displayed no growth under glycolytic conditions, confirming its proposed function to generate reduced ferredoxin for energy generation in glycolysis. Surprisingly, ΔgapN cells also did not grow under glycolytic conditions, suggesting that GAPN plays a key role in providing NADPH under these conditions. Disruption of gor and gapN had no effect on gluconeogenic growth. Growth experiments with the ΔgapDH and Δpgk strains indicated that, unlike their counterparts in the classical EM pathway, GAPDH/PGK play a major role only in gluconeogenesis. Biochemical analyses indicated that T. kodakarensis GAPN did not recognize aldehyde substrates other than d-GAP, preferred NADP(+) as cofactor and was dramatically activated with glucose 1-phosphate.
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Affiliation(s)
- Kohei Matsubara
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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30
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Nunoura T, Takaki Y, Kakuta J, Nishi S, Sugahara J, Kazama H, Chee GJ, Hattori M, Kanai A, Atomi H, Takai K, Takami H. Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res 2010; 39:3204-23. [PMID: 21169198 PMCID: PMC3082918 DOI: 10.1093/nar/gkq1228] [Citation(s) in RCA: 204] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The domain Archaea has historically been divided into two phyla, the Crenarchaeota and Euryarchaeota. Although regarded as members of the Crenarchaeota based on small subunit rRNA phylogeny, environmental genomics and efforts for cultivation have recently revealed two novel phyla/divisions in the Archaea; the 'Thaumarchaeota' and 'Korarchaeota'. Here, we show the genome sequence of Candidatus 'Caldiarchaeum subterraneum' that represents an uncultivated crenarchaeotic group. A composite genome was reconstructed from a metagenomic library previously prepared from a microbial mat at a geothermal water stream of a sub-surface gold mine. The genome was found to be clearly distinct from those of the known phyla/divisions, Crenarchaeota (hyperthermophiles), Euryarchaeota, Thaumarchaeota and Korarchaeota. The unique traits suggest that this crenarchaeotic group can be considered as a novel archaeal phylum/division. Moreover, C. subterraneum harbors an ubiquitin-like protein modifier system consisting of Ub, E1, E2 and small Zn RING finger family protein with structural motifs specific to eukaryotic system proteins, a system clearly distinct from the prokaryote-type system recently identified in Haloferax and Mycobacterium. The presence of such a eukaryote-type system is unprecedented in prokaryotes, and indicates that a prototype of the eukaryotic protein modifier system is present in the Archaea.
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Affiliation(s)
- Takuro Nunoura
- Subsurface Geobiology & Advanced Research Project, Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan.
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31
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Gooding JR, May AL, Hilliard KR, Campagna SR. Establishing a quantitative definition of quorum sensing provides insight into the information content of the autoinducer signals in Vibrio harveyi and Escherichia coli. Biochemistry 2010; 49:5621-3. [PMID: 20527983 DOI: 10.1021/bi1001163] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Extracellular autoinducer concentrations in cultures of Vibrio harveyi and Escherichia coli were monitored by liquid chromatography-tandem mass spectrometry to test whether a quantitative definition of quorum sensing could help decipher the information content of these signals. Although V. harveyi was able to keep the autoinducer-2 to cell number ratio constant, the ratio of signal to cell number for V. harveyi autoinducer-1 and E. coli autoinducer-2 varied as the cultures grew. These data indicate that V. harveyi uses autoinducer-2 for quorum sensing, while the other molecules may be used to transmit different information or are influenced by metabolic noise.
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Affiliation(s)
- Jessica R Gooding
- Department of Chemistry, University of Tennessee, 618 Buehler Hall, Knoxville, Tennessee 37996-1600, USA
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32
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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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33
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Jung J, Yeom SJ, Kim J, Kim JK, Natarajan S, Ahn YJ, Lim SB, Oh DK, Kang LW. Overexpression, crystallization and preliminary X-ray crystallographic analysis of D-ribose-5-phosphate isomerase from Clostridium thermocellum. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1141-4. [PMID: 19923736 DOI: 10.1107/s1744309109038093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 09/21/2009] [Indexed: 11/10/2022]
Abstract
Rare sugars are used for many industrial and medical purposes and are produced by the interconversion between aldoses and ketoses catalyzed by sugar and sugar-phosphate isomerases. Recently, Clostridium thermocellum d-ribose-5-phosphate isomerase (CTRPI), an aldose-ketose isomerase, was cloned in order to synthesize d-allose and its substrate specificity was further characterized for industrial usage. CTRPI has a novel substrate specificity that differs from those of other isomerases, which have broad substrate specificities. CTRPI prefers aldose substrates such as l-talose, d-ribose and d-allose. CTRPI was purified and crystallized in order to determine its three-dimensional structure and thus to elucidate its enzymatic reaction mechanism and understand its substrate specificity. The crystal belonged to the trigonal space group P3(2)21, with unit-cell parameters a = b = 69.5, c = 154.4 angstrom, and diffracted to 1.9 angstrom resolution. According to Matthews coefficient calculations, the crystallographic structure consists of a dimer in the asymmetric unit, with a V(M) of 3.2 angstrom(3) Da(-1) and a solvent content of 61.7%.
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Affiliation(s)
- Junho Jung
- Department of Advanced Technology Fusion, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul, Republic of Korea
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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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Kastenmüller G, Schenk ME, Gasteiger J, Mewes HW. Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes. Genome Biol 2009; 10:R28. [PMID: 19284550 PMCID: PMC2690999 DOI: 10.1186/gb-2009-10-3-r28] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Revised: 02/12/2009] [Accepted: 03/10/2009] [Indexed: 01/20/2023] Open
Abstract
Identifying the biochemical basis of microbial phenotypes is a main objective of comparative genomics. Here we present a novel method using multivariate machine learning techniques for comparing automatically derived metabolic reconstructions of sequenced genomes on a large scale. Applying our method to 266 genomes directly led to testable hypotheses such as the link between the potential of microorganisms to cause periodontal disease and their ability to degrade histidine, a link also supported by clinical studies.
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Affiliation(s)
- Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstraße, D-85764 Neuherberg, Germany
| | - Maria Elisabeth Schenk
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstraße, D-85764 Neuherberg, Germany
| | - Johann Gasteiger
- Computer-Chemie-Centrum, Universität Erlangen-Nürnberg, Nägelsbachstraße, D-91052 Erlangen, Germany
- Molecular Networks GmbH, Henkestraße 91, D-91052 Erlangen, Germany
| | - Hans-Werner Mewes
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstraße, D-85764 Neuherberg, Germany
- Chair for Genome-oriented Bioinformatics, Technische Universität München, Life and Food Science Center Weihenstephan, Am Forum 1, D-85354 Freising-Weihenstephan, Germany
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Kim TG, Kwon TH, Min K, Dong MS, Park YI, Ban C. Crystal structures of substrate and inhibitor complexes of ribose 5-phosphate isomerase A from Vibrio vulnificus YJ016. Mol Cells 2009; 27:99-103. [PMID: 19214439 DOI: 10.1007/s10059-009-0010-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 10/28/2008] [Indexed: 11/27/2022] Open
Abstract
Ribose-5-phosphate isomerase A (RpiA) plays an important role in interconverting between ribose-5-phosphate (R5P) and ribulose-5-phosphate in the pentose phosphate pathway and the Calvin cycle. We have determined the crystal structures of the open form RpiA from Vibrio vulnificus YJ106 (VvRpiA) in complex with the R5P and the closed form with arabinose-5-phosphate (A5P) in parallel with the apo VvRpiA at 2.0 A resolution. VvRpiA is highly similar to Eschericihia coliRpiA, and the VvRpiA-R5P complex strongly resembles the E. coli RpiA-A5P complex. Interestingly, unlike the E. coli RpiA-A5P complex, the position of A5P in the VvRpiA-A5P complex reveals a different position than the R5P binding mode. VvRpiA-A5P has a sugar ring inside the binding pocket and a phosphate group outside the binding pocket: By contrast, the sugar ring of A5P interacts with the Asp4, Lys7, Ser30, Asp118, and Lys121 residues; the phosphate group of A5P interacts with two water molecules, W51 and W82.
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Affiliation(s)
- Tae Gyun Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang, 790-784, Korea
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37
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Samland AK, Wang M, Sprenger GA. MJ0400 from Methanocaldococcus jannaschii exhibits fructose-1,6-bisphosphate aldolase activity. FEMS Microbiol Lett 2008; 281:36-41. [DOI: 10.1111/j.1574-6968.2008.01079.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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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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Grochowski LL, White RH. Promiscuous anaerobes: new and unconventional metabolism in methanogenic archaea. Ann N Y Acad Sci 2007; 1125:190-214. [PMID: 18096851 DOI: 10.1196/annals.1419.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The development of an oxygenated atmosphere on earth resulted in the polarization of life into two major groups, those that could live in the presence of oxygen and those that could not-the aerobes and the anaerobes. The evolution of aerobes from the earliest anaerobic prokaryotes resulted in a variety of metabolic adaptations. Many of these adaptations center on the need to sustain oxygen-sensitive reactions and cofactors to function in the new oxygen-containing atmosphere. Still other metabolic pathways that were not sensitive to oxygen also diverged. This is likely due to the physical separation of the organisms, based on their ability to live in the presence of oxygen, which allowed for the independent evolution of the pathways. Through the study of metabolic pathways in anaerobes and comparison to the more established pathways from aerobes, insight into metabolic evolution can be gained. This, in turn, can allow for extra- polation to those metabolic pathways occurring in the Last Universal Common Ancestor (LUCA). Some of the unique and uncanonical metabolic pathways that have been identified in the archaea with emphasis on the biochemistry of an obligate anaerobic methanogen, Methanocaldococcus jannaschii are reviewed.
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Affiliation(s)
- Laura L Grochowski
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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Gonzalez O, Gronau S, Falb M, Pfeiffer F, Mendoza E, Zimmer R, Oesterhelt D. Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism. MOLECULAR BIOSYSTEMS 2007; 4:148-59. [PMID: 18213408 DOI: 10.1039/b715203e] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a genome-scale metabolic reconstruction for the extreme halophile Halobacterium salinarum. The reconstruction represents a summary of the knowledge regarding the organism's metabolism, and has already led to new research directions and improved the existing annotation. We used the network for computational analysis and studied the aerobic growth of the organism using dynamic simulations in media with 15 available carbon and energy sources. Simulations resulted in predictions for the internal fluxes, which describe at the molecular level how the organism lives and grows. We found numerous indications that cells maximized energy production even at the cost of longer term concerns such as growth prospects. Simulations showed a very low carbon incorporation rate of only approximately 15%. All of the supplied nutrients were simultaneously degraded, unexpectedly including five which are essential. These initially surprising behaviors are likely adaptations of the organism to its natural environment where growth occurs in blooms. In addition, we also examined specific aspects of metabolism, including how each of the supplied carbon and energy sources is utilized. Finally, we investigated the consequences of the model assumptions and the network structure on the quality of the flux predictions.
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Affiliation(s)
- Orland Gonzalez
- Department of Membrane Biochemistry, Max-Planck Institute of Biochemistry, 82152, Martinsried, Germany.
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Orita I, Sato T, Yurimoto H, Kato N, Atomi H, Imanaka T, Sakai Y. The ribulose monophosphate pathway substitutes for the missing pentose phosphate pathway in the archaeon Thermococcus kodakaraensis. J Bacteriol 2006; 188:4698-704. [PMID: 16788179 PMCID: PMC1482999 DOI: 10.1128/jb.00492-06] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ribulose monophosphate (RuMP) pathway, involving 3-hexulose-6-phosphate synthase (HPS) and 6-phospho-3-hexuloisomerase (PHI), is now recognized as a widespread prokaryotic pathway for formaldehyde fixation and detoxification. Interestingly, HPS and PHI homologs are also found in a variety of archaeal strains, and recent biochemical and genome analyses have raised the possibility that the reverse reaction of formaldehyde fixation, i.e., ribulose 5-phosphate (Ru5P) synthesis from fructose 6-phosphate, may function in the biosynthesis of Ru5P in some archaeal strains whose pentose phosphate pathways are imperfect. In this study, we have taken a genetic approach to address this possibility by using the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. This strain possesses a single open reading frame (TK0475) encoding an HPS- and PHI-fused protein. The recombinant HPS-PHI-fused enzyme exhibited the expected HPS and PHI activities in both directions (formaldehyde fixing and Ru5P synthesizing). The TK0475 deletion mutant Delta hps-phi-7A did not exhibit any growth in minimal medium, while growth of the mutant strain could be recovered by the addition of nucleosides to the medium. This auxotrophic phenotype together with the catalytic properties of the HPS-PHI-fused enzyme reveal that HPS and PHI are essential for the biosynthesis of Ru5P, the precursor of nucleotides, showing that the RuMP pathway is the only relevant pathway for Ru5P biosynthesis substituting for the classical pentose phosphate pathway missing in this archaeon.
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Affiliation(s)
- Izumi Orita
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Kyoto 606-8502, Japan
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Affiliation(s)
- Robert H White
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, 24061, USA.
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