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Zhong ZP, Du J, Köstlbacher S, Pjevac P, Orlić S, Sullivan MB. Viral potential to modulate microbial methane metabolism varies by habitat. Nat Commun 2024; 15:1857. [PMID: 38424049 PMCID: PMC10904782 DOI: 10.1038/s41467-024-46109-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
Methane is a potent greenhouse gas contributing to global warming. Microorganisms largely drive the biogeochemical cycling of methane, yet little is known about viral contributions to methane metabolism (MM). We analyzed 982 publicly available metagenomes from host-associated and environmental habitats containing microbial MM genes, expanding the known MM auxiliary metabolic genes (AMGs) from three to 24, including seven genes exclusive to MM pathways. These AMGs are recovered on 911 viral contigs predicted to infect 14 prokaryotic phyla including Halobacteriota, Methanobacteriota, and Thermoproteota. Of those 24, most were encoded by viruses from rumen (16/24), with substantially fewer by viruses from environmental habitats (0-7/24). To search for additional MM AMGs from an environmental habitat, we generate metagenomes from methane-rich sediments in Vrana Lake, Croatia. Therein, we find diverse viral communities, with most viruses predicted to infect methanogens and methanotrophs and some encoding 13 AMGs that can modulate host metabolisms. However, none of these AMGs directly participate in MM pathways. Together these findings suggest that the extent to which viruses use AMGs to modulate host metabolic processes (e.g., MM) varies depending on the ecological properties of the habitat in which they dwell and is not always predictable by habitat biogeochemical properties.
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Affiliation(s)
- Zhi-Ping Zhong
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Jingjie Du
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Division of Nutritional Science, Cornell University, Ithaca, NY, USA
| | - Stephan Köstlbacher
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Petra Pjevac
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.
- Center of Excellence for Science and Technology-Integration of Mediterranean Region, Zagreb, Croatia.
| | - Matthew B Sullivan
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA.
- Department of Microbiology, Ohio State University, Columbus, OH, USA.
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA.
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Ohnuki J, Arimura Y, Kono T, Kino K, Kurumizaka H, Takano M. Electrostatic Ratchet for Successive Peptide Synthesis in Nonribosomal Molecular Machine RimK. J Am Chem Soc 2023. [PMID: 37452763 PMCID: PMC10375531 DOI: 10.1021/jacs.3c03926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
A nonribosomal peptide-synthesizing molecular machine, RimK, adds l-glutamic acids to the C-terminus of ribosomal protein S6 (RpsF) in vivo and synthesizes poly-α-glutamates in vitro. However, the mechanism of the successive glutamate addition, which is fueled by ATP, remains unclear. Here, we investigate the successive peptide-synthesizing mechanism of RimK via the molecular dynamics (MD) simulation of glutamate binding. We first show that RimK adopts three stable structural states with respect to the ATP-binding loop and the triphosphate chain of the bound ATP. We then show that a glutamate in solution preferentially binds to a positively charged belt-like region of RimK and the bound glutamate exhibits Brownian motion along the belt. The binding-energy landscape shows that the open-to-closed transition of the ATP-binding loop and the bent-to-straight transition of the triphosphate chain of ATP can function as an electrostatic ratchet that guides the bound glutamate to the active site. We then show the binding site of the second glutamate, which allows us to infer the ligation mechanism. Consistent with MD results, the crystal structure of RimK we obtained in the presence of RpsF presents an electron density that is presumed to correspond to the C-terminus of RpsF. We finally propose a mechanism for the successive peptide synthesis by RimK and discuss its similarity to other molecular machines.
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Affiliation(s)
- Jun Ohnuki
- Department of Pure and Applied Physics, Waseda University, Okubo 3-4-1, Shinjuku-Ku, Tokyo 169-8555, Japan
| | - Yasuhiro Arimura
- Institute for Quantitative Biosciences, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tomonori Kono
- Department of Applied Chemistry, Waseda University, Okubo 3-4-1, Shinjuku-Ku, Tokyo 169-8555, Japan
| | - Kuniki Kino
- Department of Applied Chemistry, Waseda University, Okubo 3-4-1, Shinjuku-Ku, Tokyo 169-8555, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Mitsunori Takano
- Department of Pure and Applied Physics, Waseda University, Okubo 3-4-1, Shinjuku-Ku, Tokyo 169-8555, Japan
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3
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Jurdzinski KT, Mehrshad M, Delgado LF, Deng Z, Bertilsson S, Andersson AF. Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity. SCIENCE ADVANCES 2023; 9:eadg2059. [PMID: 37235649 PMCID: PMC10219603 DOI: 10.1126/sciadv.adg2059] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/21/2023] [Indexed: 05/28/2023]
Abstract
The crossing of environmental barriers poses major adaptive challenges. Rareness of freshwater-marine transitions separates the bacterial communities, but how these are related to brackish counterparts remains elusive, as do the molecular adaptations facilitating cross-biome transitions. We conducted large-scale phylogenomic analysis of freshwater, brackish, and marine quality-filtered metagenome-assembled genomes (11,248). Average nucleotide identity analyses showed that bacterial species rarely existed in multiple biomes. In contrast, distinct brackish basins cohosted numerous species, but their intraspecific population structures displayed clear signs of geographic separation. We further identified the most recent cross-biome transitions, which were rare, ancient, and most commonly directed toward the brackish biome. Transitions were accompanied by systematic changes in amino acid composition and isoelectric point distributions of inferred proteomes, which evolved over millions of years, as well as convergent gains or losses of specific gene functions. Therefore, adaptive challenges entailing proteome reorganization and specific changes in gene content constrains the cross-biome transitions, resulting in species-level separation between aquatic biomes.
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Affiliation(s)
- Krzysztof T. Jurdzinski
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Luis Fernando Delgado
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Ziling Deng
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders F. Andersson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
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4
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Perween N, Pekhale K, Haval G, Khude G, Ghaskadbi S, Ghaskadbi SS. Glutathione synthetase from Hydra vulgaris: Molecular cloning, overexpression, purification and partial characterization. Protein Expr Purif 2023; 208-209:106292. [PMID: 37127055 DOI: 10.1016/j.pep.2023.106292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/03/2023]
Affiliation(s)
- Nusrat Perween
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India; Department of Zoology, M.C.E. Society's Abeda Inamdar Senior College, Pune, 411001, India
| | - Komal Pekhale
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India
| | - Gauri Haval
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India; Department of Zoology, Abasaheb Garware College, Pune, 411004, India
| | - Gaurav Khude
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India
| | - Surendra Ghaskadbi
- Developmental Biology Group, MACS-Agharkar Research Institute, Pune, 411004, India
| | - Saroj S Ghaskadbi
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India.
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Grinter R, Greening C. Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea. FEMS Microbiol Rev 2021; 45:fuab021. [PMID: 33851978 PMCID: PMC8498797 DOI: 10.1093/femsre/fuab021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway; however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.
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Affiliation(s)
- Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Chris Greening
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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6
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Subedi BP, Martin WF, Carbone V, Duin EC, Cronin B, Sauter J, Schofield LR, Sutherland-Smith AJ, Ronimus RS. Archaeal pseudomurein and bacterial murein cell wall biosynthesis share a common evolutionary ancestry. FEMS MICROBES 2021; 2:xtab012. [PMID: 37334239 PMCID: PMC10117817 DOI: 10.1093/femsmc/xtab012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 08/19/2021] [Indexed: 08/29/2023] Open
Abstract
Bacteria near-universally contain a cell wall sacculus of murein (peptidoglycan), the synthesis of which has been intensively studied for over 50 years. In striking contrast, archaeal species possess a variety of other cell wall types, none of them closely resembling murein. Interestingly though, one type of archaeal cell wall termed pseudomurein found in the methanogen orders Methanobacteriales and Methanopyrales is a structural analogue of murein in that it contains a glycan backbone that is cross-linked by a L-amino acid peptide. Here, we present taxonomic distribution, gene cluster and phylogenetic analyses that confirm orthologues of 13 bacterial murein biosynthesis enzymes in pseudomurein-containing methanogens, most of which are distantly related to their bacterial counterparts. We also present the first structure of an archaeal pseudomurein peptide ligase from Methanothermus fervidus DSM1088 (Mfer336) to a resolution of 2.5 Å and show that it possesses a similar overall tertiary three domain structure to bacterial MurC and MurD type murein peptide ligases. Taken together the data strongly indicate that murein and pseudomurein biosynthetic pathways share a common evolutionary history.
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Affiliation(s)
- Bishwa P Subedi
- AgResearch Ltd. Grasslands, Tennent Drive, Palmerston North 4442, New Zealand
- Massey University, Tennent Drive, Palmerston North 4442, New Zealand
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine University, Düsseldorf Universitätsstraße 1, D-40225, Germany
| | - Vincenzo Carbone
- AgResearch Ltd. Grasslands, Tennent Drive, Palmerston North 4442, New Zealand
| | - Eduardus C Duin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
| | - Bryan Cronin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
| | - Julia Sauter
- AgResearch Ltd. Grasslands, Tennent Drive, Palmerston North 4442, New Zealand
| | - Linley R Schofield
- AgResearch Ltd. Grasslands, Tennent Drive, Palmerston North 4442, New Zealand
| | | | - Ron S Ronimus
- AgResearch Ltd. Grasslands, Tennent Drive, Palmerston North 4442, New Zealand
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Hemmann JL, Brühwiler MR, Bortfeld-Miller M, Vorholt JA. Structural diversity of the coenzyme methylofuran and identification of enzymes for the biosynthesis of its polyglutamate side chain. J Biol Chem 2021; 296:100682. [PMID: 33894199 PMCID: PMC8141765 DOI: 10.1016/j.jbc.2021.100682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/07/2021] [Accepted: 04/18/2021] [Indexed: 11/17/2022] Open
Abstract
Methylofuran (MYFR) is a formyl-carrying coenzyme essential for the oxidation of formaldehyde in most methylotrophic bacteria. In Methylorubrum extorquens, MYFR contains a large and branched polyglutamate side chain of up to 24 glutamates. These glutamates play an essential role in interfacing the coenzyme with the formyltransferase/hydrolase complex, an enzyme that generates formate. To date, MYFR has not been identified in other methylotrophs, and it is unknown whether its structural features are conserved. Here, we examined nine bacterial strains for the presence and structure of MYFR using high-resolution liquid chromatography-mass spectrometry (LC-MS). Two of the strains produced MYFR as present in M. extorquens, while a modified MYFR containing tyramine instead of tyrosine in its core structure was detected in six strains. When M. extorquens was grown in the presence of tyramine, the compound was readily incorporated into MYFR, indicating that the biosynthetic enzymes are unable to discriminate tyrosine from tyramine. Using gene deletions in combination with LC-MS analyses, we identified three genes, orf5, orfY, and orf17 that are essential for MYFR biosynthesis. Notably, the orfY and orf5 mutants accumulated short MYFR intermediates with only one and two glutamates, respectively, suggesting that these enzymes catalyze glutamate addition. Upon homologous overexpression of orf5, a drastic increase in the number of glutamates in MYFR was observed (up to 40 glutamates), further corroborating the function of Orf5 as a glutamate ligase. We thus renamed OrfY and Orf5 to MyfA and MyfB to highlight that these enzymes are specifically involved in MYFR biosynthesis.
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Bharathi M, Senthil Kumar N, Chellapandi P. Functional Prediction and Assignment of Methanobrevibacter ruminantium M1 Operome Using a Combined Bioinformatics Approach. Front Genet 2020; 11:593990. [PMID: 33391347 PMCID: PMC7772410 DOI: 10.3389/fgene.2020.593990] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
Methanobrevibacter ruminantium M1 (MRU) is a rod-shaped rumen methanogen with the ability to use H2 and CO2, and formate as substrates for methane formation in the ruminants. Enteric methane emitted from this organism can also be influential to the loss of dietary energy in ruminants and humans. To date, there is no successful technology to reduce methane due to a lack of knowledge on its molecular machinery and 73% conserved hypothetical proteins (HPs; operome) whose functions are still not ascertained perceptively. To address this issue, we have predicted and assigned a precise function to HPs and categorize them as metabolic enzymes, binding proteins, and transport proteins using a combined bioinformatics approach. The results of our study show that 257 (34%) HPs have well-defined functions and contributed essential roles in its growth physiology and host adaptation. The genome-neighborhood analysis identified 6 operon-like clusters such as hsp, TRAM, dsr, cbs and cas, which are responsible for protein folding, sudden heat-shock, host defense, and protection against the toxicities in the rumen. The functions predicted from MRU operome comprised of 96 metabolic enzymes with 17 metabolic subsystems, 31 transcriptional regulators, 23 transport, and 11 binding proteins. Functional annotation of its operome is thus more imperative to unravel the molecular and cellular machinery at the systems-level. The functional assignment of its operome would advance strategies to develop new anti-methanogenic targets to mitigate methane production. Hence, our approach provides new insight into the understanding of its growth physiology and lifestyle in the ruminants and also to reduce anthropogenic greenhouse gas emissions worldwide.
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Affiliation(s)
- M Bharathi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, India
| | - N Senthil Kumar
- Human Genetics Lab, Department of Biotechnology, School of Life Sciences, Mizoram University (Central University), Aizawl, India
| | - P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, India
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Hassan NM, Nemat Alla MM. Kinetics of inhibition of isoproturon to glutathione-associated enzymes in wheat. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1505-1518. [PMID: 32647464 PMCID: PMC7326839 DOI: 10.1007/s12298-020-00812-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/23/2020] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
The present study aimed at investigating the kinetic of inhibition of isoproturon to the GSH-associated enzymes [γ-glutamyl-cysteine synthetase (γ-GCS), glutathione synthetase (GS), glutathione reductase (GR), glutathione-S-transferase (GST) and glutathione peroxidase (GPX)] in wheat. Isoproturon, applied to 10-day-old seedlings for the following 12 days, provoked significant reductions in shoot fresh and dry weights, protein, thiols and glutathione (GSH); however, oxidized glutathione (GSSG) was elevated while GSH/GSSG ratio was declined with concomitant significant inhibitions in the activities of γ-GCS, GS, GR, GST and GPX; the effect was time dependent. IC50 and Ki values of isoproturon were lowest for GPX, highest for both GST and GR, and moderate for both γ-GCS and GS. The herbicide markedly decreased Vmax of γ-GCS, GS and GPX but unchanged that of GST and GR; however, Km of γ-GCS, GS, GST and GR increased but unchanged for GPX. The pattern of response of changing Vmax, Km, Vmax/Km, kcat and kcat/Km for in vivo and in vitro tests of each enzyme seemed most likely similar. These results indicate that a malfunction to defense system was induced in wheat by isoproturon resulting in inhibitions in GSH-associated enzymes, the magnitude of inhibition was most pronounced in GPX followed by γ-GCS, GS, GST, and GR. These findings could conclude that isoproturon competitively inhibited GST and GR; however, the inhibition was noncompetitive for GPX but mixed for both γ-GCS and GS.
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Affiliation(s)
- Nemat M. Hassan
- Botany Department, Faculty of Science, Damietta University, PO 34517, New Damietta, Egypt
| | - Mamdouh M. Nemat Alla
- Botany Department, Faculty of Science, Damietta University, PO 34517, New Damietta, Egypt
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Siddiquee K, Zhao C, Stemler MA, Zeck B, Fishpaugh JR, Allen SP. Cell-culture growth conditions resulting in the oxidation of a recombinant antigen-binding fragment. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0270-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Abstract
Use of Quality-by-Design (QbD) tools is becoming an important part of the bioprocessing industry when developing a process for manufacturing operations to ensure the robustness and reproducibility of the biologic product. In the present study, a QbD tool, Design of Experiments (DOE), was utilized to optimize a bioprocess for the production of a CHO recombinant antigen-binding fragment (rFab) in small-scale bioreactors. DOE studies evaluated percent dissolved oxygen, temperature, and feeding strategy specific to this Chinese Hamster Ovary (CHO) clone. It was determined that these factors influenced cell viability, yield of the recombinant protein, and metabolic byproduct formation. To ensure the quality of the target molecule in the cell-culture process, small-scale purifications and analytical evaluation of the target molecule were completed prior to cell-culture scale-up to ensure that oxidation of the rFab, presence of free light chain, and truncation of thiol group were not observed. Analysis of the purified rFab by mass spectrometry indicated that rFab oxidation occurred under poor cell-culture conditions. PCR profile array results also revealed increased transcription of the oxidative genes Superoxide Dismutase 3, Myeloperoxidase, Dual Oxidase Like 2, Nuclear Receptor Coactivator 7, NADPH Oxidase Organizer 1, Mitochondria Uncouple Protein 3, Eosinophil Peroxidase, Lactoperoxidase Like, Serum Albumin Like, and Glutathione S-Transferase Pi 1 in this CHO strain. The present study suggests a mechanism and pathway for the oxidation of an rFab molecule during cell-culture bioprocess optimization. The present study also demonstrated the importance of utilizing the QbD tool of DOE to optimize the cell-culture bioprocess prior to scaling up into the large-scale production bioreactor.
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Boro P, Sultana A, Mandal K, Chattopadhyay S. Transcriptomic changes under stress conditions with special reference to glutathione contents. THE NUCLEUS 2018. [DOI: 10.1007/s13237-018-0256-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Coenzyme F 420-Dependent Glucose-6-Phosphate Dehydrogenase-Coupled Polyglutamylation of Coenzyme F 420 in Mycobacteria. J Bacteriol 2018; 200:JB.00375-18. [PMID: 30249701 DOI: 10.1128/jb.00375-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/07/2018] [Indexed: 12/15/2022] Open
Abstract
Coenzyme F420 plays a key role in the redox metabolisms of various archaea and bacteria, including Mycobacterium tuberculosis In M. tuberculosis, F420-dependent reactions have been linked to several virulence factors. F420 carries multiple glutamate residues in the side chain, forming F420-n species (n, number of glutamate residues), and the length of this side chain impacts cellular physiology. M. tuberculosis strains with F420 species carrying shorter side chains exhibit resistance to delamanid and pretomanid, two new tuberculosis (TB) drugs. Thus, the process of polyglutamylation of F420 is of great interest. It has been known from genetic analysis that in mycobacteria an F420-0 γ-glutamyl ligase (FbiB) introduces up to seven glutamate residues into F420 However, purified FbiB of M. tuberculosis (MtbFbiB) is either inefficient or incapable of incorporating more than two glutamates. We found that, in vitro, MtbFbiB synthesized side chains containing up to seven glutamate residues if F420 was presented to the enzyme in a two-electron reduced state (F420H2). Our genetic analysis in Mycobacterium bovis BCG and Mycobacterium smegmatis and an analysis of literature data on M. tuberculosis revealed that in these mycobacteria the polyglutamylation process requires the assistance of F420-dependent glucose-6-phosphate dehydrogenase (Fgd) which reduces F420 to F420H2 We hypothesize that, starting with F420-0H2, the amino-terminal domain of FbiB builds F420-2H2, which is then transferred to the carboxy-terminal domain for further glutamylation; F420-2H2 modifies the carboxy-terminal domain structurally to accommodate longer glutamyl chains. This system is analogous to folylpolyglutamate synthase, which introduces more than one glutamate residue into folate only after this vitamin is reduced to tetrahydrofolate.IMPORTANCE Coenzyme F420-dependent reactions of Mycobacterium tuberculosis, which causes tuberculosis, potentially contributes to the virulence of this bacterium. The coenzyme carries a glutamic acid-derived tail, the length of which influences the metabolism of M. tuberculosis Mutations that eliminate the production of F420 with longer tails make M. tuberculosis resistant to two new tuberculosis drugs. This report describes that the synthesis of longer glutamyl tails of F420 requires concerted actions of two enzymes, one of which reduces the coenzyme prior to the action of the other, which catalyzes polyglutamylation. This knowledge will help to develop more effective tuberculosis (TB) drugs. Remarkably, the introduction of multiple glutamate residues into the sidechain of folate (vitamin B9) requires similar concerted actions, where one enzyme reduces the vitamin to tetrahydrofolate and the other catalyzes polyglutamylation; folate is required for DNA and amino acid synthesis. Thus, the reported research has also revealed a key similarity between two important cellular systems.
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Plominsky AM, Trefault N, Podell S, Blanton JM, De la Iglesia R, Allen EE, von Dassow P, Ulloa O. Metabolic potential andin situtranscriptomic profiles of previously uncharacterized key microbial groups involved in coupled carbon, nitrogen and sulfur cycling in anoxic marine zones. Environ Microbiol 2018; 20:2727-2742. [DOI: 10.1111/1462-2920.14109] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 02/27/2018] [Accepted: 03/07/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Alvaro M. Plominsky
- Departamento de Oceanografía; Universidad de Concepción, P.O. Box 160-C; Concepción 4070386 Chile
- Instituto Milenio de Oceanografía, Universidad de Concepción; Concepción Chile
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor; Santiago 8580745 Chile
| | - Sheila Podell
- Marine Biology Research Division; Scripps Institution of Oceanography, University of California San Diego; San Diego CA 92093-0202 USA
| | - Jessica M. Blanton
- Marine Biology Research Division; Scripps Institution of Oceanography, University of California San Diego; San Diego CA 92093-0202 USA
| | - Rodrigo De la Iglesia
- Department of Molecular Genetics and Microbiology; Pontificia Universidad Católica de Chile; Santiago 8331150 Chile
| | - Eric E. Allen
- Marine Biology Research Division; Scripps Institution of Oceanography, University of California San Diego; San Diego CA 92093-0202 USA
- Division of Biological Sciences; University of California; San Diego CA USA
| | - Peter von Dassow
- Instituto Milenio de Oceanografía, Universidad de Concepción; Concepción Chile
- Department of Ecology; Pontificia Universidad Católica de Chile; Santiago 8331150 Chile
- Research Department UMI 3614, Evolutionary Biology and Ecology of Algae; CNRS UPMC; Roscoff 29680 France
| | - Osvaldo Ulloa
- Departamento de Oceanografía; Universidad de Concepción, P.O. Box 160-C; Concepción 4070386 Chile
- Instituto Milenio de Oceanografía, Universidad de Concepción; Concepción Chile
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Zhang D, Dong Y, Yu Q, Kai Z, Zhang M, Jia C, Xiao C, Zhang B, Zhang B, Li M. Function of glutaredoxin 3 (Grx3) in oxidative stress response caused by iron homeostasis disorder in Candida albicans. Future Microbiol 2017; 12:1397-1412. [DOI: 10.2217/fmb-2017-0098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Aim: Glutaredoxin is a conserved oxidoreductase in eukaryotes and prokaryotes. This study aimed to determine the role of Grx3 in cell survival, iron homeostasis and the oxidative stress response in Candida albicans. Materials & methods: A grx3Δ/Δ mutant was obtained using PCR-mediated homologs recombination. The function of Grx3 was investigated by a series of biochemical methods. Results: Deletion of GRX3 impaired growth and cell cycle, disturbance of iron homeostasis and activated the oxidative stress response. Furthermore, disruption of GRX3 caused oxidative damage and growth defects of C. albicans. Conclusion: Our findings provide new insights into the role of GRX3 in C. albicans.
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Affiliation(s)
- Dan Zhang
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yijie Dong
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
- The State Key Laboratory for Biology of Plant Disease & Insect Pests, Institute of Plant protection, Chinese Academy of Agricultural sciences, Beijing 100871, China
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhang Kai
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Meng Zhang
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Chang Jia
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Chenpeng Xiao
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Bing Zhang
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Biao Zhang
- College of language and culture, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China
| | - Mingchun Li
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
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15
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Physiology, Biochemistry, and Applications of F420- and Fo-Dependent Redox Reactions. Microbiol Mol Biol Rev 2016; 80:451-93. [PMID: 27122598 DOI: 10.1128/mmbr.00070-15] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
5-Deazaflavin cofactors enhance the metabolic flexibility of microorganisms by catalyzing a wide range of challenging enzymatic redox reactions. While structurally similar to riboflavin, 5-deazaflavins have distinctive and biologically useful electrochemical and photochemical properties as a result of the substitution of N-5 of the isoalloxazine ring for a carbon. 8-Hydroxy-5-deazaflavin (Fo) appears to be used for a single function: as a light-harvesting chromophore for DNA photolyases across the three domains of life. In contrast, its oligoglutamyl derivative F420 is a taxonomically restricted but functionally versatile cofactor that facilitates many low-potential two-electron redox reactions. It serves as an essential catabolic cofactor in methanogenic, sulfate-reducing, and likely methanotrophic archaea. It also transforms a wide range of exogenous substrates and endogenous metabolites in aerobic actinobacteria, for example mycobacteria and streptomycetes. In this review, we discuss the physiological roles of F420 in microorganisms and the biochemistry of the various oxidoreductases that mediate these roles. Particular focus is placed on the central roles of F420 in methanogenic archaea in processes such as substrate oxidation, C1 pathways, respiration, and oxygen detoxification. We also describe how two F420-dependent oxidoreductase superfamilies mediate many environmentally and medically important reactions in bacteria, including biosynthesis of tetracycline and pyrrolobenzodiazepine antibiotics by streptomycetes, activation of the prodrugs pretomanid and delamanid by Mycobacterium tuberculosis, and degradation of environmental contaminants such as picrate, aflatoxin, and malachite green. The biosynthesis pathways of Fo and F420 are also detailed. We conclude by considering opportunities to exploit deazaflavin-dependent processes in tuberculosis treatment, methane mitigation, bioremediation, and industrial biocatalysis.
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16
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Nobu MK, Narihiro T, Kuroda K, Mei R, Liu WT. Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen. ISME JOURNAL 2016; 10:2478-87. [PMID: 26943620 DOI: 10.1038/ismej.2016.33] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/22/2016] [Accepted: 01/29/2016] [Indexed: 02/06/2023]
Abstract
The ecophysiology of one candidate methanogen class WSA2 (or Arc I) remains largely uncharacterized, despite the long history of research on Euryarchaeota methanogenesis. To expand our understanding of methanogen diversity and evolution, we metagenomically recover eight draft genomes for four WSA2 populations. Taxonomic analyses indicate that WSA2 is a distinct class from other Euryarchaeota. None of genomes harbor pathways for CO2-reducing and aceticlastic methanogenesis, but all possess H2 and CO oxidation and energy conservation through H2-oxidizing electron confurcation and internal H2 cycling. As the only discernible methanogenic outlet, they consistently encode a methylated thiol coenzyme M methyltransferase. Although incomplete, all draft genomes point to the proposition that WSA2 is the first discovered methanogen restricted to methanogenesis through methylated thiol reduction. In addition, the genomes lack pathways for carbon fixation, nitrogen fixation and biosynthesis of many amino acids. Acetate, malonate and propionate may serve as carbon sources. Using methylated thiol reduction, WSA2 may not only bridge the carbon and sulfur cycles in eutrophic methanogenic environments, but also potentially compete with CO2-reducing methanogens and even sulfate reducers. These findings reveal a remarkably unique methanogen 'Candidatus Methanofastidiosum methylthiophilus' as the first insight into the sixth class of methanogens 'Candidatus Methanofastidiosa'.
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Affiliation(s)
- Masaru Konishi Nobu
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Kyohei Kuroda
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA.,Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA
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17
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Yenugudhati D, Prakash D, Kumar AK, Kumar RSS, Yennawar NH, Yennawar HP, Ferry JG. Structural and Biochemical Characterizations of Methanoredoxin from Methanosarcina acetivorans, a Glutaredoxin-Like Enzyme with Coenzyme M-Dependent Protein Disulfide Reductase Activity. Biochemistry 2015; 55:313-21. [PMID: 26684934 DOI: 10.1021/acs.biochem.5b00823] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Glutaredoxins (GRXs) are thiol-disulfide oxidoreductases abundant in prokaryotes, although little is understood of these enzymes from the domain Archaea. The numerous characterized GRXs from the domain Bacteria utilize a diversity of low-molecular-weight thiols in addition to glutathione as reductants. We report here the biochemical and structural properties of a GRX-like protein named methanoredoxin (MRX) from Methanosarcina acetivorans of the domain Archaea. MRX utilizes coenzyme M (CoMSH) as reductant for insulin disulfide reductase activity, which adds to the diversity of thiol protectants in prokaryotes. Cell-free extracts of M. acetivorans displayed CoMS-SCoM reductase activity that complements the CoMSH-dependent activity of MRX. The crystal structure exhibits a classic thioredoxin-glutaredoxin fold comprising three α-helices surrounding four antiparallel β-sheets. A pocket on the surface contains a CVWC motif, identifying the active site with architecture similar to GRXs. Although it is a monomer in solution, the crystal lattice has four monomers in a dimer of dimers arrangement. A cadmium ion is found within the active site of each monomer. Two such ions stabilize the N-terminal tails and dimer interfaces. Our modeling studies indicate that CoMSH and glutathione (GSH) bind to the active site of MRX similar to the binding of GSH in GRXs, although there are differences in the amino acid composition of the binding motifs. The results, combined with our bioinformatic analyses, show that MRX represents a class of GRX-like enzymes present in a diversity of methane-producing Archaea.
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Affiliation(s)
- Deepa Yenugudhati
- Department of Biochemistry and Molecular Biology, ‡Huck Institutes of Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Divya Prakash
- Department of Biochemistry and Molecular Biology, ‡Huck Institutes of Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Adepu K Kumar
- Department of Biochemistry and Molecular Biology, ‡Huck Institutes of Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - R Siva Sai Kumar
- Department of Biochemistry and Molecular Biology, ‡Huck Institutes of Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Neela H Yennawar
- Department of Biochemistry and Molecular Biology, ‡Huck Institutes of Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Hemant P Yennawar
- Department of Biochemistry and Molecular Biology, ‡Huck Institutes of Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, ‡Huck Institutes of Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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18
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Mutations in genes for the F420 biosynthetic pathway and a nitroreductase enzyme are the primary resistance determinants in spontaneous in vitro-selected PA-824-resistant mutants of Mycobacterium tuberculosis. Antimicrob Agents Chemother 2015; 59:5316-23. [PMID: 26100695 DOI: 10.1128/aac.00308-15] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 06/09/2015] [Indexed: 11/20/2022] Open
Abstract
Alleviating the burden of tuberculosis (TB) requires an understanding of the genetic basis that determines the emergence of drug-resistant mutants. PA-824 (pretomanid) is a bicyclic nitroimidazole class compound presently undergoing the phase III STAND clinical trial, despite lacking identifiable genetic markers for drug-specific resistant Mycobacterium tuberculosis. In the present study, we aimed to characterize the genetic polymorphisms of spontaneously generated PA-824-resistant mutant strains by surveying drug metabolism genes for potential mutations. Of the 183 independently selected PA-824-resistant M. tuberculosis mutants, 83% harbored a single mutation in one of five nonessential genes associated with either PA-824 prodrug activation (ddn, 29%; fgd1, 7%) or the tangential F420 biosynthetic pathway (fbiA, 19%; fbiB, 2%; fbiC, 26%). Crystal structure analysis indicated that identified mutations were specifically located within the protein catalytic domain that would hinder the activity of the enzymes required for prodrug activation. This systematic analysis conducted of genotypes resistant to PA-824 may contribute to future efforts in monitoring clinical strain susceptibility with this new drug therapy.
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19
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Philmus B, Decamps L, Berteau O, Begley TP. Biosynthetic versatility and coordinated action of 5'-deoxyadenosyl radicals in deazaflavin biosynthesis. J Am Chem Soc 2015; 137:5406-13. [PMID: 25781338 PMCID: PMC4416281 DOI: 10.1021/ja513287k] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Indexed: 12/30/2022]
Abstract
Coenzyme F420 is a redox cofactor found in methanogens and in various actinobacteria. Despite the major biological importance of this cofactor, the biosynthesis of its deazaflavin core (8-hydroxy-5-deazaflavin, F(o)) is still poorly understood. F(o) synthase, the enzyme involved, is an unusual multidomain radical SAM enzyme that uses two separate 5'-deoxyadenosyl radicals to catalyze F(o) formation. In this paper, we report a detailed mechanistic study on this complex enzyme that led us to identify (1) the hydrogen atoms abstracted from the substrate by the two radical SAM domains, (2) the second tyrosine-derived product, (3) the reaction product of the CofH-catalyzed reaction, (4) the demonstration that this product is a substrate for CofG, and (5) a stereochemical study that is consistent with the formation of a p-hydroxybenzyl radical at the CofH active site. These results enable us to propose a mechanism for F(o) synthase and uncover a new catalytic motif in radical SAM enzymology involving the use of two 5'-deoxyadenosyl radicals to mediate the formation of a complex heterocycle.
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Affiliation(s)
- Benjamin Philmus
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Laure Decamps
- ChemSyBio,
UMR 1319 Micalis, INRA, F-78350 Jouy-en-Josas, France
- ChemSyBio,
UMR Micalis, AgroParisTech, F-78350 Jouy-en-Josas, France
| | - Olivier Berteau
- ChemSyBio,
UMR 1319 Micalis, INRA, F-78350 Jouy-en-Josas, France
- ChemSyBio,
UMR Micalis, AgroParisTech, F-78350 Jouy-en-Josas, France
| | - Tadhg P. Begley
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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20
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21
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Wang Y, Xu H, Harich KC, White RH. Identification and Characterization of a Tyramine–Glutamate Ligase (MfnD) Involved in Methanofuran Biosynthesis. Biochemistry 2014; 53:6220-30. [DOI: 10.1021/bi500879h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Yu Wang
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Huimin Xu
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Kim C. Harich
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Robert H. White
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
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22
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Zhao G, Jin Z, Wang Y, Allewell NM, Tuchman M, Shi D. Structure and function of Escherichia coli RimK, an ATP-grasp fold, L-glutamyl ligase enzyme. Proteins 2013; 81:1847-54. [PMID: 23609986 DOI: 10.1002/prot.24311] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/04/2013] [Accepted: 04/09/2013] [Indexed: 11/11/2022]
Abstract
We report herein the crystal structure of Escherichia coli RimK at a resolution of 2.85 Å, an enzyme that catalyzes the post-translational addition of up to 15 C-terminal glutamate residues to ribosomal protein S6. The structure belongs to the ATP-grasp superfamily and is organized as a tetramer, consistent with gel filtration analysis. Each subunit consists of three distinct structural domains and the active site is located in the cleft between these domains. The catalytic reaction appears to occur at the junction between the three domains as ATP binds between the B and C domains, and other substrates bind nearby.
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Affiliation(s)
- Gengxiang Zhao
- Department of Integrative Systems Biology, Center for Genetic Medicine Research, Children's National Medical Center, The George Washington University, Washington, DC, 20010
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23
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Fawaz MV, Topper M, Firestine SM. The ATP-grasp enzymes. Bioorg Chem 2011; 39:185-91. [PMID: 21920581 PMCID: PMC3243065 DOI: 10.1016/j.bioorg.2011.08.004] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 08/12/2011] [Accepted: 08/13/2011] [Indexed: 12/17/2022]
Abstract
The ATP-grasp enzymes consist of a superfamily of 21 proteins that contain an atypical ATP-binding site, called the ATP-grasp fold. The ATP-grasp fold is comprised of two α+β domains that "grasp" a molecule of ATP between them and members of the family typically have an overall structural design containing three common conserved focal domains. The founding members of the family consist of biotin carboxylase, d-ala-d-ala ligase and glutathione synthetase, all of which catalyze the ATP-assisted reaction of a carboxylic acid with a nucleophile via the formation of an acylphosphate intermediate. While most members of the superfamily follow this mechanistic pathway, studies have demonstrated that two enzymes catalyze only the phosphoryl transfer step and thus are kinases instead of ligases. Members of the ATP-grasp superfamily are found in several metabolic pathways including de novo purine biosynthesis, gluconeogenesis, and fatty acid synthesis. Given the critical nature of these enzymes, researchers have actively sought the development of potent inhibitors of several members of the superfamily as antibacterial and anti-obseity agents. In this review, we will discuss the structure, function, mechanism, and inhibition of the ATP-grasp enzymes.
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Affiliation(s)
| | | | - Steven M. Firestine
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201
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24
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Rehan AM, Bashiri G, Paterson NG, Baker EN, Squire CJ. Cloning, expression, purification, crystallization and preliminary X-ray studies of the C-terminal domain of Rv3262 (FbiB) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1274-7. [PMID: 22102046 PMCID: PMC3212381 DOI: 10.1107/s1744309111028958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 07/18/2011] [Indexed: 11/11/2022]
Abstract
During cofactor F(420) biosynthesis, the enzyme F(420)-γ-glutamyl ligase (FbiB) catalyzes the addition of γ-linked L-glutamate residues to form polyglutamylated F(420) derivatives. In Mycobacterium tuberculosis, Rv3262 (FbiB) consists of two domains: an N-terminal domain from the F(420) ligase superfamily and a C-terminal domain with sequence similarity to nitro-FMN reductase superfamily proteins. To characterize the role of the C-terminal domain of FbiB in polyglutamyl ligation, it has been purified and crystallized in an apo form. The crystals diffracted to 2.0 Å resolution using a synchrotron source and belonged to the tetragonal space group P4(1)2(1)2 (or P4(3)2(1)2), with unit-cell parameters a = b = 136.6, c = 101.7 Å, α = β = γ = 90°.
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Affiliation(s)
- Aisyah M Rehan
- Structural Biology Laboratory, School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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25
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More than 200 genes required for methane formation from H₂ and CO₂ and energy conservation are present in Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2011; 2011:973848. [PMID: 21559116 PMCID: PMC3087415 DOI: 10.1155/2011/973848] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 12/07/2010] [Accepted: 02/18/2011] [Indexed: 12/19/2022]
Abstract
The hydrogenotrophic methanogens Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus can easily be mass cultured. They have therefore been used almost exclusively to study the biochemistry of methanogenesis from H2 and CO2, and the genomes of these two model organisms have been sequenced. The close relationship of the two organisms is reflected in their genomic architecture and coding potential. Within the 1,607 protein coding sequences (CDS) in common, we identified approximately 200 CDS required for the synthesis of the enzymes, coenzymes, and prosthetic groups involved in CO2 reduction to methane and in coupling this process with the phosphorylation of ADP. Approximately 20 additional genes, such as those for the biosynthesis of F430 and methanofuran and for the posttranslational modifications of the two methyl-coenzyme M reductases, remain to be identified.
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26
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Poly-alpha-glutamic acid synthesis using a novel catalytic activity of RimK from Escherichia coli K-12. Appl Environ Microbiol 2011; 77:2019-25. [PMID: 21278279 DOI: 10.1128/aem.02043-10] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Poly-L-α-amino acids have various applications because of their biodegradable properties and biocompatibility. Microorganisms contain several enzymes that catalyze the polymerization of L-amino acids in an ATP-dependent manner, but the products from these reactions contain amide linkages at the side residues of amino acids: e.g., poly-γ-glutamic acid, poly-ε-lysine, and cyanophycin. In this study, we found a novel catalytic activity of RimK, a ribosomal protein S6-modifying enzyme derived from Escherichia coli K-12. This enzyme catalyzed poly-α-glutamic acid synthesis from unprotected L-glutamic acid (Glu) by hydrolyzing ATP to ADP and phosphate. RimK synthesized poly-α-glutamic acid of various lengths; matrix-assisted laser desorption ionization-time of flight-mass spectrometry showed that a 46-mer of Glu (maximum length) was synthesized at pH 9. Interestingly, the lengths of polymers changed with changing pH. RimK also exhibited 86% activity after incubation at 55°C for 15 min, thus showing thermal stability. Furthermore, peptide elongation seemed to be catalyzed at the C terminus in a stepwise manner. Although RimK showed strict substrate specificity toward Glu, it also used, to a small extent, other amino acids as C-terminal substrates and synthesized heteropeptides. In addition, RimK-catalyzed modification of ribosomal protein S6 was confirmed. The number of Glu residues added to the protein varied with pH and was largest at pH 9.5.
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27
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Collard F, Stroobant V, Lamosa P, Kapanda CN, Lambert DM, Muccioli GG, Poupaert JH, Opperdoes F, Van Schaftingen E. Molecular identification of N-acetylaspartylglutamate synthase and beta-citrylglutamate synthase. J Biol Chem 2010; 285:29826-33. [PMID: 20657015 DOI: 10.1074/jbc.m110.152629] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The purpose of the present work was to determine the identity of the enzymes that synthesize N-acetylaspartylglutamate (NAAG), the most abundant dipeptide present in vertebrate central nervous system (CNS), and β-citrylglutamate, a structural analogue of NAAG present in testis and immature brain. Previous evidence suggests that NAAG is not synthesized on ribosomes but presumably is synthesized by a ligase. As attempts to detect this ligase in brain extracts failed, we searched the mammalian genomes for putative enzymes that could catalyze this type of reaction. Mammalian genomes were found to encode two putative ligases homologous to Escherichia coli RIMK, which ligates glutamates to the C terminus of ribosomal protein S6. One of them, named RIMKLA, is almost exclusively expressed in the CNS, whereas RIMKLB, which shares 65% sequence identity with RIMKLA, is expressed in CNS and testis. Both proteins were expressed in bacteria or HEK293T cells and purified. RIMKLA catalyzed the ATP-dependent synthesis of N-acetylaspartylglutamate from N-acetylaspartate and l-glutamate. RIMKLB catalyzed this reaction as well as the synthesis of β-citrylglutamate. The nature of the reaction products was confirmed by mass spectrometry and NMR. RIMKLA was shown to produce stoichiometric amounts of NAAG and ADP, in agreement with its belonging to the ATP-grasp family of ligases. The molecular identification of these two enzymes will facilitate progress in the understanding of the function of NAAG and β-citrylglutamate.
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Affiliation(s)
- François Collard
- Laboratory of Physiological Chemistry, de Duve Institute and Université Catholique de Louvain, Avenue Hippocrate 75, B-1200 Brussels, Belgium
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28
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Becker I, Lodder J, Gieselmann V, Eckhardt M. Molecular characterization of N-acetylaspartylglutamate synthetase. J Biol Chem 2010; 285:29156-64. [PMID: 20643647 DOI: 10.1074/jbc.m110.111765] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The dipeptide N-acetylaspartyl-glutamate (NAAG) is an abundant neuropeptide in the mammalian brain. Despite this fact, its physiological role is poorly understood. NAAG is synthesized by a NAAG synthetase catalyzing the ATP-dependent condensation of N-acetylaspartate and glutamate. In vitro NAAG synthetase activity has not been described, and the enzyme has not been purified. Using a bioinformatics approach we identified a putative dipeptide synthetase specifically expressed in the nervous system. Expression of the gene, which we named NAAGS (for NAAG synthetase) was sufficient to induce NAAG synthesis in primary astrocytes or CHO-K1 and HEK-293T cells when they coexpressed the NAA transporter NaDC3. Furthermore, coexpression of NAAGS and the recently identified N-acetylaspartate (NAA) synthase, Nat8l, in CHO-K1 or HEK-293T cells was sufficient to enable these cells to synthesize NAAG. Identity of the reaction product of NAAGS was confirmed by HPLC and electrospray ionization tandem mass spectrometry (ESI-MS). High expression levels of NAAGS were restricted to the brain, spinal cord, and testis. Taken together our results strongly suggest that the identified gene encodes a NAAG synthetase. Its identification will enable further studies to examine the role of this abundant neuropeptide in the vertebrate nervous system.
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Affiliation(s)
- Ivonne Becker
- Institute of Biochemistry and Molecular Biology, University of Bonn, D-53115 Bonn, Germany
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29
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Burg DW, Lauro FM, Williams TJ, Raftery MJ, Guilhaus M, Cavicchioli R. Analyzing the Hydrophobic Proteome of the Antarctic Archaeon Methanococcoides burtonii Using Differential Solubility Fractionation. J Proteome Res 2009; 9:664-76. [DOI: 10.1021/pr9007865] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dominic W. Burg
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia and Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia
| | - Federico M. Lauro
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia and Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia
| | - Timothy J. Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia and Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia
| | - Mark J. Raftery
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia and Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia
| | - Michael Guilhaus
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia and Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia and Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia
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30
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Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L. Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. MOLECULAR BIOSYSTEMS 2009; 5:1636-60. [PMID: 20023723 DOI: 10.1039/b917682a] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Recent studies have shown that the ubiquitin system had its origins in ancient cofactor/amino acid biosynthesis pathways. Preliminary studies also indicated that conjugation systems for other peptide tags on proteins, such as pupylation, have evolutionary links to cofactor/amino acid biosynthesis pathways. Following up on these observations, we systematically investigated the non-ribosomal amidoligases of the ATP-grasp, glutamine synthetase-like and acetyltransferase folds by classifying the known members and identifying novel versions. We then established their contextual connections using information from domain architectures and conserved gene neighborhoods. This showed remarkable, previously uncharacterized functional links between diverse peptide ligases, several peptidases of unrelated folds and enzymes involved in synthesis of modified amino acids. Using the network of contextual connections we were able to predict numerous novel pathways for peptide synthesis and modification, amine-utilization, secondary metabolite synthesis and potential peptide-tagging systems. One potential peptide-tagging system, which is widely distributed in bacteria, involves an ATP-grasp domain and a glutamine synthetase-like ligase, both of which are circularly permuted, an NTN-hydrolase fold peptidase and a novel alpha helical domain. Our analysis also elucidates key steps in the biosynthesis of antibiotics such as friulimicin, butirosin and bacilysin and cell surface structures such as capsular polymers and teichuronopeptides. We also report the discovery of several novel ribosomally synthesized bacterial peptide metabolites that are cyclized via amide and lactone linkages formed by ATP-grasp enzymes. We present an evolutionary scenario for the multiple convergent origins of peptide ligases in various folds and clarify the bacterial origin of eukaryotic peptide-tagging enzymes of the TTL family.
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Affiliation(s)
- Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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31
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Li W, Khullar A, Chou S, Sacramo A, Gerratana B. Biosynthesis of sibiromycin, a potent antitumor antibiotic. Appl Environ Microbiol 2009; 75:2869-78. [PMID: 19270142 PMCID: PMC2681668 DOI: 10.1128/aem.02326-08] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Accepted: 02/25/2009] [Indexed: 11/20/2022] Open
Abstract
Pyrrolobenzodiazepines, a class of natural products produced by actinomycetes, are sequence selective DNA alkylating compounds with significant antitumor properties. Among the pyrrolo[1,4]benzodiazepines (PBDs) sibiromycin, one of two identified glycosylated PBDs, displays the highest affinity for DNA and the most potent antitumor properties. Despite the promising antitumor properties clinical trials of sibiromycin were precluded by the cardiotoxicity effect in animals attributed to the presence of the C-9 hydroxyl group. As a first step toward the development of sibiromycin analogs, we have cloned and localized the sibiromycin gene cluster to a 32.7-kb contiguous DNA region. Cluster boundaries tentatively assigned by comparative genomics were verified by gene replacement experiments. The sibiromycin gene cluster consisting of 26 open reading frames reveals a "modular" strategy in which the synthesis of the anthranilic and dihydropyrrole moieties is completed before assembly by the nonribosomal peptide synthetase enzymes. In addition, the gene cluster identified includes open reading frames encoding enzymes involved in sibirosamine biosynthesis, as well as regulatory and resistance proteins. Gene replacement and chemical complementation studies are reported to support the proposed biosynthetic pathway.
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Affiliation(s)
- Wei Li
- Department of Chemistry and Biochemistry, Bldg. 091, University of Maryland, College Park, MD 20742, USA
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32
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Forouhar F, Abashidze M, Xu H, Grochowski LL, Seetharaman J, Hussain M, Kuzin A, Chen Y, Zhou W, Xiao R, Acton TB, Montelione GT, Galinier A, White RH, Tong L. Molecular insights into the biosynthesis of the F420 coenzyme. J Biol Chem 2008; 283:11832-40. [PMID: 18252724 PMCID: PMC2431047 DOI: 10.1074/jbc.m710352200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Revised: 01/28/2008] [Indexed: 11/06/2022] Open
Abstract
Coenzyme F(420), a hydride carrier, is found in Archaea and some bacteria and has crucial roles in methanogenesis, antibiotic biosynthesis, DNA repair, and activation of antitubercular compounds. CofD, 2-phospho-l-lactate transferase, catalyzes the last step in the biosynthesis of F(420)-0 (F(420) without polyglutamate), by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (Fo). CofD is highly conserved among F(420)-producing organisms, and weak sequence homologs are also found in non-F(420)-producing organisms. This superfamily does not share any recognizable sequence conservation with other proteins. Here we report the first crystal structures of CofD, the free enzyme and two ternary complexes, with Fo and P(i) or with Fo and GDP, from Methanosarcina mazei. The active site is located at the C-terminal end of a Rossmann fold core, and three large insertions make significant contributions to the active site and dimer formation. The observed binding modes of Fo and GDP can explain known biochemical properties of CofD and are also supported by our binding assays. The structures provide significant molecular insights into the biosynthesis of the F(420) coenzyme. Large structural differences in the active site region of the non-F(420)-producing CofD homologs suggest that they catalyze a different biochemical reaction.
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Affiliation(s)
- Farhad Forouhar
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, USA
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Grochowski LL, Xu H, White RH. Identification and characterization of the 2-phospho-L-lactate guanylyltransferase involved in coenzyme F420 biosynthesis. Biochemistry 2008; 47:3033-7. [PMID: 18260642 DOI: 10.1021/bi702475t] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Coenzyme F 420 is a hydride carrier cofactor functioning in methanogenesis. One step in the biosynthesis of coenzyme F 420 involves the coupling of 2-phospho- l-lactate (LP) to 7,8-didemethyl-8-hydroxy-5-deazaflavin, the F 420 chromophore. This condensation requires an initial activation of 2-phospho- l-lactate through a pyrophosphate linkage to GMP. Bioinformatic analysis identified an uncharacterized archaeal protein in the Methanocaldococcus jannaschii genome, MJ0887, which could be involved in this transformation. The predicted MJ0887-derived protein has domain similarity with other known nucleotidyl transferases. The MJ0887 gene was cloned and overexpressed, and the purified protein was found to catalyze the formation of lactyl-2-diphospho-5'-guanosine from LP and GTP. Kinetic constants were determined for the MJ0887-derived protein with both LP and GTP substrates and are as follows: V max = 3 micromol min (-1) mg (-1), GTP K M (app) = 56 microM, and k cat/ K M (app) = 2 x 10 (4) M (-1) s (-1) and LP K M (app) = 36 microM, and k cat/ K M (app) = 4 x 10 (4) M (-1) s (-1). The MJ0887 gene product has been designated CofC to indicate its involvement in the third step of coenzyme F 420 biosynthesis.
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Affiliation(s)
- Laura L Grochowski
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0308, USA
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Rouhier N, Lemaire SD, Jacquot JP. The role of glutathione in photosynthetic organisms: emerging functions for glutaredoxins and glutathionylation. ANNUAL REVIEW OF PLANT BIOLOGY 2008; 59:143-66. [PMID: 18444899 DOI: 10.1146/annurev.arplant.59.032607.092811] [Citation(s) in RCA: 238] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Glutathione, a tripeptide with the sequence gamma-Glu-Cys-Gly, exists either in a reduced form with a free thiol group or in an oxidized form with a disulfide between two identical molecules. We describe here briefly the pathways involved in the synthesis, reduction, polymerization, and degradation of glutathione, as well as its distribution throughout the plant and its redox buffering capacities. The function of glutathione in xenobiotic and heavy metal detoxification, plant development, and plant-pathogen interactions is also briefly discussed. Several lines of evidence indicate that glutathione and glutaredoxins (GRXs) are implicated in the response to oxidative stress through the regeneration of enzymes involved in peroxide and methionine sulfoxide reduction. Finally, emerging functions for plant GRXs and glutathione concern the regulation of protein activity via glutathionylation and the capacity of some GRXs to bind iron sulfur centers and for some of them to transfer FeS clusters into apoproteins.
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Affiliation(s)
- Nicolas Rouhier
- Unité Mixte de Recherches, 1136 INRA-UHP Interaction Arbres-Microorganismes, IFR 110 GEEF, Nancy University, Faculté des Sciences, 54506 Vandoeuvre Cedex, France.
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35
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Nocek B, Evdokimova E, Proudfoot M, Kudritska M, Grochowski LL, White RH, Savchenko A, Yakunin AF, Edwards A, Joachimiak A. Structure of an amide bond forming F(420):gamma-glutamyl ligase from Archaeoglobus fulgidus -- a member of a new family of non-ribosomal peptide synthases. J Mol Biol 2007; 372:456-69. [PMID: 17669425 PMCID: PMC2678844 DOI: 10.1016/j.jmb.2007.06.063] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 06/18/2007] [Accepted: 06/21/2007] [Indexed: 10/23/2022]
Abstract
F(420) is a flavin-like redox-active coenzyme commonly used by archaea and some eubacteria in a variety of biochemical reactions in methanogenesis, the formation of secondary metabolites, the degradation of nitroaromatic compounds, activation of nitroimidazofurans, and F(420)-dependent photolysis in DNA repair. Coenzyme F(420)-2 biosynthesis from 7,8-didemethyl-8-hydroxy-5-deazariboflavin (Fo) and lactaldehyde involves six enzymatic steps and five proteins (CofA, CofB, CofC, CofD, and CofE). CofE, a F(420)-0:gamma-glutamyl ligase, is responsible for the last two enzymatic steps; it catalyses the GTP-dependent addition of two L-glutamate residues to F(420)-0 to form F(420)-2. CofE is found in archaea, the aerobic actinomycetes, and cyanobacteria. Here, we report the first crystal structure of the apo-F(420)-0:gamma-glutamyl ligase (CofE-AF) from Archaeoglobus fulgidus and its complex with GDP at 2.5 A and 1.35 A resolution, respectively. The structure of CofE-AF reveals a novel protein fold with an intertwined, butterfly-like dimer formed by two-domain monomers. GDP and Mn(2+) are bound within the putative active site in a large groove at the dimer interface. We show that the enzyme adds a glutamate residue to both F(420)-0 and F(420)-1 in two distinct steps. CofE represents the first member of a new structural family of non-ribosomal peptide synthases.
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Affiliation(s)
- B. Nocek
- Midwest Center for Structural, Genomics and Structural, Biology Center, Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439, USA
| | - E. Evdokimova
- Midwest Center for Structural, Genomics and Structural, Biology Center, Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439, USA
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 1L6
| | - M. Proudfoot
- Midwest Center for Structural, Genomics and Structural, Biology Center, Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439, USA
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 1L6
| | - M. Kudritska
- Midwest Center for Structural, Genomics and Structural, Biology Center, Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439, USA
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 1L6
| | - L. L. Grochowski
- Department of Biochemistry, Virginia Polytechnic, Institute and State, University, Blacksburg, VA 24061-0308, USA
| | - R. H. White
- Department of Biochemistry, Virginia Polytechnic, Institute and State, University, Blacksburg, VA 24061-0308, USA
| | - A. Savchenko
- Midwest Center for Structural, Genomics and Structural, Biology Center, Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439, USA
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 1L6
| | - A. F. Yakunin
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 1L6
| | - A. Edwards
- Midwest Center for Structural, Genomics and Structural, Biology Center, Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439, USA
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 1L6
| | - A. Joachimiak
- Midwest Center for Structural, Genomics and Structural, Biology Center, Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439, USA
- The University of Chicago, Department of Biochemistry and Molecular Biology, University of Chicago, 920 E. 58th St., Chicago, IL 60637, USA
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36
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Guerra-Lopez D, Daniels L, Rawat M. Mycobacterium smegmatis mc2 155 fbiC and MSMEG_2392 are involved in triphenylmethane dye decolorization and coenzyme F420 biosynthesis. Microbiology (Reading) 2007; 153:2724-2732. [PMID: 17660436 DOI: 10.1099/mic.0.2006/009241-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mycobacteria can tolerate relatively high concentrations of triphenylmethane dyes such as malachite green and methyl violet. To identify mycobacterial genes involved in the decolorization of malachite green, a transposon mutant library of Mycobacterium smegmatis mc2 155 was screened for mutants unable to decolorize this dye. One of the genes identified was MSMEG_5126, an orthologue of Mycobacterium bovis fbiC encoding a 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) synthase, which is essential for the biosynthesis of the electron carrier coenzyme F420. The other gene identified was MSMEG_2392, encoding an alanine-rich protein with a DUF121 domain. The minimum inhibitory concentrations (MICs) for malachite green and methyl violet of the six fbiC mutants and two MSMEG_2392 mutants were one-third and one-fifth, respectively, of the MIC of the parent strain M. smegmatis mc2 155. Representative fbiC and MSMEG_2392 mutant strains were also sensitive to oxidative stress caused by the redox-cycling agents plumbagin and menadione, and the sensitivity was reversed in the complemented strains. HPLC analysis of representative fbiC and MSMEG_2392 strains revealed that, while the fbiC mutant lacked both coenzyme F420 and FO, the MSMEG_2392 mutant contained FO but not coenzyme F420. These results indicate that MSMEG_2392 is involved in the biosynthesis of coenzyme F420.
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Affiliation(s)
- Denise Guerra-Lopez
- Department of Biology, California State University-Fresno, Fresno, CA 937401, USA
| | - Lacy Daniels
- Irma Lerma Rangel College of Pharmacy, Texas A&M Health Science Center, Kingsville, TX 78363, USA
| | - Mamta Rawat
- Department of Biology, California State University-Fresno, Fresno, CA 937401, USA
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37
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Grochowski LL, Xu H, White RH. Identification of lactaldehyde dehydrogenase in Methanocaldococcus jannaschii and its involvement in production of lactate for F420 biosynthesis. J Bacteriol 2006; 188:2836-44. [PMID: 16585745 PMCID: PMC1447007 DOI: 10.1128/jb.188.8.2836-2844.2006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Accepted: 02/07/2006] [Indexed: 11/20/2022] Open
Abstract
One of the early steps in the biosynthesis of coenzyme F(420) in Methanocaldococcus jannaschii requires generation of 2-phospho-L-lactate, which is formed by the phosphorylation of L-lactate. Preliminary studies had shown that L-lactate in M. jannaschii is not derived from pyruvate, and thus an alternate pathway(s) for its formation was examined. Here we report that L-lactate is formed by the NAD(+)-dependent oxidation of l-lactaldehyde by the MJ1411 gene product. The lactaldehyde, in turn, was found to be generated either by the NAD(P)H reduction of methylglyoxal or by the aldol cleavage of fuculose-1-phosphate by fuculose-1-phosphate aldolase, the MJ1418 gene product.
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Affiliation(s)
- Laura L Grochowski
- Department of Biochemistry (0308), Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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38
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Skipsey M, Davis BG, Edwards R. Diversification in substrate usage by glutathione synthetases from soya bean (Glycine max), wheat (Triticum aestivum) and maize (Zea mays). Biochem J 2005; 391:567-74. [PMID: 16008521 PMCID: PMC1276957 DOI: 10.1042/bj20050718] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Revised: 06/29/2005] [Accepted: 07/11/2005] [Indexed: 11/17/2022]
Abstract
Unlike animals which accumulate glutathione (gamma-glutamyl-L-cysteinyl-glycine) alone as their major thiol antioxidant, several crops synthesize alternative forms of glutathione by varying the carboxy residue. The molecular basis of this variation is not well understood, but the substrate specificity of the respective GSs (glutathione synthetases) has been implicated. To investigate their substrate tolerance, five GS-like cDNAs have been cloned from plants that can accumulate alternative forms of glutathione, notably soya bean [hGSH (homoglutathione or gamma-glutamyl-L-cysteinyl-beta-alanine)], wheat (hydroxymethylglutathione or gamma-glutamyl-L-cysteinyl-serine) and maize (gamma-Glu-Cys-Glu). The respective recombinant GSs were then assayed for the incorporation of differing C-termini into gamma-Glu-Cys. The soya bean enzyme primarily incorporated beta-alanine to form hGSH, whereas the GS enzymes from cereals preferentially catalysed the formation of glutathione. However, when assayed with other substrates, several GSs and one wheat enzyme in particular were able to synthesize a diverse range of glutathione variants by incorporating unusual C-terminal moieties including D-serine, non-natural amino acids and alpha-amino alcohols. Our results suggest that plant GSs are capable of producing a diverse range of glutathione homologues depending on the availability of the acyl acceptor.
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Key Words
- glutathione synthetase
- glycine max (soya bean)
- homoglutathione synthetase
- hydroxymethylglutathione
- triticum aestivum (wheat)
- zea mays (maize)
- aaba, baba and gaba, α-, β- and γ-aminobutyric acid respectively
- acv synthetase, l-δ-(α-aminoadipoyl)-l-cysteinyl-d-valine synthetase
- baiba, β-aminoisobutyric acid
- γ-ec, γ-glutamyl-l-cysteine
- γ-ece, γ-glutamyl-l-cysteine-glutamic acid
- γ-ecs, γ-glutamyl-l-cysteine synthetase
- esi, electrospray ionization
- gs, glutathione synthetase
- hgs, homoglutathione synthetase
- hgsh, homoglutathione
- hmgsh, hydroxymethylglutathione
- tof, time-of-flight
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Affiliation(s)
- Mark Skipsey
- Crop Protection Group, School of Biological and Biomedical Sciences, University of Durham, South Road, Durham DH1 3LE, UK.
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George RA, Spriggs RV, Bartlett GJ, Gutteridge A, MacArthur MW, Porter CT, Al-Lazikani B, Thornton JM, Swindells MB. Effective function annotation through catalytic residue conservation. Proc Natl Acad Sci U S A 2005; 102:12299-304. [PMID: 16037208 PMCID: PMC1178014 DOI: 10.1073/pnas.0504833102] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Because of the extreme impact of genome sequencing projects, protein sequences without accompanying experimental data now dominate public databases. Homology searches, by providing an opportunity to transfer functional information between related proteins, have become the de facto way to address this. Although a single, well annotated, close relationship will often facilitate sufficient annotation, this situation is not always the case, particularly if mutations are present in important functional residues. When only distant relationships are available, the transfer of function information is more tenuous, and the likelihood of encountering several well annotated proteins with different functions is increased. The consequence for a researcher is a range of candidate functions with little way of knowing which, if any, are correct. Here, we address the problem directly by introducing a computational approach to accurately identify and segregate related proteins into those with a functional similarity and those where function differs. This approach should find a wide range of applications, including the interpretation of genomics/proteomics data and the prioritization of targets for high-throughput structure determination. The method is generic, but here we concentrate on enzymes and apply high-quality catalytic site data. In addition to providing a series of comprehensive benchmarks to show the overall performance of our approach, we illustrate its utility with specific examples that include the correct identification of haptoglobin as a nonenzymatic relative of trypsin, discrimination of acid-d-amino acid ligases from a much larger ligase pool, and the successful annotation of BioH, a structural genomics target.
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Affiliation(s)
- Richard A George
- Inpharmatica, 60 Charlotte Street, London W1T 2NU, United Kingdom
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40
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Gopal S, Borovok I, Ofer A, Yanku M, Cohen G, Goebel W, Kreft J, Aharonowitz Y. A multidomain fusion protein in Listeria monocytogenes catalyzes the two primary activities for glutathione biosynthesis. J Bacteriol 2005; 187:3839-47. [PMID: 15901709 PMCID: PMC1112035 DOI: 10.1128/jb.187.11.3839-3847.2005] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glutathione is the predominant low-molecular-weight peptide thiol present in living organisms and plays a key role in protecting cells against oxygen toxicity. Until now, glutathione synthesis was thought to occur solely through the consecutive action of two physically separate enzymes, gamma-glutamylcysteine ligase and glutathione synthetase. In this report we demonstrate that Listeria monocytogenes contains a novel multidomain protein (termed GshF) that carries out complete synthesis of glutathione. Evidence for this comes from experiments which showed that in vitro recombinant GshF directs the formation of glutathione from its constituent amino acids and the in vivo effect of a mutation in GshF that abolishes glutathione synthesis, results in accumulation of the intermediate gamma-glutamylcysteine, and causes hypersensitivity to oxidative agents. We identified GshF orthologs, consisting of a gamma-glutamylcysteine ligase (GshA) domain fused to an ATP-grasp domain, in 20 gram-positive and gram-negative bacteria. Remarkably, 95% of these bacteria are mammalian pathogens. A plausible origin for GshF-dependent glutathione biosynthesis in these bacteria was the recruitment by a GshA ancestor gene of an ATP-grasp gene and the subsequent spread of the fusion gene between mammalian hosts, most likely by horizontal gene transfer.
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Affiliation(s)
- Shubha Gopal
- Tel Aviv University, The George S. Wise Faculty of Life Sciences, Department of Molecular Microbiology and Biotechnology, Ramat Aviv, 69978, Tel Aviv, Israel
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Chistoserdova L, Rasche ME, Lidstrom ME. Novel dephosphotetrahydromethanopterin biosynthesis genes discovered via mutagenesis in Methylobacterium extorquens AM1. J Bacteriol 2005; 187:2508-12. [PMID: 15774894 PMCID: PMC1065231 DOI: 10.1128/jb.187.7.2508-2512.2005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2004] [Accepted: 12/14/2004] [Indexed: 11/20/2022] Open
Abstract
Methylobacterium extorquens AM1 was used to explore the genetics of dephosphotetrahydromethanopterin (dH(4)MPT) biosynthesis. Strains with mutations in eight "archaeal-type" genes linked on the chromosome of M. extorquens AM1 were analyzed for the ability to synthesize dH(4)MPT, and six were found to be dH(4)MPT negative. Putative functions of these genes in dH(4)MPT biosynthesis are discussed.
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Affiliation(s)
- Ludmila Chistoserdova
- 231 Wilcox Hall, Box 352125, Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA.
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42
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Abstract
The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate. The imidazole ring of GTP is hydrolytically opened, yielding a 2,5-diaminopyrimidine that is converted to 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione by a sequence of deamination, side chain reduction, and dephosphorylation. Condensation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy-2-butanone 4-phosphate obtained from ribulose 5-phosphate affords 6,7-dimethyl-8-ribityllumazine. Dismutation of the lumazine derivative yields riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, which is recycled in the biosynthetic pathway. The enzymes of the riboflavin pathway are potential targets for antibacterial agents.
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Affiliation(s)
- Markus Fischer
- Lehrstuhl für Organische Chemie und Biochemie, Technische Universität München, Lichtenbergstr. 4, D-85747, Garching, Germany.
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Buchenau B, Thauer RK. Tetrahydrofolate-specific enzymes in Methanosarcina barkeri and growth dependence of this methanogenic archaeon on folic acid or p-aminobenzoic acid. Arch Microbiol 2004; 182:313-25. [PMID: 15349715 DOI: 10.1007/s00203-004-0714-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2004] [Revised: 07/15/2004] [Accepted: 07/15/2004] [Indexed: 10/26/2022]
Abstract
Methanogenic archaea are generally thought to use tetrahydromethanopterin or tetrahydrosarcinapterin (H4SPT) rather than tetrahydrofolate (H4F) as a pterin C1 carrier. However, the genome sequence of Methanosarcina species recently revealed a cluster of genes, purN, folD, glyA and metF, that are predicted to encode for H4F-specific enzymes. We show here for folD and glyA from M. barkeri that this prediction is correct: FolD (bifunctional N5,N10-methylene-H4F dehydrogenase/N5,N10-methenyl-H4F cyclohydrolase) and GlyA (serine:H4F hydroxymethyltransferase) were heterologously overproduced in Escherichia coli, purified and found to be specific for methylene-H4F and H4F, respectively (apparent Km below 5 microM). Western blot analyses and enzyme activity measurements revealed that both enzymes were synthesized in M. barkeri. The results thus indicate that M. barkeri should contain H4F, which was supported by the finding that growth of M. barkeri was dependent on folic acid and that the vitamin could be substituted by p-aminobenzoic acid, a biosynthetic precursor of H4F. From the p-aminobenzoic acid requirement, an intracellular H4F concentration of approximately 5 M was estimated. Evidence is presented that the p-aminobenzoic acid taken up by the growing cells was not required for the biosynthesis of H4SPT, which was found to be present in the cells at a concentration above 3 mM. The presence of both H4SPT and H4F in M. barkeri is in agreement with earlier isotope labeling studies indicating that there are two separate C1 pools in these methanogens.
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Affiliation(s)
- Bärbel Buchenau
- Max-Planck-Institut für terrestrische Mikrobiologie and Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, Karl-von-Frisch-Strasse, Marburg, Germany
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