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Yurgel SN, Johnson SA, Rice J, Sa N, Bailes C, Baumgartner J, Pitzer JE, Roop RM, Roje S. A novel formamidase is required for riboflavin biosynthesis in invasive bacteria. J Biol Chem 2022; 298:102377. [PMID: 35970388 PMCID: PMC9478397 DOI: 10.1016/j.jbc.2022.102377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/03/2022] Open
Abstract
Biosynthesis of riboflavin, the precursor of the redox cofactors FMN and FAD, was thought to be well understood in bacteria, with all the pathway enzymes presumed to be known and essential. Our previous research has challenged this view by showing that, in the bacterium Sinorhizobium meliloti, deletion of the ribBA gene encoding the enzyme that catalyzes the initial steps on the riboflavin biosynthesis pathway only causes a reduction in flavin secretion rather than riboflavin auxotrophy. This finding led us to hypothesize that RibBA participates in the biosynthesis of flavins destined for secretion, while S. meliloti has another enzyme that performs this function for internal cellular metabolism. Here, we identify and biochemically characterize a novel formamidase (SMc02977) involved in the production of riboflavin for intracellular functions in S. meliloti. This catalyst, which we named Sm-BrbF, releases formate from the early riboflavin precursor 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (AFRPP) to yield 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARoPP). We show that homologs of this enzyme are present in many bacteria, are highly abundant in the Rhizobiales order, and that sequence homologs from Brucella abortus and Liberobacter solanacearum complement the riboflavin auxotrophy of the Sm1021ΔSMc02977 mutant. Furthermore, we show that the B. abortus enzyme (Bab2_0247, Ba-BrbF) is also an AFRPP formamidase, and that the bab2_0247 mutant is a riboflavin auxotroph exhibiting a lower level of intracellular infection than the wild-type strain. Finally, we show that Sm-BrbF and Ba-BrbF directly interact with other riboflavin biosynthesis pathway enzymes. Together, our results provide novel insight into the intricacies of riboflavin biosynthesis in bacteria.
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Affiliation(s)
- Svetlana N Yurgel
- Grain Legume Genetics and Physiology Research Unit, USDA, ARS, Prosser, WA, USA.
| | - Skylar A Johnson
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Jennifer Rice
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Na Sa
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Clayton Bailes
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - John Baumgartner
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Josh E Pitzer
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - R Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Sanja Roje
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
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2
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Smith MM, Beaupre BA, Fourozesh DC, Meneely KM, Lamb AL, Moran GR. Finding Ways to Relax: A Revisionistic Analysis of the Chemistry of E. coli GTP Cyclohydrolase II. Biochemistry 2021; 60:3027-3039. [PMID: 34569786 DOI: 10.1021/acs.biochem.1c00511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Guanosine triphosphate (GTP) cyclohydrolase II (RibA) is one of three enzymes that hydrolytically cleave the C8-N9 bond of the GTP guanine. RibA also catalyzes a subsequent hydrolytic attack at the base liberating formate and in addition cleaves the α-β phosphodiester bond of the triphosphate to form pyrophosphate (PPi). These hydrolytic reactions are promoted by tandem active-site metal ions, zinc and magnesium, that respectively function at the GTP guanine and triphosphate moieties. The RibA reaction is part of riboflavin biosynthesis and forms 2,5-diamino-6-β-pyrimidinone 5'-phosphate, an exocyclic pyrimidine nucleotide that ultimately forms the pyrimidine ring of the isoalloxazine of riboflavin. The stoichiometry of the RibA reaction was defined in the study that first identified this activity in Escherichia coli (Foor, F., Brown, G. M. J. Biol. Chem., 1975, 250, 9, 3545-3551) and has not been quantitatively evaluated in subsequent works. Using primarily transient state approaches we examined the interaction of RibA from E. coli with the GTP, inosine triphosphate, and PPi. Our data indicate that PPi is a slow substrate for RibA that is cleaved to form two phosphate ions (Pi). A combination of real-time enzymatically coupled Pi reporter assays and end-point 31P NMR revealed that Pi is formed at a catalytically relevant rate in the native reaction of RibA with GTP, redefining the reaction stoichiometry. Furthermore, our data indicate that both PPi and GTP stimulate conformational changes prior to hydrolytic chemistry, and we conclude that the cleavage of PPi bound as a substrate or an intermediate state results in conformational relaxation.
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Affiliation(s)
- Madison M Smith
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Dariush C Fourozesh
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Kathleen M Meneely
- Department of Chemistry, University of Texas San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
| | - Audrey L Lamb
- Department of Chemistry, University of Texas San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, Illinois 60660, United States
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3
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Kumar Y, Singh RK, Hazra AB. Characterization of a novel mesophilic CTP-dependent riboflavin kinase and rational engineering to create its thermostable homologs. Chembiochem 2021; 22:3414-3424. [PMID: 34387404 DOI: 10.1002/cbic.202100211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/20/2021] [Indexed: 11/05/2022]
Abstract
Flavins play a central role in metabolism as molecules that catalyze a wide range of redox reactions in living organisms. Several variations in flavin biosynthesis exist among the domains of life, and their analysis has revealed many new structural and mechanistic insights till date. The cytidine triphosphate (CTP)-dependent riboflavin kinase in archaea is one such example - unlike most kinases that use adenosine triphosphate, archaeal riboflavin kinases utilize CTP to phosphorylate riboflavin and produce flavin mononucleotide. In this study, we present the characterization of a new mesophilic archaeal CTP-utilizing riboflavin kinase homolog from Methanococcus maripaludis (MmpRibK), which is linked closely in sequence to the previously characterized thermophilic Methanocaldococcus jannaschii homolog. We reconstitute the activity of MmpRibK, determine its kinetic parameters and molecular factors that contribute to its unique properties, and finally establish the residues that improve its thermostability using computation and a series of experiments. Our work advances the molecular understanding of flavin biosynthesis in archaea by the characterization of the first mesophilic CTP-dependent riboflavin kinase. Finally, it validates the role of salt bridges and rigidifying amino acid residues in imparting thermostability to this unique structural fold that characterizes archaeal riboflavin kinase enzymes, with implications in enzyme engineering and biotechnological applications.
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Affiliation(s)
- Yashwant Kumar
- IISER Pune: Indian Institute of Science Education Research Pune, Chemistry, INDIA
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4
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Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea. Genes (Basel) 2021; 12:genes12070963. [PMID: 34202810 PMCID: PMC8305020 DOI: 10.3390/genes12070963] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.
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Rodionova IA, Vetting MW, Li X, Almo SC, Osterman AL, Rodionov DA. A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea. Nucleic Acids Res 2017; 45:3785-3799. [PMID: 28073944 PMCID: PMC5397151 DOI: 10.1093/nar/gkw1331] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/20/2016] [Indexed: 12/11/2022] Open
Abstract
Riboflavin (vitamin B2) is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide, which are essential coenzymes in all free-living organisms. Riboflavin biosynthesis in many Bacteria but not in Archaea is controlled by FMN-responsive riboswitches. We identified a novel bifunctional riboflavin kinase/regulator (RbkR), which controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain. Using comparative genomics, we predicted RbkR operator sites and reconstructed RbkR regulons in 94 archaeal genomes. While the identified RbkR operators showed significant variability between archaeal lineages, the conserved core of RbkR regulons includes riboflavin biosynthesis genes, known/predicted vitamin uptake transporters and the rbkR gene. The DNA motifs and CTP-dependent riboflavin kinase activity of two RbkR proteins were experimentally validated in vitro. The DNA binding activity of RbkR was stimulated by CTP and suppressed by FMN, a product of riboflavin kinase. The crystallographic structure of RbkR from Thermoplasma acidophilum was determined in complex with CTP and its DNA operator revealing key residues for operator and ligand recognition. Overall, this study contributes to our understanding of metabolic and regulatory networks for vitamin homeostasis in Archaea.
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Affiliation(s)
- Irina A Rodionova
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Xiaoqing Li
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Andrei L Osterman
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Dmitry A Rodionov
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051 Russia
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6
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Sarge S, Haase I, Illarionov B, Laudert D, Hohmann HP, Bacher A, Fischer M. Catalysis of an Essential Step in Vitamin B2Biosynthesis by a Consortium of Broad Spectrum Hydrolases. Chembiochem 2015; 16:2466-9. [DOI: 10.1002/cbic.201500352] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Sonja Sarge
- Hamburg School of Food Science; Institute of Food Chemistry; University of Hamburg; Grindelallee 117 20146 Hamburg Germany
| | - Ilka Haase
- Hamburg School of Food Science; Institute of Food Chemistry; University of Hamburg; Grindelallee 117 20146 Hamburg Germany
| | - Boris Illarionov
- Hamburg School of Food Science; Institute of Food Chemistry; University of Hamburg; Grindelallee 117 20146 Hamburg Germany
| | - Dietmar Laudert
- DSM Nutritional Products; P. O. Box 2676 4002 Basel Switzerland
| | | | - Adelbert Bacher
- Hamburg School of Food Science; Institute of Food Chemistry; University of Hamburg; Grindelallee 117 20146 Hamburg Germany
| | - Markus Fischer
- Hamburg School of Food Science; Institute of Food Chemistry; University of Hamburg; Grindelallee 117 20146 Hamburg Germany
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7
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Haase I, Gräwert T, Illarionov B, Bacher A, Fischer M. Recent advances in riboflavin biosynthesis. Methods Mol Biol 2014; 1146:15-40. [PMID: 24764086 DOI: 10.1007/978-1-4939-0452-5_2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Riboflavin is biosynthesized from GTP and ribulose 5-phosphate. Whereas the early reactions conducing to 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate show significant taxonomic variation, the subsequent reaction steps are universal in all taxonomic kingdoms. With the exception of a hitherto elusive phosphatase, all enzymes of the pathway have been characterized in some detail at the structural and mechanistic level. Some of the pathway enzymes (GTP cycloyhdrolase II, 3,4-dihydroxy-2-butanone 4-phosphate synthase, riboflavin synthase) have exceptionally complex reaction mechanisms. The commercial production of the vitamin is now entirely based on highly productive fermentation processes. Due to their absence in animals, the pathway enzymes are potential targets for the development of novel anti-infective drugs.
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Affiliation(s)
- Ilka Haase
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146, Hamburg, Germany
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8
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Gräwert T, Fischer M, Bacher A. Structures and reaction mechanisms of GTP cyclohydrolases. IUBMB Life 2013; 65:310-22. [PMID: 23457054 DOI: 10.1002/iub.1153] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 01/25/2013] [Indexed: 11/09/2022]
Abstract
GTP cyclohydrolases generate the first committed intermediates for the biosynthesis of certain vitamins/cofactors (folic acid, riboflavin, deazaflavin, and tetrahydrobiopterin), deazapurine antibiotics, some t-RNA bases (queuosine, archaeosine), and the phytotoxin, toxoflavin. They depend on divalent cations for hydrolytic opening of the imidazole ring of the substrate, guanosine triphosphate (GTP). Surprisingly, the ring opening reaction is not the rate-limiting step for GTP cyclohydrolases I and II whose mechanism have been studied in some detail. GTP cyclohydrolase I, Ib, and II are potential targets for novel anti-infectives. Genetic factors modulating the activity of human GTP cyclohydrolase are highly pleiotropic, since the signal transponders whose biosyntheses require their participation (nitric oxide, catecholamines) impact a very wide range of physiological phenomena. Recent studies suggest that human GTP cyclohydrolase may become an oncology target.
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Affiliation(s)
- Tobias Gräwert
- Hamburg School of Food Science, Institut für Lebensmittelchemie, Grindelallee 117, 20146 Hamburg, Germany
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9
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Phillips G, Grochowski LL, Bonnett S, Xu H, Bailly M, Haas-Blaby C, El Yacoubi B, Iwata-Reuyl D, White RH, de Crécy-Lagard V. Functional promiscuity of the COG0720 family. ACS Chem Biol 2012; 7:197-209. [PMID: 21999246 PMCID: PMC3262898 DOI: 10.1021/cb200329f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biosynthesis of GTP derived metabolites such as tetrahydrofolate (THF), biopterin (BH(4)), and the modified tRNA nucleosides queuosine (Q) and archaeosine (G(+)) relies on several enzymes of the Tunnel-fold superfamily. A subset of these proteins includes the 6-pyruvoyltetrahydropterin (PTPS-II), PTPS-III, and PTPS-I homologues, all members of the COG0720 family that have been previously shown to transform 7,8-dihydroneopterin triphosphate (H(2)NTP) into different products. PTPS-II catalyzes the formation of 6-pyruvoyltetrahydropterin in the BH(4) pathway, PTPS-III catalyzes the formation of 6-hydroxylmethyl-7,8-dihydropterin in the THF pathway, and PTPS-I catalyzes the formation of 6-carboxy-5,6,7,8-tetrahydropterin in the Q pathway. Genes of these three enzyme families are often misannotated as they are difficult to differentiate by sequence similarity alone. Using a combination of physical clustering, signature motif, phylogenetic codistribution analyses, in vivo complementation studies, and in vitro enzymatic assays, a complete reannotation of the COG0720 family was performed in prokaryotes. Notably, this work identified and experimentally validated dual function PTPS-I/III enzymes involved in both THF and Q biosynthesis. Both in vivo and in vitro analyses showed that the PTPS-I family could tolerate a translation of the active site cysteine and was inherently promiscuous, catalyzing different reactions on the same substrate or the same reaction on different substrates. Finally, the analysis and experimental validation of several archaeal COG0720 members confirmed the role of PTPS-I in archaeosine biosynthesis and resulted in the identification of PTPS-III enzymes with variant signature sequences in Sulfolobus species. This study reveals an expanded versatility of the COG0720 family members and illustrates that for certain protein families extensive comparative genomic analysis beyond homology is required to correctly predict function.
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Affiliation(s)
- Gabriela Phillips
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Laura L. Grochowski
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Shilah Bonnett
- Department of Chemistry, Portland State University, Portland, OR 97207
| | - Huimin Xu
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Marc Bailly
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Crysten Haas-Blaby
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Basma El Yacoubi
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Dirk Iwata-Reuyl
- Department of Chemistry, Portland State University, Portland, OR 97207
| | - Robert H. White
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
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10
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Mashhadi Z, Xu H, Grochowski LL, White RH. Archaeal RibL: a new FAD synthetase that is air sensitive. Biochemistry 2010; 49:8748-55. [PMID: 20822113 DOI: 10.1021/bi100817q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
FAD synthetases catalyze the transfer of the AMP portion of ATP to FMN to produce FAD and pyrophosphate (PP(i)). Monofunctional FAD synthetases exist in eukaryotes, while bacteria have bifunctional enzymes that catalyze both the phosphorylation of riboflavin and adenylation of FMN to produce FAD. Analyses of archaeal genomes did not reveal the presence of genes encoding either group, yet the archaea contain FAD. Our recent identification of a CTP-dependent archaeal riboflavin kinase strongly indicated the presence of a monofunctional FAD synthetase. Here we report the identification and characterization of an archaeal FAD synthetase. Methanocaldococcus jannaschii gene MJ1179 encodes a protein that is classified in the nucleotidyl transferase protein family and was previously annotated as glycerol-3-phosphate cytidylyltransferase (GCT). The MJ1179 gene was cloned and its protein product heterologously expressed in Escherichia coli. The resulting enzyme catalyzes the adenylation of FMN with ATP to produce FAD and PP(i). The MJ1179-derived protein has been designated RibL to indicate that it follows the riboflavin kinase (RibK) step in the archaeal FAD biosynthetic pathway. Aerobically isolated RibL is active only under reducing conditions. RibL was found to require divalent metals for activity, the best activity being observed with Co(2+), where the activity was 4 times greater than that with Mg(2+). Alkylation of the two conserved cysteines in the C-terminus of the protein resulted in complete inactivation. RibL was also found to catalyze cytidylation of FMN with CTP, making the modified FAD, flavin cytidine dinucleotide (FCD). Unlike other FAD synthetases, RibL does not catalyze the reverse reaction to produce FMN and ATP from FAD and PP(i). Also in contrast to other FAD synthetases, PP(i) inhibits the activity of RibL.
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Affiliation(s)
- Zahra Mashhadi
- Department of Biochemistry (0308), Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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11
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Abstract
The biosynthesis of riboflavin requires 1 equivalent of GTP and 2 equivalents of ribulose phosphate. The first committed reactions of the convergent pathway are catalyzed by GTP hydrolase II and 3,4-dihydroxy-2-butanone 4-phosphate synthase. The initial reaction steps afford 5-amino-6-ribitylaminopyrimidine 5'-phosphate, which needs to be dephosphorylated by a hitherto elusive hydrolase. The dephosphorylated pyrimidine is condensed with the carbohydrate precursor, 3,4-dihydroxy-2-butanone 4-phosphate. The resulting 6,7-dimethyl-8-ribityllumazine affords riboflavin by a mechanistically unique dismutation, i.e., by formation of a pentacyclic dimer that is subsequently fragmented.
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12
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Lehmann M, Degen S, Hohmann HP, Wyss M, Bacher A, Schramek N. Biosynthesis of riboflavin. Screening for an improved GTP cyclohydrolase II mutant. FEBS J 2009; 276:4119-29. [PMID: 19583770 DOI: 10.1111/j.1742-4658.2009.07118.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
GTP cyclohydrolase II catalyzes the first dedicated step in the biosynthesis of riboflavin and appears to be a limiting factor for the production of the vitamin by recombinant Bacillus subtilis overproducer strains. Using error-prone PCR amplification, we generated a library of the B. subtilis ribA gene selectively mutated in the GTP cyclohydrolase II domain. The ratio of the GTP cyclohydrolase II to 3,4-dihydroxy-2-butanone synthase activities of the mutant proteins was measured. A mutant designated Construct E, carrying seven point mutations, showed a two-fold increase in GTP cyclohydrolase II activity and a four-fold increase in the K(m) value with GTP as the substrate. Using the analog 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-triphosphate as the substrate, the mutant showed a rate enhancement by a factor of about two and an increase in the K(m) value by a factor of about 5. A series of UV absorption spectra obtained in stopped-flow experiments using the wild-type and mutant enzymes revealed isosbestic points indicative of apparently perfect reactions, which were similar to the findings obtained with GTP cyclohydrolase II of Escherichia coli. Initial burst velocities obtained for the mutant and wild-type proteins were similar. The data suggest that the mutations present in Construct E are jointly conducive to the acceleration of a late step in the reaction trajectory, most probably the release of product from the enzyme.
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13
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Grochowski LL, Xu H, White RH. An iron(II) dependent formamide hydrolase catalyzes the second step in the archaeal biosynthetic pathway to riboflavin and 7,8-didemethyl-8-hydroxy-5-deazariboflavin. Biochemistry 2009; 48:4181-8. [PMID: 19309161 DOI: 10.1021/bi802341p] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The early steps in the biosynthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (Fo) and riboflavin in the archaea differ from the established eukaryotic and bacterial pathways. The archaeal pathway has been proposed to begin with an archaeal-specific GTP cyclohydrolase III that hydrolyzes the imidazole ring of GTP but does not remove the resulting formyl group from the formamide [Graham, D. E., Xu, H., and White, R. H. (2002) Biochemistry 41, 15074-15084 ]. This enzyme is different than the bacterial GTP cyclohydrolase II which catalyzes both reactions. Here we describe the identification and characterization of the formamide hydrolase that catalyzes the second step in the archaeal Fo and riboflavin biosynthetic pathway. The Methanocaldococcus jannaschii MJ0116 gene was cloned and heterologously expressed, and the resulting enzyme was shown to catalyze the formation of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (APy) and formate from 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-monophosphate (FAPy). The MJ0116-derived protein has been named ArfB to indicate that it catalyzes the second step in archaeal riboflavin and Fo biosynthesis. ArfB was found to require ferrous iron for activity although metal analysis by ICP indicated the presence of zinc as well as iron in the purified protein. The identification of this enzyme confirms the involvement of GTP cyclohydrolase III (ArfA) in archaeal riboflavin and Fo 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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14
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Biosynthesis of 7-deazaguanosine-modified tRNA nucleosides: a new role for GTP cyclohydrolase I. J Bacteriol 2008; 190:7876-84. [PMID: 18931107 DOI: 10.1128/jb.00874-08] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Queuosine (Q) and archaeosine (G(+)) are hypermodified ribonucleosides found in tRNA. Q is present in the anticodon region of tRNA(GUN) in Eukarya and Bacteria, while G(+) is found at position 15 in the D-loop of archaeal tRNA. Prokaryotes produce these 7-deazaguanosine derivatives de novo from GTP through the 7-cyano-7-deazaguanine (pre-Q(0)) intermediate, but mammals import the free base, queuine, obtained from the diet or the intestinal flora. By combining the results of comparative genomic analysis with those of genetic studies, we show that the first enzyme of the folate pathway, GTP cyclohydrolase I (GCYH-I), encoded in Escherichia coli by folE, is also the first enzyme of pre-Q(0) biosynthesis in both prokaryotic kingdoms. Indeed, tRNA extracted from an E. coli DeltafolE strain is devoid of Q and the deficiency is complemented by expressing GCYH-I-encoding genes from different bacterial or archaeal origins. In a similar fashion, tRNA extracted from a Haloferax volcanii strain carrying a deletion of the GCYH-I-encoding gene contains only traces of G(+). These results link the production of a tRNA-modified base to primary metabolism and further clarify the biosynthetic pathway for these complex modified nucleosides.
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Römisch-Margl W, Eisenreich W, Haase I, Bacher A, Fischer M. 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate synthases of fungi and archaea. FEBS J 2008; 275:4403-14. [PMID: 18671734 DOI: 10.1111/j.1742-4658.2008.06586.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The pathway of riboflavin (vitamin B2) biosynthesis is significantly different in archaea, eubacteria, fungi and plants. Specifically, the first committed intermediate, 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, can either undergo hydrolytic cleavage of the position 2 amino group by a deaminase (in plants and most eubacteria) or reduction of the ribose side chain by a reductase (in fungi and archaea). We compare 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate synthases from the yeast Candida glabrata, the archaeaon Methanocaldococcus jannaschii and the eubacterium Aquifex aeolicus. All three enzymes convert 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate into 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate, as shown by 13C-NMR spectroscopy using [2,1',2',3',4',5'-13C6]2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate as substrate. The beta anomer was found to be the authentic substrate, and the alpha anomer could serve as substrate subsequent to spontaneous anomerisation. The M. jannaschii and C. glabrata enzymes were shown to be A-type reductases catalysing the transfer of deuterium from the 4(R) position of NADPH to the 1' (S) position of the substrate. These results are in agreement with the known three-dimensional structure of the M. jannaschii enzyme.
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Affiliation(s)
- Werner Römisch-Margl
- Lehrstuhl für Organische Chemie und Biochemie, Technische Universität München, Garching, Germany
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16
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Mashhadi Z, Zhang H, Xu H, White RH. Identification and characterization of an archaeon-specific riboflavin kinase. J Bacteriol 2008; 190:2615-8. [PMID: 18245297 PMCID: PMC2293203 DOI: 10.1128/jb.01900-07] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Accepted: 01/25/2008] [Indexed: 11/20/2022] Open
Abstract
The riboflavin kinase in Methanocaldococcus jannaschii has been identified as the product of the MJ0056 gene. Recombinant expression of the MJ0056 gene in Escherichia coli led to a large increase in the amount of flavin mononucleotide (FMN) in the E. coli cell extract. The unexpected features of the purified recombinant enzyme were its use of CTP as the phosphoryl donor and the absence of a requirement for added metal ion to catalyze the formation of FMN. Identification of this riboflavin kinase fills another gap in the archaeal flavin biosynthetic pathway. Some divalent metals were found to be potent inhibitors of the reaction. The enzyme represents a unique CTP-dependent family of kinases.
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Affiliation(s)
- Zahra Mashhadi
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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Abstract
In spite of their common hypersaline environment, halophilic archaea are surprisingly different in their nutritional demands and metabolic pathways. The metabolic diversity of halophilic archaea was investigated at the genomic level through systematic metabolic reconstruction and comparative analysis of four completely sequenced species: Halobacterium salinarum, Haloarcula marismortui, Haloquadratum walsbyi, and the haloalkaliphile Natronomonas pharaonis. The comparative study reveals different sets of enzyme genes amongst halophilic archaea, e.g. in glycerol degradation, pentose metabolism, and folate synthesis. The carefully assessed metabolic data represent a reliable resource for future system biology approaches as it also links to current experimental data on (halo)archaea from the literature.
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El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. Discovery of a New Prokaryotic Type I GTP Cyclohydrolase Family. J Biol Chem 2006; 281:37586-93. [PMID: 17032654 DOI: 10.1074/jbc.m607114200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
GTP cyclohydrolase I (GCYH-I) is the first enzyme of the de novo tetrahydrofolate biosynthetic pathway present in bacteria, fungi, and plants, and encoded in Escherichia coli by the folE gene. It is also the first enzyme of the biopterin (BH4) pathway in Homo sapiens, where it is encoded by a homologous folE gene. A homology-based search of GCYH-I orthologs in all sequenced bacteria revealed a group of microbes, including several clinically important pathogens, that encoded all of the enzymes of the tetrahydrofolate biosynthesis pathway but GCYH-I, suggesting that an alternate family was present in these organisms. A prediction based on phylogenetic occurrence and physical clustering identified the COG1469 family as a potential candidate for this missing enzyme family. The GCYH-I activity of COG1469 family proteins from a variety of sources (Thermotoga maritima, Bacillus subtilis, Acinetobacter baylyi, and Neisseria gonorrhoeae) was experimentally verified in vivo and/or in vitro. Although there is no detectable sequence homology with the canonical GCYH-I, protein fold recognition based on sequence profiles, secondary structure, and solvation potential information suggests that, like GCYH-I proteins, COG1469 proteins are members of the tunnel-fold (T-fold) structural superfamily. This new GCYH-I family is found in approximately 20% of sequenced bacteria and is prevalent in Archaea, but the family is to this date absent in Eukarya.
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Affiliation(s)
- Basma El Yacoubi
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, USA
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19
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Spoonamore JE, Dahlgran AL, Jacobsen NE, Bandarian V. Evolution of new function in the GTP cyclohydrolase II proteins of Streptomyces coelicolor. Biochemistry 2006; 45:12144-55. [PMID: 17002314 PMCID: PMC3227873 DOI: 10.1021/bi061005x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The genome sequence of Streptomyces coelicolor contains three open reading frames (sco1441, sco2687, and sco6655) that encode proteins with significant (>40%) amino acid identity to GTP cyclohydrolase II (GCH II), which catalyzes the committed step in the biosynthesis of riboflavin. The physiological significance of the redundancy of these proteins in S. coelicolor is not known. However, the gene contexts of the three proteins are different, suggesting that they may serve alternate biological niches. Each of the three proteins was overexpressed in Escherichia coli and characterized to determine if their functions are biologically overlapping. As purified, each protein contains 1 molar equiv of zinc/mol of protein and utilizes guanosine 5'-triphosphate (GTP) as substrate. Two of these proteins (SCO 1441 and SCO 2687) produce the canonical product of GCH II, 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (APy). Remarkably, however, one of the three proteins (SCO 6655) converts GTP to 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (FAPy), as shown by UV-visible spectrophotometry, mass spectrometry, and NMR. This activity has been reported for a GTP cyclohydrolase III protein from Methanocaldococcus jannaschii [Graham, D. E., Xu, H., and White, R. H. (2002) Biochemistry 41, 15074-15084], which has no amino acid sequence homology to SCO 6655. Comparison of the sequences of these proteins and mapping onto the structure of the E. coli GCH II protein [Ren, J., Kotaka, M., Lockyer, M., Lamb, H. K., Hawkins, A. R., and Stammers, D. K. (2005) J. Biol. Chem. 280, 36912-36919] allowed identification of a switch residue, Met120, which appears to be responsible for the altered fate of GTP observed with SCO 6655; a Tyr is found in the analogous position of all proteins that have been shown to catalyze the conversion of GTP to APy. The Met120Tyr variant of SCO 6655 acquires the ability to catalyze the conversion of GTP to APy, suggesting a role for Tyr120 in the late phase of the reaction. Our data are consistent with duplication of GCH II in S. coelicolor promoting evolution of a new function. The physiological role(s) of the gene clusters that house GCH II homologues will be discussed.
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Affiliation(s)
- James E. Spoonamore
- Department of Biochemistry and Molecular Biophysics, University of Arizona, 1041 East Lowell Street, Arizona 85721
| | - Annie L. Dahlgran
- Department of Biochemistry and Molecular Biophysics, University of Arizona, 1041 East Lowell Street, Arizona 85721
| | - Neil E. Jacobsen
- Department of Chemistry, University of Arizona, 1306 East University Avenue, Tucson, Arizona 85721
| | - Vahe Bandarian
- Department of Biochemistry and Molecular Biophysics, University of Arizona, 1041 East Lowell Street, Arizona 85721
- Department of Chemistry, University of Arizona, 1306 East University Avenue, Tucson, Arizona 85721
- Corresponding author. Telephone: (520) 626-0389. Fax: (520) 621-1697. E-mail:
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20
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Chatwell L, Krojer T, Fidler A, Römisch W, Eisenreich W, Bacher A, Huber R, Fischer M. Biosynthesis of Riboflavin: Structure and Properties of 2,5-Diamino-6-ribosylamino-4(3H)-pyrimidinone 5′-phosphate Reductase of Methanocaldococcus jannaschii. J Mol Biol 2006; 359:1334-51. [PMID: 16730025 DOI: 10.1016/j.jmb.2006.04.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Revised: 04/19/2006] [Accepted: 04/20/2006] [Indexed: 10/24/2022]
Abstract
The pyrimidine reductase of the riboflavin biosynthetic pathway (MjaRED) specified by the open reading frame MJ0671 of Methanocaldococcus jannaschii was expressed in Escherichia coli using a synthetic gene. The synthetic open reading frame that was optimized for expression in E. coli directed the synthesis of abundant amounts of the enzyme with an apparent subunit mass of 25 kDa. The enzyme was purified to apparent homogeneity and was shown to catalyze the conversion of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate into 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate at a rate of 0.8 micromol min(-1) mg(-1) at pH 8.0 and at 30 degrees C. The protein is a homodimer as shown by sedimentation equilibrium analysis and sediments at an apparent velocity of 3.5 S. The structure of the enzyme in complex with the cofactor nicotinamide adenine dinucleotide phosphate was determined by X-ray crystallography at a resolution of 2.5 Angstroms. The folding pattern resembles that of dihydrofolate reductase with the Thermotoga maritima ortholog as the most similar structure. The substrate, 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, was modeled into the putative active site. The model suggests the transfer of the pro-R hydrogen of C-4 of NADPH to C-1' of the substrate.
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Affiliation(s)
- Lorenz Chatwell
- Max-Planck Institut für Biochemie, Abteilung für Strukturforschung, Martinsried, Germany.
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21
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Fischer M, Haase I, Feicht R, Schramek N, Köhler P, Schieberle P, Bacher A. Evolution of vitamin B2 biosynthesis: riboflavin synthase of Arabidopsis thaliana and its inhibition by riboflavin. Biol Chem 2005; 386:417-28. [PMID: 15927885 DOI: 10.1515/bc.2005.050] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A synthetic gene specifying the catalytic domain of the Arabidopsis thaliana riboflavin synthase was expressed with high efficiency in a recombinant Escherichia coli strain. The recombinant pseudomature protein was shown to convert 6,7-dimethyl-8-ribityllumazine into riboflavin at a rate of 0.027 s-1 at 25 degrees C. The protein sediments at a rate of 3.9 S. Sedimentation equilibrium analysis afforded a molecular mass of 67.5 kDa, indicating a homotrimeric structure, analogous to the riboflavin synthases of Eubacteria and fungi. The protein binds its product riboflavin with relatively high affinity (Kd =1.1 microM). Product inhibition results in a characteristic sigmoidal velocity versus substrate concentration relationship. Characterization of the enzyme/product complex by circular dichroism and UV absorbance spectroscopy revealed a shift of the absorption maxima of riboflavin from 370 and 445 to 399 and 465 nm, respectively. Complete or partial sequences for riboflavin synthase orthologs were analyzed from 11 plant species. In each case for which the complete plant gene sequence was available, the catalytic domain was preceded by a sequence of 1-72 amino acid residues believed to function as plastid targeting signals. Comparison of all available riboflavin synthase sequences indicates that hypothetical gene duplication conducive to the two-domain architecture occurred very early in evolution.
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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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22
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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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23
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Van Lanen SG, Reader JS, Swairjo MA, de Crécy-Lagard V, Lee B, Iwata-Reuyl D. From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold. Proc Natl Acad Sci U S A 2005; 102:4264-9. [PMID: 15767583 PMCID: PMC555470 DOI: 10.1073/pnas.0408056102] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2004] [Indexed: 11/18/2022] Open
Abstract
The enzyme YkvM from Bacillus subtilis was identified previously along with three other enzymes (YkvJKL) in a bioinformatics search for enzymes involved in the biosynthesis of queuosine, a 7-deazaguanine modified nucleoside found in tRNA(GUN) of Bacteria and Eukarya. Genetic analysis of ykvJKLM mutants in Acinetobacter confirmed that each was essential for queuosine biosynthesis, and the genes were renamed queCDEF. QueF exhibits significant homology to the type I GTP cyclohydrolases characterized by FolE. Given that GTP is the precursor to queuosine and that a cyclohydrolase-like reaction was postulated as the initial step in queuosine biosynthesis, QueF was proposed to be the putative cyclohydrolase-like enzyme responsible for this reaction. We have cloned the queF genes from B. subtilis and Escherichia coli and characterized the recombinant enzymes. Contrary to the predictions based on sequence analysis, we discovered that the enzymes, in fact, catalyze a mechanistically unrelated reaction, the NADPH-dependent reduction of 7-cyano-7-deazaguanineto7-aminomethyl-7-deazaguanine, a late step in the biosynthesis of queuosine. We report here in vitro and in vivo studies that demonstrate this catalytic activity, as well as preliminary biochemical and bioinformatics analysis that provide insight into the structure of this family of enzymes.
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Affiliation(s)
- Steven G Van Lanen
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, OR 97207, USA
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24
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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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25
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Caccamo MA, Malone CS, Rasche ME. Biochemical characterization of a dihydromethanopterin reductase involved in tetrahydromethanopterin biosynthesis in Methylobacterium extorquens AM1. J Bacteriol 2004; 186:2068-73. [PMID: 15028691 PMCID: PMC374392 DOI: 10.1128/jb.186.7.2068-2073.2004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2003] [Accepted: 12/11/2003] [Indexed: 11/20/2022] Open
Abstract
During growth on one-carbon (C1) compounds, the aerobic alpha-proteobacterium Methylobacterium extorquens AM1 synthesizes the tetrahydromethanopterin (H4MPT) derivative dephospho-H4MPT as a C1 carrier in addition to tetrahydrofolate. The enzymes involved in dephospho-H4MPT biosynthesis have not been identified in bacteria. In archaea, the final step in the proposed pathway of H4MPT biosynthesis is the reduction of dihydromethanopterin (H2MPT) to H4MPT, a reaction analogous to the reaction of the bacterial dihydrofolate reductase. A gene encoding a dihydrofolate reductase homolog has previously been reported for M. extorquens and assigned as the putative H2MPT reductase gene (dmrA). In the present work, we describe the biochemical characterization of H2MPT reductase (DmrA), which is encoded by dmrA. The gene was expressed with a six-histidine tag in Escherichia coli, and the recombinant protein was purified by nickel affinity chromatography and gel filtration. Purified DmrA catalyzed the NAD(P)H-dependent reduction of H2MPT with a specific activity of 2.8 micromol of NADPH oxidized per min per mg of protein at 30 degrees C and pH 5.3. Dihydrofolate was not a substrate for DmrA at the physiological pH of 6.8. While the existence of an H2MPT reductase has been proposed previously, this is the first biochemical evidence for such an enzyme in any organism, including archaea. Curiously, no DmrA homologs have been identified in the genomes of known methanogenic archaea, suggesting that bacteria and archaea produce two evolutionarily distinct forms of dihydromethanopterin reductase. This may be a consequence of different electron donors, NAD(P)H versus reduced F420, used, respectively, in bacteria and methanogenic archaea.
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Affiliation(s)
- Marco A Caccamo
- Microbiology and Cell Science Department, University of Florida, Gainesville, Florida 32611-0700, USA
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26
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Rasche ME, Havemann SA, Rosenzvaig M. Characterization of two methanopterin biosynthesis mutants of Methylobacterium extorquens AM1 by use of a tetrahydromethanopterin bioassay. J Bacteriol 2004; 186:1565-70. [PMID: 14973120 PMCID: PMC344399 DOI: 10.1128/jb.186.5.1565-1570.2004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2003] [Accepted: 11/12/2003] [Indexed: 11/20/2022] Open
Abstract
An enzymatic assay was developed to measure tetrahydromethanopterin (H(4)MPT) levels in wild-type and mutant cells of Methylobacterium extorquens AM1. H(4)MPT was detectable in wild-type cells but not in strains with a mutation of either the orf4 or the dmrA gene, suggesting a role for these two genes in H(4)MPT biosynthesis. The protein encoded by orf4 catalyzed the reaction of ribofuranosylaminobenzene 5'-phosphate synthase, the first committed step of H(4)MPT biosynthesis. These results provide the first biochemical evidence for H(4)MPT biosynthesis genes in bacteria.
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Affiliation(s)
- Madeline E Rasche
- Microbiology and Cell Science Department, University of Florida, Gainesville, Florida 32611-0700, USA.
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27
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Graupner M, White RH. Methanococcus jannaschii coenzyme F420 analogs contain a terminal alpha-linked glutamate. J Bacteriol 2003; 185:4662-5. [PMID: 12867481 PMCID: PMC165758 DOI: 10.1128/jb.185.15.4662-4665.2003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2003] [Accepted: 05/12/2003] [Indexed: 11/20/2022] Open
Abstract
Analyses of the F(420)s present in Methanococcus jannaschii have shown that these cells contain a series of gamma-glutamyl-linked F(420)s capped with a single, terminal alpha-linked L-glutamate. The predominant form of F(420) was designated as alpha-F(420)-3 and represented 86% of the F(420)s in these cells. Analyses of Methanosarcina thermophila, Methanosarcina barkeri, Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, and Mycobacterium smegmatis showed that they contained only gamma-glutamyl-linked F(420)s.
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Affiliation(s)
- Marion Graupner
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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28
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Li H, Xu H, Graham DE, White RH. The Methanococcus jannaschii dCTP deaminase is a bifunctional deaminase and diphosphatase. J Biol Chem 2003; 278:11100-6. [PMID: 12538648 DOI: 10.1074/jbc.m212460200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most bacteria produce the dUMP precursor for thymine nucleotide biosynthesis using two enzymes: a dCTP deaminase catalyzes the formation of dUTP and a dUTP diphosphatase catalyzes pyrophosphate release. Although these two hydrolytic enzymes appear to catalyze very different reactions, they are encoded by homologous genes. The hyperthermophilic archaeon Methanococcus jannaschii has two members of this gene family. One gene, at locus MJ1102, encodes a dUTP diphosphatase, which can scavenge deoxyuridine nucleotides that inhibit archaeal DNA polymerases. The second gene, at locus MJ0430, encodes a novel dCTP deaminase that releases dUMP, ammonia, and pyrophosphate. Therefore this enzyme can singly catalyze both steps in dUMP biosynthesis, precluding the formation of free, mutagenic dUTP. Besides differing from the previously characterized Salmonella typhimurium dCTP deaminase in its reaction products, this archaeal enzyme has a higher affinity for dCTP and its steady-state turnover is faster than the bacterial enzyme. Kinetic studies suggest: 1) the archaeal enzyme specifically recognizes dCTP; 2) dCTP deamination and dUTP diphosphatase activities occur independently at the same active site, and 3) both activities depend on Mg(2+). The bifunctional activity of this M. jannaschii enzyme illustrates the evolution of a suprafamily of related enzymes that catalyze mechanistically distinct reactions.
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Affiliation(s)
- Hong Li
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0308, USA
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29
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Bechard ME, Chhatwal S, Garcia RE, Rasche ME. Application of a Colorimetric Assay to Identify Putative Ribofuranosylaminobenzene 5'-Phosphate Synthase Genes Expressed with Activity in Escherichia coli. Biol Proced Online 2003; 5:69-77. [PMID: 12734554 PMCID: PMC152576 DOI: 10.1251/bpo48] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2003] [Revised: 02/14/2003] [Accepted: 02/14/2003] [Indexed: 11/23/2022] Open
Abstract
Tetrahydromethanopterin (H(4)MPT) is a tetrahydrofolate analog originally discovered in methanogenic archaea, but later found in other archaea and bacteria. The extent to which H(4)MPT occurs among living organisms is unknown. The key enzyme which distinguishes the biosynthetic pathways of H(4)MPT and tetrahydrofolate is ribofuranosylaminobenzene 5'-phosphate synthase (RFAP synthase). Given the importance of RFAP synthase in H(4)MPT biosynthesis, the identification of putative RFAP synthase genes and measurement of RFAP synthase activity would provide an indication of the presence of H(4)MPT in untested microorganisms. Investigation of putative archaeal RFAP synthase genes has been hampered by the tendency of the resulting proteins to form inactive inclusion bodies in Escherichia coli. The current work describes a colorimetric assay for measuring RFAP synthase activity, and two modified procedures for expressing recombinant RFAP synthase genes to produce soluble, active enzyme. By lowering the incubation temperature during expression, RFAP synthase from Archaeoglobus fulgidus was produced in E. coli and purified to homogeneity. The production of active RFAP synthase from Methanothermobacter thermautotrophicus was achieved by coexpression of the gene MTH0830 with a molecular chaperone. This is the first direct biochemical identification of a methanogen gene that codes for an active RFAP synthase.
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Affiliation(s)
- Matthew E. Bechard
- Microbiology and Cell Science Department, University of Florida. Gainesville, FL 32611-0700. USA
| | - Sonya Chhatwal
- Microbiology and Cell Science Department, University of Florida. Gainesville, FL 32611-0700. USA
| | - Rosemarie E. Garcia
- Microbiology and Cell Science Department, University of Florida. Gainesville, FL 32611-0700. USA
| | - Madeline E. Rasche
- Microbiology and Cell Science Department, University of Florida. Gainesville, FL 32611-0700. USA
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