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Galindo LJ, Torruella G, López-García P, Ciobanu M, Gutiérrez-Preciado A, Karpov SA, Moreira D. Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies. Syst Biol 2022:6651083. [PMID: 35900180 DOI: 10.1093/sysbio/syac054] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/12/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
The supergroup Holomycota, composed of Fungi and several related lineages of unicellular organisms (Nucleariida, Rozellida, Microsporidia, and Aphelida), represents one of the major branches in the phylogeny of eukaryotes. Nevertheless, except for the well-established position of Nucleariida as the first holomycotan branch to diverge, the relationships among the other lineages have so far remained unresolved largely owing to the lack of molecular data for some groups. This was notably the case aphelids, a poorly known group of endobiotic phagotrophic protists that feed on algae with cellulose walls. The first molecular phylogenies including aphelids supported their sister relationship with Rozellida and Microsporidia which, collectively, formed a new group called Opisthosporidia (the 'Opisthosporidia hypothesis'). However, recent phylogenomic analyses including massive sequence data from two aphelid genera, Paraphelidium and Amoeboaphelidium, suggested that the aphelids are sister to fungi (the 'Aphelida+Fungi hypothesis'). Should this position be confirmed, aphelids would be key to understanding the early evolution of Holomycota and the origin of Fungi. Here, we carry out phylogenomic analyses with an expanded taxonomic sampling for aphelids after sequencing the transcriptomes of two species of the genus Aphelidium (A. insulamus and A. tribonematis) in order to test these competing hypotheses. Our new phylogenomic analyses including species from the three known aphelid genera strongly rejected the Opisthosporidia hypothesis. Furthermore, comparative genomic analyses further supported the Aphelida+Fungi hypothesis via the identification of 19 orthologous genes exclusively shared by these two lineages. Seven of them originated from ancient horizontal gene transfer events predating the aphelid-fungal split and the remaining 12 likely evolved de novo, constituting additional molecular synapomorphies for this clade. Ancestral trait reconstruction based on our well-resolved phylogeny of Holomycota suggests that the progenitor of both fungi and rozellids, was aphelid-like, having an amoeboflagellate state and likely preying endobiotically on cellulose-containing, cell-walled organisms. Two lineages, which we propose to call Phytophagea and Opisthophagea, evolved from this ancestor. Phytophagea, grouping aphelids and classical fungi, mainly specialized in endobiotic predation of algal cells. Fungi emerged from this lineage after losing phagotrophy in favour of osmotrophy. Opisthophagea, grouping rozellids and Microsporidia, became parasites, mostly of chitin-containing hosts. This lineage entered a progressive reductive process that resulted in a unique lifestyle, especially in the highly derived Microsporidia.
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Affiliation(s)
- Luis Javier Galindo
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Guifré Torruella
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Purificación López-García
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Maria Ciobanu
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Ana Gutiérrez-Preciado
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Sergey A Karpov
- Zoological Institute RAS, Universitetskaya emb. 1, and St Petersburg State University, Universitetskaya emb. 7/9, St Petersburg 199034, Russia
| | - David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
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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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Yadav S, Shinde RN, Singh S, Karthikeyan S, Singh B. Structurally disordered C-terminal residues of GTP cyclohydrolase II are essential for its enzymatic activity. J Biomol Struct Dyn 2021; 40:9318-9331. [PMID: 34032179 DOI: 10.1080/07391102.2021.1926326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
GTP cyclohydrolase II (GCHII) is one of the rate limiting enzymes in riboflavin biosynthesis pathway and is shown to be a potential drug target for most of the pathogens. Previous biochemical and structural studies have identified the active site residues and elucidated the steps involved in the catalytic mechanism of GCHII. However, the last ∼20-25 C-terminal residues of GCHII remains unstructured in all the crystal structures determined to date and their role in the catalytic activity, if any, remains elusive. Therefore, to understand the role of these unstructured C-terminal residues, a series of C-terminal deletion mutants of GCHII from Helicobacter pylori (hGCHII) were generated and their catalytic activity was compared with its wild-type. Surprisingly, none of the C-terminal deletion mutants shows any enzymatic activity indicating that these are essential for GCHII function. To get additional insights for such loss of activity, homology models of full-length and deletion mutants of hGCHII in complex with GTP, Mg2+, and Zn2+ were generated and subjected to molecular dynamics simulation studies. The simulation studies show that a conserved histidine at 190th position from the unstructured C-terminal region of hGCHII interacts with α-phosphate of GTP. We propose that His-190 may play a role in the hydrolysis of pyrophosphate from GTP and in releasing the product, DARP. In summary, we demonstrate that the unstructured C-terminal residues of GCHII are important for its enzymatic activity and must be considered during rational drug designing. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Savita Yadav
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Ranajit Nivrutti Shinde
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Suruchi Singh
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Subramanian Karthikeyan
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Balvinder Singh
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
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Enhancement of marinacarboline A biosynthesis by optimizing the riboflavin supplement in marine derived Nocardiopsis flavescens CGMCC 4.5723. Biotechnol Lett 2019; 41:1033-1041. [DOI: 10.1007/s10529-019-02698-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 06/09/2019] [Indexed: 12/24/2022]
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Joo M, Yoo HG, Kim HJ, Kwon HJ. ToxB encodes a canonical GTP cyclohydrolase II in toxoflavin biosynthesis and ribA expression restored toxoflavin production in a ΔtoxB mutant. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s13765-015-0116-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Yadav S, Karthikeyan S. Structural and biochemical characterization of GTP cyclohydrolase II from Helicobacter pylori reveals its redox dependent catalytic activity. J Struct Biol 2015; 192:100-15. [PMID: 26272484 DOI: 10.1016/j.jsb.2015.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 08/01/2015] [Accepted: 08/10/2015] [Indexed: 01/10/2023]
Abstract
GTP cyclohydrolase II (GCHII), catalyzes the conversion of GTP to 2,5-diamino-6-β-ribosyl-4(3H)-pyrimidinone-5'-phosphate and has been shown to be essential for pathogens. Here we describe the biochemical, kinetic and structural characterization of GCHII from Helicobacter pylori (hGCHII). The crystal structure of hGCHII, unlike other GCHII structures, revealed that cysteines at the active site existed in oxidized state forming two disulfide bonds and lacked Zn(2+) that was shown to be indispensable for catalytic activity in other species. However, incubation of hGCHII with hydrogen peroxide, an oxidizing agent, followed by PAR-assay showed that Zn(2+) was intrinsically present, indicating that all cysteines at the catalytic site remained in reduced state. Moreover, site directed mutagenesis of catalytic site cysteines revealed that only three, out of four cysteines were essential for hGCHII activity. These results, though, indicated that hGCHII crystallized in oxidized form, the expulsion of Zn(2+) upon oxidation of catalytic cysteines revealed its ability to act in response to the redox environment. Exploring further, incubation of hGCHII with reversible thiol modifying agent S-methyl-methane-thiosulfonate resulted in loss of GCHII activity due to oxidation of its cysteine residues as revealed by mass spectrometry studies. However, addition of reducing agent DTT partially restored the hGCHII catalytic activity. Taken together, these results demonstrate that hGCHII can regulate its catalytic activity depending on the redox environment, a function hitherto unknown for GCHII.
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Affiliation(s)
- Savita Yadav
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh 160 036, India
| | - Subramanian Karthikeyan
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh 160 036, India.
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Singh M, Kumar P, Yadav S, Gautam R, Sharma N, Karthikeyan S. The crystal structure reveals the molecular mechanism of bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II (Rv1415) fromMycobacterium tuberculosis. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1633-44. [DOI: 10.1107/s0907444913011402] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/26/2013] [Indexed: 11/10/2022]
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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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Arabidopsis RIBA proteins: two out of three isoforms have lost their bifunctional activity in riboflavin biosynthesis. Int J Mol Sci 2012. [PMID: 23203051 PMCID: PMC3509567 DOI: 10.3390/ijms131114086] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Riboflavin serves as a precursor for flavocoenzymes (FMN and FAD) and is essential for all living organisms. The two committed enzymatic steps of riboflavin biosynthesis are performed in plants by bifunctional RIBA enzymes comprised of GTP cyclohydrolase II (GCHII) and 3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS). Angiosperms share a small RIBA gene family consisting of three members. A reduction of AtRIBA1 expression in the Arabidopsis rfd1mutant and in RIBA1 antisense lines is not complemented by the simultaneously expressed isoforms AtRIBA2 and AtRIBA3. The intensity of the bleaching leaf phenotype of RIBA1 deficient plants correlates with the inactivation of AtRIBA1 expression, while no significant effects on the mRNA abundance of AtRIBA2 and AtRIBA3 were observed. We examined reasons why both isoforms fail to sufficiently compensate for a lack of RIBA1 expression. All three RIBA isoforms are shown to be translocated into chloroplasts as GFP fusion proteins. Interestingly, both AtRIBA2 and AtRIBA3 have amino acid exchanges in conserved peptides domains that have been found to be essential for the two enzymatic functions. In vitro activity assays of GCHII and DHBPS with all of the three purified recombinant AtRIBA proteins and complementation of E. coli ribA and ribB mutants lacking DHBPS and GCHII expression, respectively, confirmed the loss of bifunctionality for AtRIBA2 and AtRIBA3. Phylogenetic analyses imply that the monofunctional, bipartite RIBA3 proteins, which have lost DHBPS activity, evolved early in tracheophyte evolution.
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Abbas CA, Sibirny AA. Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers. Microbiol Mol Biol Rev 2011; 75:321-60. [PMID: 21646432 PMCID: PMC3122625 DOI: 10.1128/mmbr.00030-10] [Citation(s) in RCA: 239] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Riboflavin [7,8-dimethyl-10-(1'-d-ribityl)isoalloxazine, vitamin B₂] is an obligatory component of human and animal diets, as it serves as the precursor of flavin coenzymes, flavin mononucleotide, and flavin adenine dinucleotide, which are involved in oxidative metabolism and other processes. Commercially produced riboflavin is used in agriculture, medicine, and the food industry. Riboflavin synthesis starts from GTP and ribulose-5-phosphate and proceeds through pyrimidine and pteridine intermediates. Flavin nucleotides are synthesized in two consecutive reactions from riboflavin. Some microorganisms and all animal cells are capable of riboflavin uptake, whereas many microorganisms have distinct systems for riboflavin excretion to the medium. Regulation of riboflavin synthesis in bacteria occurs by repression at the transcriptional level by flavin mononucleotide, which binds to nascent noncoding mRNA and blocks further transcription (named the riboswitch). In flavinogenic molds, riboflavin overproduction starts at the stationary phase and is accompanied by derepression of enzymes involved in riboflavin synthesis, sporulation, and mycelial lysis. In flavinogenic yeasts, transcriptional repression of riboflavin synthesis is exerted by iron ions and not by flavins. The putative transcription factor encoded by SEF1 is somehow involved in this regulation. Most commercial riboflavin is currently produced or was produced earlier by microbial synthesis using special selected strains of Bacillus subtilis, Ashbya gossypii, and Candida famata. Whereas earlier RF overproducers were isolated by classical selection, current producers of riboflavin and flavin nucleotides have been developed using modern approaches of metabolic engineering that involve overexpression of structural and regulatory genes of the RF biosynthetic pathway as well as genes involved in the overproduction of the purine precursor of riboflavin, GTP.
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Affiliation(s)
| | - Andriy A. Sibirny
- Institute of Cell Biology, NAS of Ukraine, Lviv 79005, Ukraine
- University of Rzeszow, Rzeszow 35-601, Poland
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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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12
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McCarty RM, Bandarian V. Deciphering deazapurine biosynthesis: pathway for pyrrolopyrimidine nucleosides toyocamycin and sangivamycin. ACTA ACUST UNITED AC 2008; 15:790-8. [PMID: 18721750 DOI: 10.1016/j.chembiol.2008.07.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 06/03/2008] [Accepted: 07/07/2008] [Indexed: 11/28/2022]
Abstract
Pyrrolopyrimidine nucleosides analogs, collectively referred to as deazapurines, are an important class of structurally diverse compounds found in a wide variety of biological niches. In this report, a cluster of genes from Streptomyces rimosus (ATCC 14673) involved in production of the deazapurine antibiotics sangivamycin and toyocamycin was identified. The cluster includes toyocamycin nitrile hydratase, an enzyme that catalyzes the conversion of toyocamycin to sangivamycin. In addition to this rare nitrile hydratase, the cluster encodes a GTP cyclohydrolase I, linking the biosynthesis of deazapurines to folate biosynthesis, and a set of purine salvage/biosynthesis genes, which presumably convert the guanine moiety from GTP to the adenine-like deazapurine base found in toyocamycin and sangivamycin. The gene cluster presented here could potentially serve as a model to allow identification of deazapurine biosynthetic pathways in other bacterial species.
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Affiliation(s)
- Reid M McCarty
- Department of Biochemistry and Molecular Biophysics, University of Arizona, 1041 E. Lowell Street, Tucson, AZ 85721, USA
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Spoonamore JE, Roberts SA, Heroux A, Bandarian V. Structure of a 6-pyruvoyltetrahydropterin synthase homolog from Streptomyces coelicolor. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:875-9. [PMID: 18931427 PMCID: PMC2564891 DOI: 10.1107/s1744309108027048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Accepted: 08/21/2008] [Indexed: 11/11/2022]
Abstract
The X-ray crystal structure of the 6-pyruvoyltetrahydropterin synthase (PTPS) homolog from Streptomyces coelicolor, SCO 6650, was solved at 1.5 A resolution. SCO 6650 forms a hexameric T-fold that closely resembles other PTPS proteins. The biological activity of SCO 6650 is unknown, but it lacks both a required active-site zinc metal ion and the essential catalytic triad and does not catalyze the PTPS reaction. However, SCO 6650 maintains active-site residues consistent with binding a pterin-like substrate.
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Affiliation(s)
- James E. Spoonamore
- Departments of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
| | - Sue A. Roberts
- Departments of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
| | - Annie Heroux
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Vahe Bandarian
- Departments of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
- Department of Chemistry, University of Arizona, Tucson, AZ 85721, USA
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Grill S, Yamaguchi H, Wagner H, Zwahlen L, Kusch U, Mack M. Identification and characterization of two Streptomyces davawensis riboflavin biosynthesis gene clusters. Arch Microbiol 2007; 188:377-87. [PMID: 17541777 DOI: 10.1007/s00203-007-0258-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 04/19/2007] [Accepted: 05/04/2007] [Indexed: 10/23/2022]
Abstract
In Streptomyces davawensis roseoflavin is synthesized from GTP and ribulose-5-phosphate through riboflavin. As a first step towards the molecular analysis of flavin metabolism in S. davawensis the genes involved in riboflavin biosynthesis were cloned by hybridization of heterologous probes to a genomic library on a high-density colony-array. The genes ribB (riboflavin synthase, alpha-chain; EC 2.5.1.9), ribM (putative membrane protein), ribA (bifunctional GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate synthase; EC 3.5.4.25) and ribH (lumazine synthase; EC 2.5.1.9) are organized in an operon-like cluster. Northern blot analysis of this cluster revealed two transcripts of 1.7 and 3.1 kb, respectively. The gene ribB was overexpressed in Escherichia coli. The specific riboflavin synthase activity in a cell-free extract of a recombinant strain was 0.246 nmol mg(-1 )min(-1). Overexpression of ribM enhanced the transport of riboflavin in the corresponding recombinant E. coli strain. Furthermore, overexpression of ribM increased roseoflavin sensitivity of E. coli. On another subgenomic fragment a putative S. davawensis ribG gene coding for the missing pyrimidine deaminase/reductase (EC 3.5.4.26 and EC 1.1.1.193) of the riboflavin biosynthetic pathway and ribY coding for a second (monofunctional) GTP cyclohydrolase II were identified.
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Affiliation(s)
- Simon Grill
- Institute for Technical Microbiology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany
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