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Joshi J, Hasnain G, Logue T, Lynch M, Wu S, Guan JC, Alseekh S, Fernie AR, Hanson AD, McCarty DR. A Core Metabolome Response of Maize Leaves Subjected to Long-Duration Abiotic Stresses. Metabolites 2021; 11:metabo11110797. [PMID: 34822455 PMCID: PMC8625080 DOI: 10.3390/metabo11110797] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 11/16/2022] Open
Abstract
Abiotic stresses reduce crop growth and yield in part by disrupting metabolic homeostasis and triggering responses that change the metabolome. Experiments designed to understand the mechanisms underlying these metabolomic responses have usually not used agriculturally relevant stress regimes. We therefore subjected maize plants to drought, salt, or heat stresses that mimic field conditions and analyzed leaf responses at metabolome and transcriptome levels. Shared features of stress metabolomes included synthesis of raffinose, a compatible solute implicated in tolerance to dehydration. In addition, a marked accumulation of amino acids including proline, arginine, and γ-aminobutyrate combined with depletion of key glycolysis and tricarboxylic acid cycle intermediates indicated a shift in balance of carbon and nitrogen metabolism in stressed leaves. Involvement of the γ-aminobutyrate shunt in this process is consistent with its previously proposed role as a workaround for stress-induced thiamin-deficiency. Although convergent metabolome shifts were correlated with gene expression changes in affected pathways, patterns of differential gene regulation induced by the three stresses indicated distinct signaling mechanisms highlighting the plasticity of plant metabolic responses to abiotic stress.
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Affiliation(s)
- Jaya Joshi
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA; (J.J.); (T.L.); (M.L.); (S.W.); (J.-C.G.); (A.D.H.)
| | - Ghulam Hasnain
- Department of Biology, University of North Georgia, Oakwood, GA 30566, USA;
| | - Taylor Logue
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA; (J.J.); (T.L.); (M.L.); (S.W.); (J.-C.G.); (A.D.H.)
| | - Madeline Lynch
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA; (J.J.); (T.L.); (M.L.); (S.W.); (J.-C.G.); (A.D.H.)
| | - Shan Wu
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA; (J.J.); (T.L.); (M.L.); (S.W.); (J.-C.G.); (A.D.H.)
| | - Jiahn-Chou Guan
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA; (J.J.); (T.L.); (M.L.); (S.W.); (J.-C.G.); (A.D.H.)
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (S.A.); (A.R.F.)
- Center for Plant Systems Biology, 4000 Plovdiv, Bulgaria
| | - Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (S.A.); (A.R.F.)
- Center for Plant Systems Biology, 4000 Plovdiv, Bulgaria
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA; (J.J.); (T.L.); (M.L.); (S.W.); (J.-C.G.); (A.D.H.)
| | - Donald R. McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA; (J.J.); (T.L.); (M.L.); (S.W.); (J.-C.G.); (A.D.H.)
- Correspondence:
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Guan JC, Hasnain G, Garrett TJ, Chase CD, Gregory J, Hanson AD, McCarty DR. Corrigendum: Divisions of labor in the thiamin biosynthetic pathway among organs of maize. Front Plant Sci 2018; 9:148. [PMID: 29491877 PMCID: PMC5826395 DOI: 10.3389/fpls.2018.00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 01/29/2018] [Indexed: 06/08/2023]
Abstract
[This corrects the article on p. 370 in vol. 5, PMID: 25136345.].
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Affiliation(s)
- Jiahn-Chou Guan
- Genetics Institute and Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Ghulam Hasnain
- Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Timothy J. Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Christine D. Chase
- Genetics Institute and Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Jesse Gregory
- Department of Food Science and Human Nutrition, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Andrew D. Hanson
- Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Donald R. McCarty
- Genetics Institute and Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
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Mimura M, Zallot R, Niehaus TD, Hasnain G, Gidda SK, Nguyen TND, Anderson EM, Mullen RT, Brown G, Yakunin AF, de Crécy-Lagard V, Gregory JF, McCarty DR, Hanson AD. Arabidopsis TH2 Encodes the Orphan Enzyme Thiamin Monophosphate Phosphatase. Plant Cell 2016; 28:2683-2696. [PMID: 27677881 PMCID: PMC5134987 DOI: 10.1105/tpc.16.00600] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/20/2016] [Accepted: 09/26/2016] [Indexed: 05/18/2023]
Abstract
To synthesize the cofactor thiamin diphosphate (ThDP), plants must first hydrolyze thiamin monophosphate (ThMP) to thiamin, but dedicated enzymes for this hydrolysis step were unknown and widely doubted to exist. The classical thiamin-requiring th2-1 mutation in Arabidopsis thaliana was shown to reduce ThDP levels by half and to increase ThMP levels 5-fold, implying that the THIAMIN REQUIRING2 (TH2) gene product could be a dedicated ThMP phosphatase. Genomic and transcriptomic data indicated that TH2 corresponds to At5g32470, encoding a HAD (haloacid dehalogenase) family phosphatase fused to a TenA (thiamin salvage) family protein. Like the th2-1 mutant, an insertional mutant of At5g32470 accumulated ThMP, and the thiamin requirement of the th2-1 mutant was complemented by wild-type At5g32470 Complementation tests in Escherichia coli and enzyme assays with recombinant proteins confirmed that At5g32470 and its maize (Zea mays) orthologs GRMZM2G148896 and GRMZM2G078283 are ThMP-selective phosphatases whose activity resides in the HAD domain and that the At5g32470 TenA domain has the expected thiamin salvage activity. In vitro and in vivo experiments showed that alternative translation start sites direct the At5g32470 protein to the cytosol and potentially also to mitochondria. Our findings establish that plants have a dedicated ThMP phosphatase and indicate that modest (50%) ThDP depletion can produce severe deficiency symptoms.
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Affiliation(s)
- Manaki Mimura
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Rémi Zallot
- Microbiology and Cell Science Department, University of Florida, Gainesville, Florida 32611
| | - Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Ghulam Hasnain
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Satinder K Gidda
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Thuy N D Nguyen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Erin M Anderson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | | | - Jesse F Gregory
- Food Science and Human Nutrition Department, University of Florida, Gainesville, Florida 32611
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
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Henry CS, Lerma-Ortiz C, Gerdes SY, Mullen JD, Colasanti R, Zhukov A, Frelin O, Thiaville JJ, Zallot R, Niehaus TD, Hasnain G, Conrad N, Hanson AD, de Crécy-Lagard V. Systematic identification and analysis of frequent gene fusion events in metabolic pathways. BMC Genomics 2016; 17:473. [PMID: 27342196 PMCID: PMC4921024 DOI: 10.1186/s12864-016-2782-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/26/2016] [Indexed: 11/19/2022] Open
Abstract
Background Gene fusions are the most powerful type of in silico-derived functional associations. However, many fusion compilations were made when <100 genomes were available, and algorithms for identifying fusions need updating to handle the current avalanche of sequenced genomes. The availability of a large fusion dataset would help probe functional associations and enable systematic analysis of where and why fusion events occur. Results Here we present a systematic analysis of fusions in prokaryotes. We manually generated two training sets: (i) 121 fusions in the model organism Escherichia coli; (ii) 131 fusions found in B vitamin metabolism. These sets were used to develop a fusion prediction algorithm that captured the training set fusions with only 7 % false negatives and 50 % false positives, a substantial improvement over existing approaches. This algorithm was then applied to identify 3.8 million potential fusions across 11,473 genomes. The results of the analysis are available in a searchable database at http://modelseed.org/projects/fusions/. A functional analysis identified 3,000 reactions associated with frequent fusion events and revealed areas of metabolism where fusions are particularly prevalent. Conclusions Customary definitions of fusions were shown to be ambiguous, and a stricter one was proposed. Exploring the genes participating in fusion events showed that they most commonly encode transporters, regulators, and metabolic enzymes. The major rationales for fusions between metabolic genes appear to be overcoming pathway bottlenecks, avoiding toxicity, controlling competing pathways, and facilitating expression and assembly of protein complexes. Finally, our fusion dataset provides powerful clues to decipher the biological activities of domains of unknown function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2782-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA. .,Computation Institute, The University of Chicago, Chicago, IL, 60637, USA.
| | - Claudia Lerma-Ortiz
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Svetlana Y Gerdes
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA.,Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Jeffrey D Mullen
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Ric Colasanti
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Aleksey Zhukov
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Océane Frelin
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Jennifer J Thiaville
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Rémi Zallot
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Ghulam Hasnain
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Neal Conrad
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Valérie de Crécy-Lagard
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA.
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5
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Thiaville JJ, Frelin O, García-Salinas C, Harrison K, Hasnain G, Horenstein NA, Díaz de la Garza RI, Henry CS, Hanson AD, de Crécy-Lagard V. Experimental and Metabolic Modeling Evidence for a Folate-Cleaving Side-Activity of Ketopantoate Hydroxymethyltransferase (PanB). Front Microbiol 2016; 7:431. [PMID: 27065985 PMCID: PMC4814558 DOI: 10.3389/fmicb.2016.00431] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 03/17/2016] [Indexed: 01/07/2023] Open
Abstract
Tetrahydrofolate (THF) and its one-carbon derivatives, collectively termed folates, are essential cofactors, but are inherently unstable. While it is clear that chemical oxidation can cleave folates or damage their pterin precursors, very little is known about enzymatic damage to these molecules or about whether the folate biosynthesis pathway responds adaptively to damage to its end-products. The presence of a duplication of the gene encoding the folate biosynthesis enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (FolK) in many sequenced bacterial genomes combined with a strong chromosomal clustering of the folK gene with panB, encoding the 5,10-methylene-THF-dependent enzyme ketopantoate hydroxymethyltransferase, led us to infer that PanB has a side activity that cleaves 5,10-methylene-THF, yielding a pterin product that is recycled by FolK. Genetic and metabolic analyses of Escherichia coli strains showed that overexpression of PanB leads to accumulation of the likely folate cleavage product 6-hydroxymethylpterin and other pterins in cells and medium, and—unexpectedly—to a 46% increase in total folate content. In silico modeling of the folate biosynthesis pathway showed that these observations are consistent with the in vivo cleavage of 5,10-methylene-THF by a side-activity of PanB, with FolK-mediated recycling of the pterin cleavage product, and with regulation of folate biosynthesis by folates or their damage products.
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Affiliation(s)
- Jennifer J Thiaville
- Department of Microbiology and Cell Science, University of Florida Gainesville, FL, USA
| | - Océane Frelin
- Horticultural Sciences Department, University of Florida Gainesville, FL, USA
| | | | - Katherine Harrison
- Department of Microbiology and Cell Science, University of Florida Gainesville, FL, USA
| | - Ghulam Hasnain
- Horticultural Sciences Department, University of Florida Gainesville, FL, USA
| | | | | | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National LaboratoryArgonne, IL, USA; Computation Institute, The University of ChicagoChicago, IL, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida Gainesville, FL, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of FloridaGainesville, FL, USA; Genetics Institute, University of FloridaGainesville, FL, USA
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6
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Kuznetsova E, Nocek B, Brown G, Makarova KS, Flick R, Wolf YI, Khusnutdinova A, Evdokimova E, Jin K, Tan K, Hanson AD, Hasnain G, Zallot R, de Crécy-Lagard V, Babu M, Savchenko A, Joachimiak A, Edwards AM, Koonin EV, Yakunin AF. Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS. J Biol Chem 2015; 290:18678-98. [PMID: 26071590 DOI: 10.1074/jbc.m115.657916] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 12/15/2022] Open
Abstract
The haloacid dehalogenase (HAD)-like enzymes comprise a large superfamily of phosphohydrolases present in all organisms. The Saccharomyces cerevisiae genome encodes at least 19 soluble HADs, including 10 uncharacterized proteins. Here, we biochemically characterized 13 yeast phosphatases from the HAD superfamily, which includes both specific and promiscuous enzymes active against various phosphorylated metabolites and peptides with several HADs implicated in detoxification of phosphorylated compounds and pseudouridine. The crystal structures of four yeast HADs provided insight into their active sites, whereas the structure of the YKR070W dimer in complex with substrate revealed a composite substrate-binding site. Although the S. cerevisiae and Escherichia coli HADs share low sequence similarities, the comparison of their substrate profiles revealed seven phosphatases with common preferred substrates. The cluster of secondary substrates supporting significant activity of both S. cerevisiae and E. coli HADs includes 28 common metabolites that appear to represent the pool of potential activities for the evolution of novel HAD phosphatases. Evolution of novel substrate specificities of HAD phosphatases shows no strict correlation with sequence divergence. Thus, evolution of the HAD superfamily combines the conservation of the overall substrate pool and the substrate profiles of some enzymes with remarkable biochemical and structural flexibility of other superfamily members.
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Affiliation(s)
- Ekaterina Kuznetsova
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Boguslaw Nocek
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Greg Brown
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Kira S Makarova
- the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Robert Flick
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Yuri I Wolf
- the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Anna Khusnutdinova
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Elena Evdokimova
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Ke Jin
- the Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada, and
| | - Kemin Tan
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Andrew D Hanson
- the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Ghulam Hasnain
- the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Rémi Zallot
- the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Valérie de Crécy-Lagard
- the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Mohan Babu
- the Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada, and
| | - Alexei Savchenko
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Andrzej Joachimiak
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Aled M Edwards
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Eugene V Koonin
- the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Alexander F Yakunin
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada,
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7
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Guan JC, Hasnain G, Garrett TJ, Chase CD, Gregory J, Hanson AD, McCarty DR. Divisions of labor in the thiamin biosynthetic pathway among organs of maize. Front Plant Sci 2014; 5:370. [PMID: 25136345 PMCID: PMC4120688 DOI: 10.3389/fpls.2014.00370] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/11/2014] [Indexed: 05/06/2023]
Abstract
The B vitamin thiamin is essential for central metabolism in all cellular organisms including plants. While plants synthesize thiamin de novo, organs vary widely in their capacities for thiamin synthesis. We use a transcriptomics approach to appraise the distribution of de novo synthesis and thiamin salvage pathways among organs of maize. We identify at least six developmental contexts in which metabolically active, non-photosynthetic organs exhibit low expression of one or both branches of the de novo thiamin biosynthetic pathway indicating a dependence on inter-cellular transport of thiamin and/or thiamin precursors. Neither the thiazole (THI4) nor pyrimidine (THIC) branches of the pathway are expressed in developing pollen implying a dependence on import of thiamin from surrounding floral and inflorescence organs. Consistent with that hypothesis, organs of the male inflorescence and flowers are shown to have high relative expression of the thiamin biosynthetic pathway and comparatively high thiamin contents. By contrast, divergent patterns of THIC and THI4 expression occur in the shoot apical meristem, embyro sac, embryo, endosperm, and root-tips suggesting that these sink organs acquire significant amounts of thiamin via salvage pathways. In the root and shoot meristems, expression of THIC in the absence of THI4 indicates a capacity for thiamin synthesis via salvage of thiazole, whereas the opposite pattern obtains in embryo and endosperm implying that seed storage organs are poised for pyrimidine salvage. Finally, stable isotope labeling experiments set an upper limit on the rate of de novo thiamin biosynthesis in maize leaf explants. Overall, the observed patterns of thiamin biosynthetic gene expression mirror the strategies for thiamin acquisition that have evolved in bacteria.
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Affiliation(s)
- Jiahn-Chou Guan
- Genetics Institute and Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of FloridaGainesville, FL, USA
| | - Ghulam Hasnain
- Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of FloridaGainesville, FL, USA
| | - Timothy J. Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of FloridaGainesville, FL, USA
| | - Christine D. Chase
- Genetics Institute and Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of FloridaGainesville, FL, USA
| | - Jesse Gregory
- Department of Food Science and Human Nutrition, Institute of Food and Agricultural Sciences, University of FloridaGainesville, FL, USA
| | - Andrew D. Hanson
- Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of FloridaGainesville, FL, USA
| | - Donald R. McCarty
- Genetics Institute and Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of FloridaGainesville, FL, USA
- *Correspondence: Donald R. McCarty, Genetics Institute and Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, PO 110690, Gainesville, FL 32611, USA e-mail:
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Van Moerkercke A, Fabris M, Pollier J, Baart GJE, Rombauts S, Hasnain G, Rischer H, Memelink J, Oksman-Caldentey KM, Goossens A. CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data. Plant Cell Physiol 2013; 54:673-85. [PMID: 23493402 DOI: 10.1093/pcp/pct039] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The medicinal plant Madagascar periwinkle (Catharanthus roseus) synthesizes numerous terpenoid indole alkaloids (TIAs), such as the anticancer drugs vinblastine and vincristine. The TIA pathway operates in a complex metabolic network that steers plant growth and survival. Pathway databases and metabolic networks reconstructed from 'omics' sequence data can help to discover missing enzymes, study metabolic pathway evolution and, ultimately, engineer metabolic pathways. To date, such databases have mainly been built for model plant species with sequenced genomes. Although genome sequence data are not available for most medicinal plant species, next-generation sequencing is now extensively employed to create comprehensive medicinal plant transcriptome sequence resources. Here we report on the construction of CathaCyc, a detailed metabolic pathway database, from C. roseus RNA-Seq data sets. CathaCyc (version 1.0) contains 390 pathways with 1,347 assigned enzymes and spans primary and secondary metabolism. Curation of the pathways linked with the synthesis of TIAs and triterpenoids, their primary metabolic precursors, and their elicitors, the jasmonate hormones, demonstrated that RNA-Seq resources are suitable for the construction of pathway databases. CathaCyc is accessible online (http://www.cathacyc.org) and offers a range of tools for the visualization and analysis of metabolic networks and 'omics' data. Overlay with expression data from publicly available RNA-Seq resources demonstrated that two well-characterized C. roseus terpenoid pathways, those of TIAs and triterpenoids, are subject to distinct regulation by both developmental and environmental cues. We anticipate that databases such as CathaCyc will become key to the study and exploitation of the metabolism of medicinal plants.
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9
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Hasnain G, Frelin O, Roje S, Ellens KW, Ali K, Guan JC, Garrett TJ, de Crécy-Lagard V, Gregory JF, McCarty DR, Hanson AD. Identification and characterization of the missing pyrimidine reductase in the plant riboflavin biosynthesis pathway. Plant Physiol 2013; 161:48-56. [PMID: 23150645 PMCID: PMC3532277 DOI: 10.1104/pp.112.208488] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 11/08/2012] [Indexed: 05/21/2023]
Abstract
Riboflavin (vitamin B₂) is the precursor of the flavin coenzymes flavin mononucleotide and flavin adenine dinucleotide. In Escherichia coli and other bacteria, sequential deamination and reduction steps in riboflavin biosynthesis are catalyzed by RibD, a bifunctional protein with distinct pyrimidine deaminase and reductase domains. Plants have two diverged RibD homologs, PyrD and PyrR; PyrR proteins have an extra carboxyl-terminal domain (COG3236) of unknown function. Arabidopsis (Arabidopsis thaliana) PyrD (encoded by At4g20960) is known to be a monofunctional pyrimidine deaminase, but no pyrimidine reductase has been identified. Bioinformatic analyses indicated that plant PyrR proteins have a catalytically competent reductase domain but lack essential zinc-binding residues in the deaminase domain, and that the Arabidopsis PyrR gene (At3g47390) is coexpressed with riboflavin synthesis genes. These observations imply that PyrR is a pyrimidine reductase without deaminase activity. Consistent with this inference, Arabidopsis or maize (Zea mays) PyrR (At3g47390 or GRMZM2G090068) restored riboflavin prototrophy to an E. coli ribD deletant strain when coexpressed with the corresponding PyrD protein (At4g20960 or GRMZM2G320099) but not when expressed alone; the COG3236 domain was unnecessary for complementing activity. Furthermore, recombinant maize PyrR mediated NAD(P)H-dependent pyrimidine reduction in vitro. Import assays with pea (Pisum sativum) chloroplasts showed that PyrR and PyrD are taken up and proteolytically processed. Ablation of the maize PyrR gene caused early seed lethality. These data argue that PyrR is the missing plant pyrimidine reductase, that it is plastid localized, and that it is essential. The role of the COG3236 domain remains mysterious; no evidence was obtained for the possibility that it catalyzes the dephosphorylation that follows pyrimidine reduction.
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Affiliation(s)
- Ghulam Hasnain
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Océane Frelin
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Sanja Roje
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Kenneth W. Ellens
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Kashif Ali
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Jiahn-Chou Guan
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Timothy J. Garrett
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Valérie de Crécy-Lagard
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Jesse F. Gregory
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Donald R. McCarty
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Andrew D. Hanson
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
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Hasnain G, Waller JC, Alvarez S, Ravilious GE, Jez JM, Hanson AD. Mutational analysis of YgfZ, a folate-dependent protein implicated in iron/sulphur cluster metabolism. FEMS Microbiol Lett 2011; 326:168-72. [DOI: 10.1111/j.1574-6968.2011.02448.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 10/25/2011] [Accepted: 10/25/2011] [Indexed: 11/27/2022] Open
Affiliation(s)
- Ghulam Hasnain
- Plant Molecular and Cellular Biology Program; University of Florida; Gainesville; FL; USA
| | - Jeffrey C. Waller
- Plant Molecular and Cellular Biology Program; University of Florida; Gainesville; FL; USA
| | - Sophie Alvarez
- Donald Danforth Plant Science Center; St. Louis; MO; USA
| | | | - Joseph M. Jez
- Department of Biology; Washington University; St. Louis; MO; USA
| | - Andrew D. Hanson
- Plant Molecular and Cellular Biology Program; University of Florida; Gainesville; FL; USA
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Levine BF, Bethea CG, Hasnain G, Walker J, Malik RJ, Vandenberg JM. Coherent enhancement of the hot-electron mean free path by superlattice transmission resonances. Phys Rev Lett 1989; 63:899-902. [PMID: 10041214 DOI: 10.1103/physrevlett.63.899] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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