101
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Mashalidis EH, Mukherjee T, Śledź P, Matak-Vinković D, Boshoff H, Abell C, Barry CE. Rv2607 from Mycobacterium tuberculosis is a pyridoxine 5'-phosphate oxidase with unusual substrate specificity. PLoS One 2011; 6:e27643. [PMID: 22110704 PMCID: PMC3215729 DOI: 10.1371/journal.pone.0027643] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 10/21/2011] [Indexed: 11/26/2022] Open
Abstract
Despite intensive effort, the majority of the annotated Mycobacterium tuberculosis genome consists of genes encoding proteins of unknown or poorly understood function. For example, there are seven conserved hypothetical proteins annotated as homologs of pyridoxine 5′-phosphate oxidase (PNPOx), an enzyme that oxidizes pyridoxine 5′-phosphate (PNP) or pyridoxamine 5′-phosphate (PMP) to form pyridoxal 5′-phosphate (PLP). We have characterized the function of Rv2607 from Mycobacterium tuberculosis H37Rv and shown that it encodes a PNPOx that oxidizes PNP to PLP. The kcat and KM for this reaction were 0.01 s−1 and 360 µM, respectively. Unlike many PNPOx enzymes, Rv2607 does not recognize PMP as a substrate.
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Affiliation(s)
- Ellene H. Mashalidis
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tathagata Mukherjee
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Paweł Śledź
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Helena Boshoff
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (CA); (CEB)
| | - Clifton E. Barry
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (CA); (CEB)
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102
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di Salvo ML, Contestabile R, Safo MK. Vitamin B6 salvage enzymes: Mechanism, structure and regulation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1597-608. [DOI: 10.1016/j.bbapap.2010.12.006] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 12/13/2010] [Indexed: 10/18/2022]
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103
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Mukherjee T, Hanes J, Tews I, Ealick SE, Begley TP. Pyridoxal phosphate: biosynthesis and catabolism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1585-96. [PMID: 21767669 DOI: 10.1016/j.bbapap.2011.06.018] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 06/26/2011] [Accepted: 06/29/2011] [Indexed: 11/19/2022]
Abstract
Vitamin B(6) is an essential cofactor that participates in a large number of biochemical reactions. Pyridoxal phosphate is biosynthesized de novo by two different pathways (the DXP dependent pathway and the R5P pathway) and can also be salvaged from the environment. It is one of the few cofactors whose catabolic pathway has been comprehensively characterized. It is also known to function as a singlet oxygen scavenger and has protective effects against oxidative stress in fungi. Enzymes utilizing vitamin B(6) are important targets for therapeutic agents. This review provides a concise overview of the mechanistic enzymology of vitamin B(6) biosynthesis and catabolism. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.
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Affiliation(s)
- Tathagata Mukherjee
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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104
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Herrero S, González E, Gillikin JW, Vélëz H, Daub ME. Identification and characterization of a pyridoxal reductase involved in the vitamin B6 salvage pathway in Arabidopsis. PLANT MOLECULAR BIOLOGY 2011; 76:157-69. [PMID: 21533842 DOI: 10.1007/s11103-011-9777-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 04/08/2011] [Indexed: 05/22/2023]
Abstract
Vitamin B6 (pyridoxal phosphate) is an essential cofactor in enzymatic reactions involved in numerous cellular processes and also plays a role in oxidative stress responses. In plants, the pathway for de novo synthesis of pyridoxal phosphate has been well characterized, however only two enzymes, pyridoxal (pyridoxine, pyridoxamine) kinase (SOS4) and pyridoxamine (pyridoxine) 5' phosphate oxidase (PDX3), have been identified in the salvage pathway that interconverts between the six vitamin B6 vitamers. A putative pyridoxal reductase (PLR1) was identified in Arabidopsis based on sequence homology with the protein in yeast. Cloning and expression of the AtPLR1 coding region in a yeast mutant deficient for pyridoxal reductase confirmed that the enzyme catalyzes the NADPH-mediated reduction of pyridoxal to pyridoxine. Two Arabidopsis T-DNA insertion mutant lines with insertions in the promoter sequences of AtPLR1 were established and characterized. Quantitative RT-PCR analysis of the plr1 mutants showed little change in expression of the vitamin B6 de novo pathway genes, but significant increases in expression of the known salvage pathway genes, PDX3 and SOS4. In addition, AtPLR1 was also upregulated in pdx3 and sos4 mutants. Analysis of vitamer levels by HPLC showed that both plr1 mutants had lower levels of total vitamin B6, with significantly decreased levels of pyridoxal, pyridoxal 5'-phosphate, pyridoxamine, and pyridoxamine 5'-phosphate. By contrast, there was no consistent significant change in pyridoxine and pyridoxine 5'-phosphate levels. The plr1 mutants had normal root growth, but were significantly smaller than wild type plants. When assayed for abiotic stress resistance, plr1 mutants did not differ from wild type in their response to chilling and high light, but showed greater inhibition when grown on NaCl or mannitol, suggesting a role in osmotic stress resistance. This is the first report of a pyridoxal reductase in the vitamin B6 salvage pathway in plants.
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Affiliation(s)
- Sonia Herrero
- Department of Plant Biology, North Carolina State University, Raleigh, NC 27695-7612, USA
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105
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Raschke M, Boycheva S, Crèvecoeur M, Nunes-Nesi A, Witt S, Fernie AR, Amrhein N, Fitzpatrick TB. Enhanced levels of vitamin B(6) increase aerial organ size and positively affect stress tolerance in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 66:414-32. [PMID: 21241390 DOI: 10.1111/j.1365-313x.2011.04499.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Vitamin B₆ is an essential nutrient in the human diet derived primarily from plant sources. While it is well established as a cofactor for numerous metabolic enzymes, more recently, vitamin B₆ has been implicated as a potent antioxidant. The de novo vitamin B₆ biosynthesis pathway in plants has recently been unraveled and involves only two proteins, PDX1 and PDX2. To provide more insight into the effect of the compound on plant development and its role as an antioxidant, we have overexpressed the PDX proteins in Arabidopsis, generating lines with considerably higher levels of the vitamin in comparison with other recent attempts to achieve this goal. Interestingly, it was possible to increase the level of only one of the two catalytically active PDX1 proteins at the protein level, providing insight into the mechanism of vitamin B₆ homeostasis in planta. Vitamin B₆ enhanced lines have considerably larger vegetative and floral organs and although delayed in pre-reproductive development, do not have an altered overall morphology. The vitamin was observed to accumulate in seeds and the enhancement of its levels was correlated with an increase in their size and weight. This phenotype is predominantly a consequence of embryo enlargement as reflected by larger cells. Furthermore, plants that overaccumulate the vitamin have an increased tolerance to oxidative stress providing in vivo evidence for the antioxidant functionality of vitamin B₆. In particular, the plants show an increased resistance to paraquat and photoinhibition, and they attenuate the cell death response observed in the conditional flu mutant.
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Affiliation(s)
- Maja Raschke
- ETH Zurich, Institute of Plant Sciences, 8092 Zurich, Switzerland
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106
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Ristilä M, Strid H, Eriksson LA, Strid A, Sävenstrand H. The role of the pyridoxine (vitamin B6) biosynthesis enzyme PDX1 in ultraviolet-B radiation responses in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2011; 49:284-92. [PMID: 21288732 DOI: 10.1016/j.plaphy.2011.01.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 12/15/2010] [Accepted: 01/02/2011] [Indexed: 05/08/2023]
Abstract
Ultraviolet-B radiation regulates plant growth and morphology at low and ambient fluence rates but can severely impact on plants at higher doses. Some plant UV-B responses are related to the formation of reactive oxygen species (ROS) and pyridoxine (vitamin B(6)) has been reported to be a quencher of ROS. UV-B irradiation of Arabidopsis Col-0 plants resulted in increased levels of PDX1 protein, compared with UV-A-exposed plants. This was shown by immunoblot analysis using specific polyclonal antibodies raised against the recombinant PDX1.3 protein and confirmed by mass spectrometry analysis of immunoprecipitated PDX1. The protein was located mainly in the cytosol but also to a small extent in the membrane fraction of plant leaves. Immunohistochemical analysis performed in pea revealed that PDX1 is present in UV-B-exposed leaf mesophyll and palisade parenchyma but not in epidermal cells. Pyridoxine production increased in Col-0 plants exposed to 3 days of UV-B, whereas in an Arabidopsis pdx1.3 mutant UV-B did not induce pyridoxine biosynthesis. In gene expression studies performed after UV-B exposure, the pdx1.3 mutant showed elevated transcript levels for the LHCB1*3 gene (encoding a chlorophyll a/b-binding protein of the photosystem II light-harvesting antenna complex) and the pathogenesis-related protein 5 (PR-5) gene, compared with wild type.
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Affiliation(s)
- Mikael Ristilä
- School of Science and Technology and Örebro Life Science Centre, Örebro University, Örebro, Sweden
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107
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Moccand C, Kaufmann M, Fitzpatrick TB. It takes two to tango: defining an essential second active site in pyridoxal 5'-phosphate synthase. PLoS One 2011; 6:e16042. [PMID: 21283685 PMCID: PMC3024981 DOI: 10.1371/journal.pone.0016042] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 12/09/2010] [Indexed: 11/24/2022] Open
Abstract
The prevalent de novo biosynthetic pathway of vitamin B6 involves only two enzymes (Pdx1 and Pdx2) that form an ornate multisubunit complex functioning as a glutamine amidotransferase. The synthase subunit, Pdx1, utilizes ribose 5-phosphate and glyceraldehyde 3-phosphate, as well as ammonia derived from the glutaminase activity of Pdx2 to directly form the cofactor vitamer, pyridoxal 5′-phosphate. Given the fact that a single enzyme performs the majority of the chemistry behind this reaction, a complicated mechanism is anticipated. Recently, the individual steps along the reaction co-ordinate are beginning to be unraveled. In particular, the binding of the pentose substrate and the first steps of the reaction have been elucidated but it is not known if the latter part of the chemistry, involving the triose sugar, takes place in the same or a disparate site. Here, we demonstrate through the use of enzyme assays, enzyme kinetics, and mutagenesis studies that indeed a second site is involved in binding the triose sugar and moreover, is the location of the final vitamin product, pyridoxal 5′-phosphate. Furthermore, we show that product release is triggered by the presence of a PLP-dependent enzyme. Finally, we provide evidence that a single arginine residue of the C terminus of Pdx1 is responsible for coordinating co-operativity in this elaborate protein machinery.
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Affiliation(s)
- Cyril Moccand
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Markus Kaufmann
- Bio-Molecular Analysis Platform, University of Geneva, Geneva, Switzerland
| | - Teresa B. Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- * E-mail:
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108
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Structural insights into the catalytic mechanism of the yeast pyridoxal 5-phosphate synthase Snz1. Biochem J 2011; 432:445-50. [PMID: 20919991 DOI: 10.1042/bj20101241] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In most eubacteria, fungi, apicomplexa, plants and some metazoans, the active form of vitamin B6, PLP (pyridoxal 5-phosphate), is de novo synthesized from three substrates, R5P (ribose 5-phosphate), DHAP (dihydroxyacetone phosphate) and ammonia hydrolysed from glutamine by a complexed glutaminase. Of the three active sites of DXP (deoxyxylulose 5-phosphate)independent PLP synthase (Pdx1), the R5P isomerization site has been assigned, but the sites for DHAP isomerization and PLP formation remain unknown. In the present study, we present the crystal structures of yeast Pdx1/Snz1, in apo-, G3P (glyceraldehyde 3-phosphate)- and PLP-bound forms, at 2.3, 1.8 and 2.2 Å (1 Å=0.1 nm) respectively. Structural and biochemical analysis enabled us to assign the PLP-formation site, a G3P-binding site and a G3P-transfer site. We propose a putative catalytic mechanism for Pdx1/Snz1 in which R5P and DHAP are isomerized at two distinct sites and transferred along well-defined routes to a final destination for PLP synthesis.
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109
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Sang Y, Locy RD, Goertzen LR, Rashotte AM, Si Y, Kang K, Singh NK. Expression, in vivo localization and phylogenetic analysis of a pyridoxine 5'-phosphate oxidase in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2011; 49:88-95. [PMID: 21051239 DOI: 10.1016/j.plaphy.2010.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Revised: 09/29/2010] [Accepted: 10/08/2010] [Indexed: 05/30/2023]
Abstract
Pyridoxal phosphate (PLP), a vitamin B(6) vitamer, is an essential cofactor for numerous enzymes. Pyridoxine/pyridoxamine phosphate oxidase (PPOX) catalyzes the synthesis of pyridoxal phosphate from pyridoxine phosphate (PNP) and/or pyridoxamine phosphate (PMP). The At5g49970 locus in Arabidopsis thaliana encodes an AtPPOX, a PNP/PMP oxidase. The expression of the AtPPOX gene varied in different tissues of Arabidopsis examined, being up-regulated by light, heat shock, ABA, and ethylene treatments, and down-regulated by exposure to drought and NaCl. Monoclonal antibodies raised against two different domains of AtPPOX recognized different sizes of AtPPOX, suggesting that AtPPOX proteins are produced as splice variants of the AtPPOX gene in Arabidopsis. Phylogenetic analysis of AtPPOX across all domains of life demonstrated that plant AtPPOX homologs have an additional Yjef_N domain preceding the Pyridox_Oxidase domain at the C-terminal end of the protein, while AtPPOX homologs from bacteria, fungi and animals have only Pyridox_Oxidase domain. The presence of the Yjef_N domain in plant AtPPOX homologs suggests that acquisition of this domain, and its fusion with the pyridox_oxidase domain began with the endosymbiotic acquisition of the chloroplast. Bioinformatic analysis suggested that AtPPOX is localized in chloroplast, but the monoclonal antibody could not be used for subcellular localization of this protein. A GFP-AtPPOX fusion construct introduced into the Arabidopsis protoplast confirmed localization of AtPPOX into the chloroplast. An RNAi mutant of AtPPOX showed sensitivity to high light suggesting a role for PPOX in resistance to photooxidative damage, and alteration in root growth in the presence of sucrose suggests a role for PPOX in root development.
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Affiliation(s)
- Yuying Sang
- Department of Biological Sciences, 101 Rouse Life Sciences Building, Auburn University, AL 36849, USA
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110
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Rudolph J, Kim J, Copley SD. Multiple turnovers of the nicotino-enzyme PdxB require α-keto acids as cosubstrates. Biochemistry 2010; 49:9249-55. [PMID: 20831184 PMCID: PMC3295541 DOI: 10.1021/bi101291d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PdxB catalyzes the second step in the biosynthesis of pyridoxal phosphate by oxidizing 4-phospho-d-erythronate (4PE) to 2-oxo-3-hydroxy-4-phosphobutanoate (OHPB) with concomitant reduction of NAD(+) to NADH. PdxB is a nicotino-enzyme wherein the NAD(H) cofactor remains tightly bound to PdxB. It has been a mystery how PdxB performs multiple turnovers since addition of free NAD(+) does not reoxidize the enzyme-bound NADH following conversion of 4PE to OHPB. We have solved this mystery by demonstrating that a variety of physiologically available α-keto acids serve as oxidants of PdxB to sustain multiple turnovers. In a coupled assay using the next two enzymes of the biosynthetic pathway for pyridoxal phosphate (SerC and PdxA), we have found that α-ketoglutarate, oxaloacetic acid, and pyruvate are equally good substrates for PdxB (k(cat)/K(m) values ~1 × 10(4) M⁻¹s⁻¹). The kinetic parameters for the substrate 4PE include a k(cat) of 1.4 s⁻¹, a K(m) of 2.9 μM, and a k(cat)/K(m) of 6.7 × 10(6) M⁻¹s⁻¹. Additionally, we have characterized the stereochemistry of α-ketoglutarate reduction by showing that d-2-HGA, but not l-2-HGA, is a competitive inhibitor vs 4PE and a noncompetitive inhibitor vs α-ketoglutarate.
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Affiliation(s)
- Johannes Rudolph
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
| | - Juhan Kim
- Cooperative Institute for Research in Environmental Sciences. University of Colorado at Boulder, Boulder, CO, USA
| | - Shelley D. Copley
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO, USA
- Cooperative Institute for Research in Environmental Sciences. University of Colorado at Boulder, Boulder, CO, USA
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111
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Asensi-Fabado MA, Munné-Bosch S. Vitamins in plants: occurrence, biosynthesis and antioxidant function. TRENDS IN PLANT SCIENCE 2010; 15:582-92. [PMID: 20729129 DOI: 10.1016/j.tplants.2010.07.003] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 07/13/2010] [Accepted: 07/22/2010] [Indexed: 05/03/2023]
Abstract
Plant-derived vitamins are of great interest because of their impact on human health. They are essential for metabolism because of their redox chemistry and role as enzymatic cofactors, not only in animals but also in plants. Several vitamins have strong antioxidant potential, including both water-soluble (vitamins B and C) and lipid-soluble (vitamins A, E and K) compounds. Here, we review recent advances in the understanding of antioxidant roles of vitamins and present an overview of their occurrence within the plant kingdom, different organs and subcellular location; their major biosynthetic pathways, including common precursors and competitive pathways; and their antioxidant function. In particular, we discuss novel evidence for, as well as evidence against, a role of B vitamins as important antioxidants.
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Affiliation(s)
- M Amparo Asensi-Fabado
- Departament de Biologia Vegetal, Universitat de Barcelona, Facultat de Biologia, Avinguda Diagonal 645, E-08028 Barcelona, Spain
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112
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Fitzpatrick TB, Moccand C, Roux C. Vitamin B6 biosynthesis: charting the mechanistic landscape. Chembiochem 2010; 11:1185-93. [PMID: 20397182 DOI: 10.1002/cbic.201000084] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, Sciences III, 30 Quai Ernest Ansermet, 1211 Geneva 4, Switzerland.
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113
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Dick T, Manjunatha U, Kappes B, Gengenbacher M. Vitamin B6 biosynthesis is essential for survival and virulence of Mycobacterium tuberculosis. Mol Microbiol 2010; 78:980-8. [PMID: 20815826 DOI: 10.1111/j.1365-2958.2010.07381.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
With 500000 cases of multidrug-resistant tuberculosis there is an urgent need for attractive targets to enable the discovery of novel antimycobacterials. The biosynthesis of essential cofactors is of particular interest as these pathways are absent in man and their inhibition is expected to affect the metabolism of Mycobacterium tuberculosis at multiple sites. Our data demonstrate that the pathogen synthesizes pyridoxal 5-phosphate (PLP), the bioactive form of vitamin B6, by a heteromeric PLP synthase composed of Pdx1 (Rv2606c) and Pdx2 (Rv2604c). Disruption of the pdx1 gene generated a strictly B6 auxotrophic M. tuberculosis mutant, Δpdx1. Removal of the cofactor during exponential growth or stationary phase demonstrated the essentiality of vitamin B6 biosynthesis for growth and survival of the pathogen in culture. In a tuberculosis dormancy model based on gradual oxygen depletion, de novo biosynthesis of PLP was required for regrowth of the bacillus after direct oxygen exposure. The Δpdx1 mutant showed a severe growth defect in immunocompetent mice: bacilli applied intranasally failed to persist in host tissues and were quickly cleared. We conclude that vitamin B6 biosynthesis is required for survival of M. tuberculosis in vivo and thus might represent a candidate pathway for the development of new antitubercular agents.
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Affiliation(s)
- Thomas Dick
- Novartis Institute for Tropical Diseases Pte. Ltd., 10 Biopolis Road, #05-01 Chromos, Singapore 138670, Singapore
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114
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Leuendorf JE, Osorio S, Szewczyk A, Fernie AR, Hellmann H. Complex assembly and metabolic profiling of Arabidopsis thaliana plants overexpressing vitamin B₆ biosynthesis proteins. MOLECULAR PLANT 2010; 3:890-903. [PMID: 20675613 DOI: 10.1093/mp/ssq041] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In plants, vitamin B₆ biosynthesis requires the activity of PDX1 and PDX2 proteins. Arabidopsis thaliana encodes for three PDX1 proteins, named PDX1.1, 1.2, and 1.3, but only one PDX2. Here, we show in planta complex assembly of PDX proteins, based on split-YFP and FPLC assays, and can demonstrate their presence in higher complexes of around 750 kDa. Metabolic profiling of plants ectopically expressing the different PDX proteins indicates a negative influence of PDX1.2 on vitamin B₆ biosynthesis and a correlation between aberrant vitamin B6 content, PDX1 gene expression, and light sensitivity specifically for PDX1.3. These findings provide first insights into in planta vitamin B₆ synthase complex assembly and new information on how the different PDX proteins affect plant metabolism.
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115
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Vitamin B6 is required for full motility and virulence in Helicobacter pylori. mBio 2010; 1. [PMID: 21151756 PMCID: PMC3000542 DOI: 10.1128/mbio.00112-10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 07/15/2010] [Indexed: 12/16/2022] Open
Abstract
Despite recent advances in our understanding of how Helicobacter pylori causes disease, the factors that allow this pathogen to persist in the stomach have not yet been fully characterized. To identify new virulence factors in H. pylori, we generated low-infectivity variants of a mouse-colonizing H. pylori strain using the classical technique of in vitro attenuation. The resulting variants and their highly infectious progenitor bacteria were then analyzed by global gene expression profiling. The gene expression levels of five open reading frames (ORFs) were significantly reduced in low-infectivity variants, with the most significant changes observed for ORFs HP1583 and HP1582. These ORFs were annotated as encoding homologs of the Escherichia coli vitamin B6 biosynthesis enzymes PdxA and PdxJ. Functional complementation studies with E. coli confirmed H. pylori PdxA and PdxJ to be bona fide homologs of vitamin B6 biosynthesis enzymes. Importantly, H. pylori PdxA was required for optimal growth in vitro and was shown to be essential for chronic colonization in mice. In addition to having a well-known metabolic role, vitamin B6 is necessary for the synthesis of glycosylated flagella and for flagellum-based motility in H. pylori. Thus, for the first time, we identify vitamin B6 biosynthesis enzymes as novel virulence factors in bacteria. Interestingly, pdxA and pdxJ orthologs are present in a number of human pathogens, but not in mammalian cells. We therefore propose that PdxA/J enzymes may represent ideal candidates for therapeutic targets against bacterial pathogens. Approximately half of the world’s population is infected with H. pylori, yet how H. pylori bacteria establish chronic infections in human hosts remains elusive. From gene array studies, we identified two genes as representing potentially novel colonization factors for H. pylori. These genes encoded enzymes involved in the synthesis of vitamin B6, an important molecule for many metabolic reactions in living organisms. Little is currently known regarding vitamin B6 biosynthesis in human pathogens. We showed that mutant H. pylori bacteria lacking an enzyme involved in de novo vitamin B6 biosynthesis, PdxA, were unable to synthesize motility appendages (flagella) and were unable to establish chronic colonization in mice. Thus, this work identifies vitamin B6 biosynthesis enzymes as novel virulence factors for bacterial pathogens. Interestingly, a number of human pathogens, but not their mammalian hosts, possess these genes, which suggests that Pdx enzymes may represent ideal candidates for new therapeutic targets.
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116
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Abstract
Conserved hypothetical proteins, i.e. conserved proteins whose functions are still unknown,
pose a challenge not just to functional genomics but also to general biology. For many
conserved proteins, computational analysis provides only a general prediction of
biochemical function; their exact biological functions have to be established through
direct experimentation. In the few cases when this has been accomplished, the results were
remarkable, revealing the deoxyxylulose pathway and a new essential enzyme, the ITP
pyrophosphatase. Comparative genome analysis is also instrumental in illuminating
unsolved problems in biology, e.g. the mechanism of FtsZ-independent cell division in
Chlamydia, Ureaplasma and Aeropyrum or the role of uncharacterized conserved domains
in signal transduction.
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Affiliation(s)
- M Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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117
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Mooney S, Hellmann H. Vitamin B6: Killing two birds with one stone? PHYTOCHEMISTRY 2010; 71:495-501. [PMID: 20089286 DOI: 10.1016/j.phytochem.2009.12.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 12/23/2009] [Accepted: 12/30/2009] [Indexed: 05/24/2023]
Abstract
Vitamin B6 comprises a group of compounds that are involved in a surprisingly high diversity of biochemical reactions. Actually, most of these reactions are co-catalyzed by a single B6 vitamer, pyridoxal 5'-phosphate, making it a crucial and versatile co-factor in many metabolic processes in the cell. In addition, it has been demonstrated in recent years that vitamin B6 has a second important function by being an effective antioxidant. Because of these two characteristics the vitamin is an interesting compound to study in plants. This review provides a brief overview and update on such important aspects like vitamin B6-dependent enzymes and known biosynthetic pathways in plants, phenotypes of plant mutants affected in vitamin B6 biosynthesis, and the potential benefits of modifying vitamin B6 content in plants.
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Affiliation(s)
- Sutton Mooney
- Washington State University, Pullman, Abelson Hall, WA 99164, USA
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Müller IB, Hyde JE, Wrenger C. Vitamin B metabolism in Plasmodium falciparum as a source of drug targets. Trends Parasitol 2009; 26:35-43. [PMID: 19939733 DOI: 10.1016/j.pt.2009.10.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 09/25/2009] [Accepted: 10/22/2009] [Indexed: 10/20/2022]
Abstract
The malaria parasite Plasmodium falciparum depends primarily on nutrient sources from its human host. Most compounds, such as glucose, purines, amino acids, as well as cofactors and vitamins, are abundantly available in the host cell, and can be readily salvaged by the parasite. However, in some cases the parasite can also synthesize cofactors de novo in reactions that appear to be essential. Importantly, the three biosynthetic pathways that produce vitamins B(1), B(6) and B(9) are absent from the host, but are well established in P. falciparum. This review summarizes and updates the current knowledge of vitamin B de novo synthesis and salvage in P. falciparum and focuses on their potential as targets for drug intervention.
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Affiliation(s)
- Ingrid B Müller
- Department of Biochemistry, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
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120
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Bueno C, Pavez P, Salazar R, Encinas MV. Photophysics and photochemical studies of the vitamin B6 group and related derivatives. Photochem Photobiol 2009; 86:39-46. [PMID: 19930123 DOI: 10.1111/j.1751-1097.2009.00643.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: 11/27/2022]
Abstract
The photophysics and photochemical properties of vitamin B6 constituents and analogs were studied as function of pH and solvent. The pK of the phenolic oxygen and the pyridine ring nitrogen depends on the electron donor-acceptor ability of the 4-substituent, and agrees with the calculated proton affinity. For all studied compounds, the fluorescence properties showed that the phenolic oxygen is 8 units more acidic in the lowest singlet excited state than in the ground state. The pyridine N-atom is slightly more basic in the excited state. At pH of biological significance, pH 6-8, pyridoxamine and 4-pyridoxic acid are the more efficient chromophores with higher fluorescence yield and longer lifetime. Spectroscopic studies showed that the tautomeric equilibrium depends on the nature of the 4-substituent. The quenching of the singlet excited state of pyridoxamine and 4-pyridoxic acid by amino acids, free or in a peptide, and DNA bases at pH 7 was studied by time-resolved fluorescence techniques. The quenching rate constants are well correlated with the redox properties of the pyridoxinic compound and amino acids, and are related to the free energy change in the electron transfer process. Guanosine and pyrimidine bases also are efficient quenchers, involving an electron transfer reaction.
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Affiliation(s)
- Claudia Bueno
- Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
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Havaux M, Ksas B, Szewczyk A, Rumeau D, Franck F, Caffarri S, Triantaphylidès C. Vitamin B6 deficient plants display increased sensitivity to high light and photo-oxidative stress. BMC PLANT BIOLOGY 2009; 9:130. [PMID: 19903353 PMCID: PMC2777905 DOI: 10.1186/1471-2229-9-130] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 11/10/2009] [Indexed: 05/18/2023]
Abstract
BACKGROUND Vitamin B6 is a collective term for a group of six interconvertible compounds: pyridoxine, pyridoxal, pyridoxamine and their phosphorylated derivatives. Vitamin B6 plays essential roles as a cofactor in a range of biochemical reactions. In addition, vitamin B6 is able to quench reactive oxygen species in vitro, and exogenously applied vitamin B6 protects plant cells against cell death induced by singlet oxygen (1O2). These results raise the important question as to whether plants employ vitamin B6 as an antioxidant to protect themselves against reactive oxygen species. RESULTS The pdx1.3 mutation affects the vitamin B6 biosynthesis enzyme, pyridoxal synthase (PDX1), and leads to a reduction of the vitamin B6 concentration in Arabidopsis thaliana leaves. Although leaves of the pdx1.3 Arabidopsis mutant contained less chlorophyll than wild-type leaves, we found that vitamin B6 deficiency did not significantly impact photosynthetic performance or shoot and root growth. Chlorophyll loss was associated with an increase in the chlorophyll a/b ratio and a selective decrease in the abundance of several PSII antenna proteins (Lhcb1/2, Lhcb6). These changes were strongly dependent on light intensity, with high light amplifying the difference between pdx1.3 and the wild type. When leaf discs were exposed to exogenous 1O2, lipid peroxidation in pdx1.3 was increased relative to the wild type; this effect was not observed with superoxide or hydrogen peroxide. When leaf discs or whole plants were exposed to excess light energy, 1O2-mediated lipid peroxidation was enhanced in leaves of the pdx1.3 mutant relative to the wild type. High light also caused an increased level of 1O2 in vitamin B6-deficient leaves. Combining the pdx1.3 mutation with mutations affecting the level of 'classical' quenchers of 1O2 (zeaxanthin, tocopherols) resulted in a highly photosensitive phenotype. CONCLUSION This study demonstrates that vitamin B6 has a function in the in vivo antioxidant defense of plants. Thus, the antioxidant activity of vitamin B6 inferred from in vitro studies is confirmed in planta. Together with the finding that chloroplasts contain vitamin B6 compounds, the data show that vitamin B6 functions as a photoprotector that limits 1O2 accumulation in high light and prevents 1O2-mediated oxidative damage.
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Affiliation(s)
- Michel Havaux
- Commissariat à l'Energie Atomique (CEA), Institut de Biologie Environnementale et de Biotechnologie, Laboratoire d'Ecophysiologie Moléculaire des Plantes, 13108 Saint-Paul-lez-Durance, France
- Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche Biologie Végétale et Microbiologie Environnementales, 13108 Saint-Paul-lez-Durance, France
- Université Aix-Marseille, 13108 Saint-Paul-lez-Durance, France
| | - Brigitte Ksas
- Commissariat à l'Energie Atomique (CEA), Institut de Biologie Environnementale et de Biotechnologie, Laboratoire d'Ecophysiologie Moléculaire des Plantes, 13108 Saint-Paul-lez-Durance, France
- Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche Biologie Végétale et Microbiologie Environnementales, 13108 Saint-Paul-lez-Durance, France
- Université Aix-Marseille, 13108 Saint-Paul-lez-Durance, France
| | - Agnieszka Szewczyk
- Pharmaceutical Faculty of the Collegium Medicum, Jagiellonian University, Krakow, Poland
| | - Dominique Rumeau
- Commissariat à l'Energie Atomique (CEA), Institut de Biologie Environnementale et de Biotechnologie, Laboratoire d'Ecophysiologie Moléculaire des Plantes, 13108 Saint-Paul-lez-Durance, France
- Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche Biologie Végétale et Microbiologie Environnementales, 13108 Saint-Paul-lez-Durance, France
- Université Aix-Marseille, 13108 Saint-Paul-lez-Durance, France
| | - Fabrice Franck
- Laboratory of Plant Biochemistry and Photobiology, Institute of Plant Biology, University of Liège, 4000-Liège, Belgium
| | - Stefano Caffarri
- Commissariat à l'Energie Atomique (CEA), Institut de Biologie Environnementale et de Biotechnologie, Laboratoire d'Ecophysiologie Moléculaire des Plantes, 13108 Saint-Paul-lez-Durance, France
- Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche Biologie Végétale et Microbiologie Environnementales, 13108 Saint-Paul-lez-Durance, France
- Université Aix-Marseille, 13108 Saint-Paul-lez-Durance, France
| | - Christian Triantaphylidès
- Commissariat à l'Energie Atomique (CEA), Institut de Biologie Environnementale et de Biotechnologie, Laboratoire d'Ecophysiologie Moléculaire des Plantes, 13108 Saint-Paul-lez-Durance, France
- Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche Biologie Végétale et Microbiologie Environnementales, 13108 Saint-Paul-lez-Durance, France
- Université Aix-Marseille, 13108 Saint-Paul-lez-Durance, France
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Benabdellah K, Azcón-Aguilar C, Valderas A, Speziga D, Fitzpatrick TB, Ferrol N. GintPDX1 encodes a protein involved in vitamin B6 biosynthesis that is up-regulated by oxidative stress in the arbuscular mycorrhizal fungus Glomus intraradices. THE NEW PHYTOLOGIST 2009; 184:682-693. [PMID: 19674326 DOI: 10.1111/j.1469-8137.2009.02978.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Vitamin B6 is an essential metabolite that has recently been implicated in defense against cellular oxidative stress. In fungi, the de novo biosynthetic pathway of vitamin B6 involves two genes, PDX1 and PDX2. Here, we report a component of the PDX1/PDX2 vitamin B6 biosynthetic pathway in an arbuscular mycorrhizal (AM) fungus. Using rapid amplification of cDNA ends, we isolated the full-length cDNA of a PDX-like gene, GintPDX1, from Glomus intraradices. GintPDX1 expression was analysed by real-time reverse transcription-polymerase chain reaction (RT-PCR). GintPDX1 activity and function were investigated by heterologous complementation of the yeast strainDeltasnz1, which is deficient in vitamin B6 biosynthesis. Sequence data revealed that GintPDX1 is highly homologous to other identified PDX1 proteins. GintPDX1 restores prototrophy to the vitamin B6 auxotrophic yeast mutant and reverts its superoxide sensitivity. GintPDX1 is expressed throughout the fungal life cycle, with the highest transcription levels found in the intraradical fungal structures. GintPDX1 expression was induced in response to hydrogen peroxide, paraquat and copper. The results demonstrate that AM fungi possess at least one component of the machinery necessary for vitamin B6 biosynthesis. Transcriptional regulation of GintPDX1 suggests a role for vitamin B6 as an antioxidant and modulator of reactive oxygen species in G. intraradices.
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Affiliation(s)
- Karim Benabdellah
- Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, Granada 18008, Spain
| | | | - Ascensión Valderas
- Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, Granada 18008, Spain
| | - Davide Speziga
- Institute of Plant Biology, University of Zurich, 8008 Zurich, Switzerland
| | | | - Nuria Ferrol
- Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, Granada 18008, Spain
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123
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Argueso JL, Carazzolle MF, Mieczkowski PA, Duarte FM, Netto OVC, Missawa SK, Galzerani F, Costa GGL, Vidal RO, Noronha MF, Dominska M, Andrietta MGS, Andrietta SR, Cunha AF, Gomes LH, Tavares FCA, Alcarde AR, Dietrich FS, McCusker JH, Petes TD, Pereira GAG. Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production. Genome Res 2009; 19:2258-70. [PMID: 19812109 DOI: 10.1101/gr.091777.109] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Bioethanol is a biofuel produced mainly from the fermentation of carbohydrates derived from agricultural feedstocks by the yeast Saccharomyces cerevisiae. One of the most widely adopted strains is PE-2, a heterothallic diploid naturally adapted to the sugar cane fermentation process used in Brazil. Here we report the molecular genetic analysis of a PE-2 derived diploid (JAY270), and the complete genome sequence of a haploid derivative (JAY291). The JAY270 genome is highly heterozygous (approximately 2 SNPs/kb) and has several structural polymorphisms between homologous chromosomes. These chromosomal rearrangements are confined to the peripheral regions of the chromosomes, with breakpoints within repetitive DNA sequences. Despite its complex karyotype, this diploid, when sporulated, had a high frequency of viable spores. Hybrid diploids formed by outcrossing with the laboratory strain S288c also displayed good spore viability. Thus, the rearrangements that exist near the ends of chromosomes do not impair meiosis, as they do not span regions that contain essential genes. This observation is consistent with a model in which the peripheral regions of chromosomes represent plastic domains of the genome that are free to recombine ectopically and experiment with alternative structures. We also explored features of the JAY270 and JAY291 genomes that help explain their high adaptation to industrial environments, exhibiting desirable phenotypes such as high ethanol and cell mass production and high temperature and oxidative stress tolerance. The genomic manipulation of such strains could enable the creation of a new generation of industrial organisms, ideally suited for use as delivery vehicles for future bioenergy technologies.
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Affiliation(s)
- Juan Lucas Argueso
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA.
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124
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Matxain JM, Padro D, Ristilä M, Strid A, Eriksson LA. Evidence of high *OH radical quenching efficiency by vitamin B6. J Phys Chem B 2009; 113:9629-32. [PMID: 19558175 DOI: 10.1021/jp903023c] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecules acting as antioxidants capable of scavenging reactive oxygen species (ROS) are of the utmost importance in the living cell. The antioxidative properties of pyridoxine (vitamin B6) have recently been discovered. Previous theoretical calculations have shown a high reactivity of pyridoxine toward hydroxyl radicals, where the latter preferably abstract H from either carbon of the two methanol substituents (C8 or C9). In this study, we have explored the reactivity of pyridoxine toward further hydroxyl radicals, considering as the first step the H abstraction from either C8 or C9, also including addition reactions and cyclization. Many of the reactions display similar DeltaG, and hence, the quenching of hydroxyl radicals by pyridoxine may undergo different pathways leading to a mix of products. In addition, we observe that pyridoxine, under high hydroxyl radical concentrations, may scavenge up to eight radicals, supporting its observed high antioxidant activity.
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125
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Chen H, Xiong L. Enhancement of vitamin B(6) levels in seeds through metabolic engineering. PLANT BIOTECHNOLOGY JOURNAL 2009; 7:673-81. [PMID: 19656333 DOI: 10.1111/j.1467-7652.2009.00433.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
As a versatile cofactor for many enzymes catalyzing important biochemical reactions, vitamin B(6) is required for all cellular organisms. In contrast to bacteria, fungi and plants, which have the ability to synthesize vitamin B(6)de novo, animals have to take up the vitamin from their diet. Plants are the major source of vitamin B(6) for animals. The recent identification of vitamin B(6) biosynthetic enzymes PDX1 and PDX2 in plants makes it possible to regulate the biosynthesis of this important vitamin. In this study, we generated Arabidopsis plants overexpressing the PDX1 and/or PDX2 gene and used a liquid chromatography/mass spectrometry/mass spectrometry method to determine the levels of different forms of vitamin B(6) in these transgenic plants. It was found that expression of the PDX genes under control of the CaMV 35S promoter caused only a limited increase in pyridoxine contents in dry seeds but not in shoots or roots. When using the Arabidopsis seed-specific 12S promoter to drive the expression of the PDX genes, the levels of vitamin B(6) increased more than twofold in transgenic plants. Our work demonstrates that it is feasible to enhance vitamin B(6) content in seeds by metabolic engineering.
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Affiliation(s)
- Hao Chen
- Donald Danforth Plant Science Center, St Louis, MO, USA
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126
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Wallner S, Neuwirth M, Flicker K, Tews I, Macheroux P. Dissection of contributions from invariant amino acids to complex formation and catalysis in the heteromeric pyridoxal 5-phosphate synthase complex from Bacillus subtilis. Biochemistry 2009; 48:1928-35. [PMID: 19152323 DOI: 10.1021/bi801887r] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyridoxal 5-phosphate (PLP), an active form of vitamin B(6), is one of the most versatile cofactors and is involved in numerous biochemical reactions. The main pathway for de novo PLP biosynthesis leads to direct formation of PLP from a pentose and triose. This reaction is catalyzed by the heteromeric PLP synthase, consisting of the synthase subunit Pdx1 and the glutaminase subunit Pdx2. l-Glutamine hydrolysis by Pdx2 supplies ammonia to Pdx1 for incorporation into PLP. Autonomous glutaminase Pdx2 is inactive; however, interaction with Pdx1 leads to enzymatic activity. Oxyanion hole formation in the active site of Pdx2 is required for substrate binding and was suggested as the prime event of enzyme activation. Here, we dissect interactions required for complex formation from interactions required for catalytic activation of the glutaminase. The three-dimensional structural analysis suggested a number of invariant residues that regulate complex formation and enzyme activation. We have replaced several of these invariant residues by site-directed mutagenesis in an effort to understand their function. In addition to the biochemical characterization of enzyme activity, the generated protein variants were studied by isothermal calorimetry to investigate their role in complex formation. The assembled data describe a multistep activation mechanism. Residues of helix alphaN of Pdx1 are essential for formation of the Pdx1-Pdx2 complex and also stabilize the oxyanion hole. Thus, these interactions describe the encounter complex. On the other hand, residues at the N-terminal face of the (betaalpha)(8) barrel of Pdx1 contribute to interface formation and are required for the organization of the catalytic center; thus, these interactions describe the Michaelis complex. However, the main players for formation of the Michaelis complex reside on Pdx2, as replacement of residues at the N-terminal face of the (betaalpha)(8) barrel of Pdx1 leads to reduction but not complete inactivation of the glutaminase.
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Affiliation(s)
- Silvia Wallner
- Technische Universität Graz, Institut für Biochemie, Petersgasse 12/2, A-8010 Graz, Austria
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127
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Neuwirth M, Strohmeier M, Windeisen V, Wallner S, Deller S, Rippe K, Sinning I, Macheroux P, Tews I. X-ray crystal structure of Saccharomyces cerevisiae Pdx1 provides insights into the oligomeric nature of PLP synthases. FEBS Lett 2009; 583:2179-86. [PMID: 19523954 DOI: 10.1016/j.febslet.2009.06.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Revised: 06/01/2009] [Accepted: 06/04/2009] [Indexed: 10/20/2022]
Abstract
The universal enzymatic cofactor vitamin B6 can be synthesized as pyridoxal 5-phosphate (PLP) by the glutamine amidotransferase Pdx1. We show that Saccharomyces cerevisiae Pdx1 is hexameric by analytical ultracentrifugation and by crystallographic 3D structure determination. Bacterial homologues were previously reported to exist in hexamer:dodecamer equilibrium. A small sequence insertion found in yeast Pdx1 elevates the dodecamer dissociation constant when introduced into Bacillus subtilis Pdx1. Further, we demonstrate that the yeast Pdx1 C-terminus contacts an adjacent subunit, and deletion of this segment decreases enzymatic activity 3.5-fold, suggesting a role in catalysis.
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Affiliation(s)
- Martina Neuwirth
- Technische Universität Graz, Institut für Biochemie, Graz, Austria
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128
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You BJ, Lee MH, Chung KR. Gene-specific disruption in the filamentous fungus Cercospora nicotianae using a split-marker approach. Arch Microbiol 2009; 191:615-22. [PMID: 19506835 DOI: 10.1007/s00203-009-0489-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Revised: 04/22/2009] [Accepted: 05/25/2009] [Indexed: 12/24/2022]
Abstract
To determine if DNA configuration, gene locus, and flanking sequences will affect homologous recombination in the phytopathogenic fungus Cercospora nicotianae, we evaluated and compared disruption efficiency targeting four cercosporin toxin biosynthetic genes encoding a polyketide synthase (CTB1), a monooxygenase/O-methyltransferase (CTB3), a NADPH-dependent oxidoreductase (CTB5), and a FAD/FMN-dependent oxidoreductase (CTB7). Transformation of C. nicotianae using a circular plasmid resulted in low disruption frequency. The use of endonucleases or a selectable marker DNA fragment flanked by homologous sequence either at one end or at both ends in the transformation procedures, increased disruption efficiency in some but not all CTB genes. A split-marker approach, using two DNA fragments overlapping within the selectable marker, increased the frequency of targeted gene disruption and homologous integration as high as 50%, depending on the target gene and on the length of homologous DNA sequence flanking the selectable marker. The results indicate that the split-marker approach favorably decreased ectopic integration and thus, greatly facilitated targeted gene disruption in this important fungal pathogen.
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Affiliation(s)
- Bang-Jau You
- School of Chinese Medicine Resources, College of Pharmacy, China Medical University, 91 Hsueh-Shih Road, Taichung 404, Taiwan
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129
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Triantaphylidès C, Havaux M. Singlet oxygen in plants: production, detoxification and signaling. TRENDS IN PLANT SCIENCE 2009; 14:219-28. [PMID: 19303348 DOI: 10.1016/j.tplants.2009.01.008] [Citation(s) in RCA: 410] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 01/19/2009] [Accepted: 01/22/2009] [Indexed: 05/18/2023]
Abstract
Singlet oxygen ((1)O(2)) is a singular reactive oxygen species (ROS) that is produced constitutively in plant leaves in light via chlorophylls that act as photosensitizers. This (1)O(2) production is spatially resolved within thylakoid membranes and is enhanced under light stress conditions. (1)O(2) can also be produced by phytotoxins during plant-pathogen interactions. (1)O(2) is highly reactive, can be toxic to cells and can be involved in the signaling of programmed cell death or acclimation processes. Here, we summarize current knowledge on (1)O(2) management in plants and on the biological effects of this peculiar ROS. Compared with other ROS, (1)O(2) has received relatively little attention, but recent developments indicate that it has a crucial role in the responses of plants to light.
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Affiliation(s)
- Christian Triantaphylidès
- CEA, IBEB, SBVME, Laboratoire d'Ecophysiologie Moléculaire des Plantes, 13108 Saint-Paul-lez-Durance, France
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130
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Knöckel J, Jordanova R, Müller IB, Wrenger C, Groves MR. Mobility of the conserved glycine 155 is required for formation of the active plasmodial Pdx1 dodecamer. Biochim Biophys Acta Gen Subj 2009; 1790:347-50. [PMID: 19272411 DOI: 10.1016/j.bbagen.2009.02.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 02/19/2009] [Accepted: 02/23/2009] [Indexed: 11/25/2022]
Abstract
BACKGROUND Vitamin B6 synthesis requires a functional Pdx1 assembly that is dodecameric in vivo. We have previously shown that mutation of a catalytic lysine in the plasmodial Pdx1 protein results in a protein that is both inactive and hexameric in vitro. METHODS Static and dynamic light scattering, circular dichroism, co-purification and enzyme assays are used to investigate the role of a glycine conserved in all Pdx1 family members. RESULTS Static light scattering indicates that a glycine to alanine mutant is present as a hexamer in vitro. Subsequent circular dichroism experiments demonstrate that a significant change in secondary structure content is induced by this mutation. However, this mutant is still competent to bind and support Pdx2 activity. CONCLUSIONS As the mutated glycine occupies an unrestricted region of the Ramachandran plot the additional stereo-chemical restrictions imposed on alanine residues strongly support our hypothesis that significant structural rearrangement of Pdx1 is required during the transition from hexamer to dodecamer. GENERAL SIGNIFICANCE The presented results demonstrate that reduction in the mobility of this region in Pdx1 proteins is required for formation of the in vivo dodecamer, negatively affecting the activity of Pdx1, opening the possibility of allosteric Pdx1 inhibitors.
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Affiliation(s)
- Julia Knöckel
- Bernhard Nocht Institute for Tropical Medicine, Department of Biochemistry, Bernhard Nocht Strasse 74, D-20359 Hamburg, Germany
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131
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Mooney S, Leuendorf JE, Hendrickson C, Hellmann H. Vitamin B6: a long known compound of surprising complexity. Molecules 2009; 14:329-51. [PMID: 19145213 PMCID: PMC6253932 DOI: 10.3390/molecules14010329] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 01/07/2009] [Accepted: 01/09/2009] [Indexed: 12/31/2022] Open
Abstract
In recent years vitamin B6 has become a focus of research describing the compound’s critical function in cellular metabolism and stress response. For many years the sole function of vitamin B6 was considered to be that of an enzymatic cofactor. However, recently it became clear that it is also a potent antioxidant that effectively quenches reactive oxygen species and is thus of high importance for cellular well-being. In view of the recent findings, the current review takes a look back and summarizes the discovery of vitamin B6 and the elucidation of its structure and biosynthetic pathways. It provides a detailed overview on vitamin B6 both as a cofactor and a protective compound. Besides these general characteristics of the vitamin, the review also outlines the current literature on vitamin B6 derivatives and elaborates on recent findings that provide new insights into transport and catabolism of the compound and on its impact on human health.
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Affiliation(s)
- Sutton Mooney
- School of Biological Sciences, Washington State University, Pullman, WA, USA; E-mail: (S. M.), (C. H.)
| | - Jan-Erik Leuendorf
- Angewandte Genetik, Freie Universität Berlin, 14195 Berlin, Germany E-mail: (J-E. L.)
| | - Christopher Hendrickson
- School of Biological Sciences, Washington State University, Pullman, WA, USA; E-mail: (S. M.), (C. H.)
| | - Hanjo Hellmann
- School of Biological Sciences, Washington State University, Pullman, WA, USA; E-mail: (S. M.), (C. H.)
- Author to whom correspondence should be addressed; E-Mail:
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Bluhm BH, Dhillon B, Lindquist EA, Kema GH, Goodwin SB, Dunkle LD. Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae-maydis identify novel genes expressed during vegetative, infectious, and reproductive growth. BMC Genomics 2008; 9:523. [PMID: 18983654 PMCID: PMC2596140 DOI: 10.1186/1471-2164-9-523] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Accepted: 11/04/2008] [Indexed: 11/18/2022] Open
Abstract
Background The ascomycete fungus Cercospora zeae-maydis is an aggressive foliar pathogen of maize that causes substantial losses annually throughout the Western Hemisphere. Despite its impact on maize production, little is known about the regulation of pathogenesis in C. zeae-maydis at the molecular level. The objectives of this study were to generate a collection of expressed sequence tags (ESTs) from C. zeae-maydis and evaluate their expression during vegetative, infectious, and reproductive growth. Results A total of 27,551 ESTs was obtained from five cDNA libraries constructed from vegetative and sporulating cultures of C. zeae-maydis. The ESTs, grouped into 4088 clusters and 531 singlets, represented 4619 putative unique genes. Of these, 36% encoded proteins similar (E value ≤ 10-05) to characterized or annotated proteins from the NCBI non-redundant database representing diverse molecular functions and biological processes based on Gene Ontology (GO) classification. We identified numerous, previously undescribed genes with potential roles in photoreception, pathogenesis, and the regulation of development as well as Zephyr, a novel, actively transcribed transposable element. Differential expression of selected genes was demonstrated by real-time PCR, supporting their proposed roles in vegetative, infectious, and reproductive growth. Conclusion Novel genes that are potentially involved in regulating growth, development, and pathogenesis were identified in C. zeae-maydis, providing specific targets for characterization by molecular genetics and functional genomics. The EST data establish a foundation for future studies in evolutionary and comparative genomics among species of Cercospora and other groups of plant pathogenic fungi.
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Affiliation(s)
- Burton H Bluhm
- Department of Plant Pathology, University of Arkansas, Fayetteville, Arkansas 72701, USA.
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Filamentous fungi for production of food additives and processing aids. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008. [PMID: 18253709 DOI: 10.1007/10_2007_094] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Filamentous fungi are metabolically versatile organisms with a very wide distribution in nature. They exist in association with other species, e.g. as lichens or mycorrhiza, as pathogens of animals and plants or as free-living species. Many are regarded as nature's primary degraders because they secrete a wide variety of hydrolytic enzymes that degrade waste organic materials. Many species produce secondary metabolites such as polyketides or peptides and an increasing range of fungal species is exploited commercially as sources of enzymes and metabolites for food or pharmaceutical applications. The recent availability of fungal genome sequences has provided a major opportunity to explore and further exploit fungi as sources of enzymes and metabolites. In this review chapter we focus on the use of fungi in the production of food additives but take a largely pre-genomic, albeit a mainly molecular, view of the topic.
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134
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Craig JP, Bekal S, Hudson M, Domier L, Niblack T, Lambert KN. Analysis of a horizontally transferred pathway involved in vitamin B6 biosynthesis from the soybean cyst nematode Heterodera glycines. Mol Biol Evol 2008; 25:2085-98. [PMID: 18586696 DOI: 10.1093/molbev/msn141] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Heterodera glycines is an obligate plant parasite capable of biochemically and developmentally altering its host's cells in order to create a specialized feeding cell. Although the exact mechanism of feeding cell morphogenesis remains a mystery, the nematode's ability to manipulate the plant is thought to be due in part to horizontal gene transfers (HGTs). A bioinformatic screen of the nematode genome has revealed homologues of the genes SNZ and SNO, which comprise a metabolic pathway for the de novo biosynthesis of pyridoxal 5'-phosphate, the active form of vitamin B(6) (VB(6)). Analysis of the 2 genes, HgSNZ and HgSNO, show that they contain nematode-like introns, generate polyadenylated mRNAs, and map to the soybean cyst nematode genetic linkage map, indicating that they are part of the nematode genome. However, gene synteny, protein homology, and phylogenetic evidence suggest prokaryotic origin. This would represent the first case of the HGT of a complete pathway into a nematode or terrestrial animal. VB(6) acts as a cofactor in over 140 different enzymes, and recent studies point toward an important role as a potent quencher of reactive oxygen species. With H. glycines' penchant for acquiring parasitism genes through HGT along with the absence of this pathway in other land-based animals suggests a specific need for VB(6) which may involve the parasite-host interaction.
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Affiliation(s)
- James P Craig
- Department of Crop Sciences, University of Illinois, Urbana, USA
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135
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You BJ, Lee MH, Chung KR. Production of cercosporin toxin by the phytopathogenic Cercospora fungi is affected by diverse environmental signals. Can J Microbiol 2008; 54:259-69. [PMID: 18388998 DOI: 10.1139/w08-002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cercosporin is a polyketide phytotoxin produced by many phytopathogenic Cercospora spp. We investigated environmental signals that have elaborate control of cercosporin production. Light is the most critical factor for cercosporin production. Cercospora nicotianae accumulated substantial quantities of cercosporin only when grown on a particular potato dextrose agar under light but produced little cercosporin on other brands of potato dextrose agar or media with defined ingredients. In addition to light regulation, numerous factors including salts, buffers, and ions markedly affected cercosporin production. By contrast, pH had little effect on cercosporin production. Depletion or alteration of the carbon or nitrogen sources also affected cercosporin production. Production of cercosporin was elevated to varying levels by metal ions, such as cobalt, ferric, manganese, and zinc. Significant differences in cercosporin production were observed among various Cercospora species. Further, regulation of cercosporin production by phosphate buffer, ammonium, LiCl, but not metal ions appeared to occur at transcriptional levels. Expression of the genes involved in cercosporin biosynthesis and regulation decreased markedly and was closely concomitant with the amounts of cercosporin reduced as the fungus was grown on medium containing phosphate, LiCl, ammonium, or dimethyl sulfoxide. The results reveal the complexity of cercosporin production at the physiological and genetic levels. A model delineating regulatory controls of cercosporin biosynthesis is proposed and discussed.
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Affiliation(s)
- Bang-Jau You
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850, USA
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136
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Leuendorf JE, Genau A, Szewczyk A, Mooney S, Drewke C, Leistner E, Hellmann H. The Pdx1 family is structurally and functionally conserved between Arabidopsis thaliana and Ginkgo biloba. FEBS J 2008; 275:960-9. [PMID: 18298794 DOI: 10.1111/j.1742-4658.2008.06275.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Vitamin B6 is one of the most important compounds in living organisms, and its biosynthesis has only recently been understood. Because it is required for more than 100 biochemical reactions, lack of the vitamin is fatal. This is of special importance to mammals and humans, which cannot biosynthesize the vitamin and thus depend on its external uptake. Here we describe the cloning of a vitamin B6 biosynthetic gene GbPDX1 from Ginkgo biloba. The gene is expressed in seeds, leaf and trunk tissue. Using yeast 2-hybrid and pull-down assays, we show that the protein can interact with itself and with members of Arabidopsis thaliana AtPDX1 and AtPDX2 families. Furthermore, we prove the function of GbPDX1 in vitamin B6 biosynthesis by complementation of an Arabidopsis AtPDX1.3 mutant rsr4-1, at the phenotypical level and increasing vitamin B6 levels caused by ectopic GbPDX1 expression in the mutant background. Overall, this study provides a first description of Ginkgo vitamin B6 metabolism, and demonstrates a high degree of conservation between Ginkgo and Arabidopsis.
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137
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Begley TP, Chatterjee A, Hanes JW, Hazra A, Ealick SE. Cofactor biosynthesis--still yielding fascinating new biological chemistry. Curr Opin Chem Biol 2008; 12:118-25. [PMID: 18314013 DOI: 10.1016/j.cbpa.2008.02.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 02/05/2008] [Accepted: 02/06/2008] [Indexed: 11/26/2022]
Abstract
This mini review covers recent advances in the mechanistic enzymology of cofactor biosynthesis.
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Affiliation(s)
- Tadhg P Begley
- Cornell University, Department of Chemistry and Chemical Biology, 120 Baker Lab, Ithaca, NY 14853, United States.
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138
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Said ZM, Subramanian VS, Vaziri ND, Said HM. Pyridoxine uptake by colonocytes: a specific and regulated carrier-mediated process. Am J Physiol Cell Physiol 2008; 294:C1192-7. [PMID: 18353902 DOI: 10.1152/ajpcell.00015.2008] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The water-soluble vitamin B6 (pyridoxine) is important for normal cellular functions, growth, and development. The vitamin is obtained from two exogenous sources: a dietary source, which is absorbed in the small intestine, and a bacterial source, where the vitamin is synthesized in significant quantities by the normal microflora of the large intestine. Evidence exists to suggest the bioavailability of the latter source of the vitamin, but nothing is known about the mechanism involved and its regulation. In this study, we addressed these issues using young adult mouse colonic epithelial (YAMC) cells and human colonic apical membrane vesicles (AMV) as models and using [3H]pyridoxine as the uptake substrate. The results showed the initial rate of [3H]pyridoxine uptake by YAMC cells to be 1) energy- and temperature- (but not Na-) dependent and to occur without metabolic alteration in the transported substrate; 2) saturable as a function of concentration with an apparent Km and Vmax of 2.1 +/- 0.5 muM and 53.4 +/- 4.3 pmol.mg protein(-1).3 min(-1), respectively; 3) cis-inhibited by unlabeled pyridoxine and its structural analogs, but not by the unrelated compounds theophylline, penicillamine, and isoniazid; 4) trans-stimulated by unlabeled pyridoxine; 5) amiloride sensitive; and 6) regulated by extracellular and intracellular factors. Uptake of pyridoxine by native human colonic AMV was also found to involve a carrier-mediated process. These studies demonstrate, for the first time, the functional existence of a specific and regulatable carrier-mediated process for pyridoxine uptake by mammalian colonocytes.
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Affiliation(s)
- Zainab M Said
- Department of Medicine and Physiology, University of California, Irvine, California, USA
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139
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Müller IB, Knöckel J, Groves MR, Jordanova R, Ealick SE, Walter RD, Wrenger C. The assembly of the plasmodial PLP synthase complex follows a defined course. PLoS One 2008; 3:e1815. [PMID: 18350152 PMCID: PMC2266796 DOI: 10.1371/journal.pone.0001815] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Accepted: 02/14/2008] [Indexed: 11/26/2022] Open
Abstract
Background Plants, fungi, bacteria and the apicomplexan parasite Plasmodium falciparum are able to synthesize vitamin B6 de novo, whereas mammals depend upon the uptake of this essential nutrient from their diet. The active form of vitamin B6 is pyridoxal 5-phosphate (PLP). For its synthesis two enzymes, Pdx1 and Pdx2, act together, forming a multimeric complex consisting of 12 Pdx1 and 12 Pdx2 protomers. Methodology/Principal Findings Here we report amino acid residues responsible for stabilization of the structural and enzymatic integrity of the plasmodial PLP synthase, identified by using distinct mutational analysis and biochemical approaches. Residues R85, H88 and E91 (RHE) are located at the Pdx1:Pdx1 interface and play an important role in Pdx1 complex assembly. Mutation of these residues to alanine impedes both Pdx1 activity and Pdx2 binding. Furthermore, changing D26, K83 and K151 (DKK), amino acids from the active site of Pdx1, to alanine obstructs not only enzyme activity but also formation of the complex. In contrast to the monomeric appearance of the RHE mutant, alteration of the DKK residues results in a hexameric assembly, and does not affect Pdx2 binding or its activity. While the modelled position of K151 is distal to the Pdx1:Pdx1 interface, it affects the assembly of hexameric Pdx1 into a functional dodecamer, which is crucial for PLP synthesis. Conclusions/Significance Taken together, our data suggest that the assembly of a functional Pdx1:Pdx2 complex follows a defined pathway and that inhibition of this assembly results in an inactive holoenzyme.
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Affiliation(s)
- Ingrid B. Müller
- Department of Biochemistry, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Julia Knöckel
- Department of Biochemistry, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Matthew R. Groves
- European Molecular Biology Laboratory-Hamburg Outstation, Hamburg, Germany
| | - Rositsa Jordanova
- European Molecular Biology Laboratory-Hamburg Outstation, Hamburg, Germany
| | - Steven E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States of America
| | - Rolf D. Walter
- Department of Biochemistry, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Carsten Wrenger
- Department of Biochemistry, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- * E-mail:
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140
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Hanes JW, Burns KE, Hilmey DG, Chatterjee A, Dorrestein PC, Begley TP. Mechanistic studies on pyridoxal phosphate synthase: the reaction pathway leading to a chromophoric intermediate. J Am Chem Soc 2008; 130:3043-52. [PMID: 18271580 DOI: 10.1021/ja076604l] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two routes for the de novo biosynthesis of pyridoxal-5'-phosphate (PLP) have been discovered and reconstituted in vitro. The most common pathway that organisms use is dependent upon the activity of just two enzymes, known as Pdx1 (YaaD) and Pdx2 (YaaE) in bacteria. Pdx2 has been shown to have glutaminase activity and most likely channels ammonia to the active site of the PLP synthase subunit, Pdx1, where ribose-5-phosphate (R5P), glyceraldehyde-3-phosphate (G3P), and ammonia are condensed in a complex series of reactions. In this report we investigated the early steps in the mechanism of PLP formation. Under pre-steady-state conditions, a chromophoric intermediate (I320) is observed that accumulates upon addition of only two of the substrates, R5P and glutamine. The intermediate is covalently bound to the protein. We synthesized C5 monodeuterio (pro-R, pro-S) and dideuterio R5P and showed that there is a primary kinetic isotope effect on the formation of this intermediate using the pro-R but not the pro-S labeled isomer. Furthermore, it was shown that the phosphate unit of R5P is eliminated rather than hydrolyzed in route to intermediate formation and also that there is an observed C5-deuterium kinetic isotope effect on this elimination step. Interestingly, it was observed that the formation of the intermediate could be triggered in the absence of Pdx2 by the addition of high concentrations of NH4Cl to a preincubated solution of Pdx1 and R5P. The formation of I320 was also monitored using high-resolution electrospray ionization Fourier transform mass spectrometry and revealed a species of mass 34,304 Da (Pdx1 + 95 Da). These results allow us to narrow the mechanistic possibilities for the complex series of reactions involved in PLP formation.
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Affiliation(s)
- Jeremiah W Hanes
- Department of Chemistry and Chemical Biology, 120 Baker Laboratory, Cornell University, Ithaca, New York 14853, USA
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141
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Wrenger C, Knöckel J, Walter RD, Müller IB. Vitamin B1 and B6 in the malaria parasite: requisite or dispensable? ACTA ACUST UNITED AC 2008; 41:82-8. [PMID: 18235965 DOI: 10.1590/s0100-879x2008005000006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Accepted: 12/06/2007] [Indexed: 11/21/2022]
Abstract
Vitamins are essential compounds mainly involved in acting as enzyme co-factors or in response to oxidative stress. In the last two years it became apparent that apicomplexan parasites are able to generate B vitamers such as vitamin B1 and B6 de novo. The biosynthesis pathways responsible for vitamin generation are considered as drug targets, since both provide a high degree of selectivity due to their absence in the human host. This report updates the current knowledge about vitamin B1 and B6 biosynthesis in malaria and other apicomplexan parasites. Owing to the urgent need for novel antimalarials, the significance of the biosynthesis and salvage of these vitamins is critically discussed in terms of parasite survival and their exploitation for drug development.
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Affiliation(s)
- C Wrenger
- Department of Biochemistry, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
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142
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Chen HQ, Lee MH, Chung KR. Functional characterization of three genes encoding putative oxidoreductases required for cercosporin toxin biosynthesis in the fungus Cercospora nicotianae. MICROBIOLOGY-SGM 2007; 153:2781-2790. [PMID: 17660442 DOI: 10.1099/mic.0.2007/007294-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cercosporin is a non-host-selective, photoactivated polyketide toxin produced by many phytopathogenic Cercospora species, which plays a crucial role during pathogenesis on host plants. Upon illumination, cercosporin converts oxygen molecules to toxic superoxide and singlet oxygen that damage various cellular components and induce lipid peroxidation and electrolyte leakage. Three genes (CTB5, CTB6 and CTB7) encoding putative FAD/FMN- or NADPH-dependent oxidoreductases in the cercosporin toxin biosynthetic pathway of C. nicotianae were functionally analysed. Replacement of each gene via double recombination was utilized to create null mutant strains that were completely impaired in cercosporin production as a consequence of specific interruption at the CTB5, CTB6 or CTB7 locus. Expression of CTB1, CTB5, CTB6, CTB7 and CTB8 was drastically reduced or nearly abolished when CTB5, CTB6 or CTB7 was disrupted. Production of cercosporin was revived when a functional gene cassette was introduced into the respective mutants. All ctb5, ctb6 and ctb7 null mutants retained wild-type levels of resistance against toxicity of cercosporin or singlet-oxygen-generating compounds, indicating that none of the genes plays a role in self-protection.
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Affiliation(s)
- Hui-Qin Chen
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS), University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
| | - Miin-Huey Lee
- Department of Plant Pathology, National Chung-Hsing University, Taichung 402, Taiwan
| | - Kuang-Ren Chung
- Department of Plant Pathology, Institute of Food and Agricultural Sciences (IFAS), University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS), University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
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143
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Fitzpatrick TB, Amrhein N, Kappes B, Macheroux P, Tews I, Raschle T. Two independent routes of de novo vitamin B6 biosynthesis: not that different after all. Biochem J 2007; 407:1-13. [PMID: 17822383 DOI: 10.1042/bj20070765] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Vitamin B6 is well known in its biochemically active form as pyridoxal 5'-phosphate, an essential cofactor of numerous metabolic enzymes. The vitamin is also implicated in numerous human body functions ranging from modulation of hormone function to its recent discovery as a potent antioxidant. Its de novo biosynthesis occurs only in bacteria, fungi and plants, making it an essential nutrient in the human diet. Despite its paramount importance, its biosynthesis was predominantly investigated in Escherichia coli, where it is synthesized from the condensation of deoxyxylulose 5-phosphate and 4-phosphohydroxy-L-threonine catalysed by the concerted action of PdxA and PdxJ. However, it has now become clear that the majority of organisms capable of producing this vitamin do so via a different route, involving precursors from glycolysis and the pentose phosphate pathway. This alternative pathway is characterized by the presence of two genes, Pdx1 and Pdx2. Their discovery has sparked renewed interest in vitamin B6, and numerous studies have been conducted over the last few years to characterize the new biosynthesis pathway. Indeed, enormous progress has been made in defining the nature of the enzymes involved in both pathways, and important insights have been provided into their mechanisms of action. In the present review, we summarize the recent advances in our knowledge of the biosynthesis of this versatile molecule and compare the two independent routes to the biosynthesis of vitamin B6. Surprisingly, this comparison reveals that the key biosynthetic enzymes of both pathways are, in fact, very similar both structurally and mechanistically.
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144
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González E, Danehower D, Daub ME. Vitamer levels, stress response, enzyme activity, and gene regulation of Arabidopsis lines mutant in the pyridoxine/pyridoxamine 5'-phosphate oxidase (PDX3) and the pyridoxal kinase (SOS4) genes involved in the vitamin B6 salvage pathway. PLANT PHYSIOLOGY 2007; 145:985-96. [PMID: 17873088 PMCID: PMC2048783 DOI: 10.1104/pp.107.105189] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Accepted: 09/08/2007] [Indexed: 05/17/2023]
Abstract
PDX3 and SALT OVERLY SENSITIVE4 (SOS4), encoding pyridoxine/pyridoxamine 5'-phosphate oxidase and pyridoxal kinase, respectively, are the only known genes involved in the salvage pathway of pyridoxal 5'-phosphate in plants. In this study, we determined the phenotype, stress responses, vitamer levels, and regulation of the vitamin B(6) pathway genes in Arabidopsis (Arabidopsis thaliana) plants mutant in PDX3 and SOS4. sos4 mutant plants showed a distinct phenotype characterized by chlorosis and reduced plant size, as well as hypersensitivity to sucrose in addition to the previously noted NaCl sensitivity. This mutant had higher levels of pyridoxine, pyridoxamine, and pyridoxal 5'-phosphate than the wild type, reflected in an increase in total vitamin B(6) observed through HPLC analysis and yeast bioassay. The sos4 mutant showed increased activity of PDX3 as well as of the B(6) de novo pathway enzyme PDX1, correlating with increased total B(6) levels. Two independent lines with T-DNA insertions in the promoter region of PDX3 (pdx3-1 and pdx3-2) had decreased PDX3 activity. Both also had decreased activity of PDX1, which correlated with lower levels of total vitamin B(6) observed using the yeast bioassay; however, no differences were noted in levels of individual vitamers by HPLC analysis. Both pdx3 mutants showed growth reduction in vitro and in vivo as well as an inability to increase growth under high light conditions. Increased expression of salvage and some of the de novo pathway genes was observed in both the pdx3 and sos4 mutants. In all mutants, increased expression was more dramatic for the salvage pathway genes.
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Affiliation(s)
- Eugenia González
- Department of Plant Biology, North Carolina State University, Raleigh, North Carolina 27695-7612, USA
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145
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Herrero S, Amnuaykanjanasin A, Daub ME. Identification of genes differentially expressed in the phytopathogenic fungus Cercospora nicotianae between cercosporin toxin-resistant and -susceptible strains. FEMS Microbiol Lett 2007; 275:326-37. [PMID: 17850326 DOI: 10.1111/j.1574-6968.2007.00903.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Plant pathogens from the genus Cercospora produce cercosporin, a photoactivated fungal toxin that generates toxic reactive oxygen species. Mechanisms governing toxin auto-resistance in Cercospora spp. are poorly understood. In this work, suppressive subtractive hybridization was used to identify genes differentially expressed between the cercosporin-resistant wild-type (WT) Cercospora nicotianae and a sensitive strain lacking a transcription factor (CRG1) that regulates resistance. Out of 338 sequences recovered, 185 unique expressed sequence tags (ESTs) were obtained and classified into functional categories. The majority of genes showed predicted expression differences, and 38.5% were differentially expressed at least twofold between the WT and mutant strain. ESTs were recovered with homology to genes involved in detoxification of noxious compounds, multidrug membrane transporters and antioxidant and polyketide biosynthetic enzymes as well as to ATPases and ATP synthases. The findings suggest that CRG1 regulates genes involved in pH responses in addition to those involved in toxin resistance and biosynthesis.
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Affiliation(s)
- Sonia Herrero
- Department of Plant Biology, North Carolina State University, Raleigh, NC, USA
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146
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Salzano AM, Febbraio F, Farias T, Cetrangolo GP, Nucci R, Scaloni A, Manco G. Redox stress proteins are involved in adaptation response of the hyperthermoacidophilic archaeon Sulfolobus solfataricus to nickel challenge. Microb Cell Fact 2007; 6:25. [PMID: 17692131 PMCID: PMC1995220 DOI: 10.1186/1475-2859-6-25] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Accepted: 08/12/2007] [Indexed: 11/21/2022] Open
Abstract
Background Exposure to nickel (Ni) and its chemical derivatives has been associated with severe health effects in human. On the contrary, poor knowledge has been acquired on target physiological processes or molecular mechanisms of this metal in model organisms, including Bacteria and Archaea. In this study, we describe an analysis focused at identifying proteins involved in the recovery of the archaeon Sulfolobus solfataricus strain MT4 from Ni-induced stress. Results To this purpose, Sulfolobus solfataricus was grown in the presence of the highest nickel sulphate concentration still allowing cells to survive; crude extracts from treated and untreated cells were compared at the proteome level by using a bi-dimensional chromatography approach. We identified several proteins specifically repressed or induced as result of Ni treatment. Observed up-regulated proteins were largely endowed with the ability to trigger recovery from oxidative and osmotic stress in other biological systems. It is noteworthy that most of the proteins induced following Ni treatment perform similar functions and a few have eukaryal homologue counterparts. Conclusion These findings suggest a series of preferential gene expression pathways activated in adaptation response to metal challenge.
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Affiliation(s)
- Anna M Salzano
- Laboratorio di Proteomica e Spettrometria di Massa, ISPAAM, Consiglio Nazionale delle Ricerche, 80147 Napoli, Italy
| | - Ferdinando Febbraio
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Tiziana Farias
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giovanni P Cetrangolo
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Roberto Nucci
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Andrea Scaloni
- Laboratorio di Proteomica e Spettrometria di Massa, ISPAAM, Consiglio Nazionale delle Ricerche, 80147 Napoli, Italy
| | - Giuseppe Manco
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Naples, Italy
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147
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Kleine T, Kindgren P, Benedict C, Hendrickson L, Strand A. Genome-wide gene expression analysis reveals a critical role for CRYPTOCHROME1 in the response of Arabidopsis to high irradiance. PLANT PHYSIOLOGY 2007; 144:1391-406. [PMID: 17478635 PMCID: PMC1914119 DOI: 10.1104/pp.107.098293] [Citation(s) in RCA: 175] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Exposure to high irradiance results in dramatic changes in nuclear gene expression in plants. However, little is known about the mechanisms by which changes in irradiance are sensed and how the information is transduced to the nucleus to initiate the genetic response. To investigate whether the photoreceptors are involved in the response to high irradiance, we analyzed expression of EARLY LIGHT-INDUCIBLE PROTEIN1 (ELIP1), ELIP2, ASCORBATE PEROXIDASE2 (APX2), and LIGHT-HARVESTING CHLOROPHYLL A/B-BINDING PROTEIN2.4 (LHCB2.4) in the phytochrome A (phyA), phyB, cryptochrome1 (cry1), and cry2 photoreceptor mutants and long hypocotyl5 (hy5) and HY5 homolog (hyh) transcription factor mutants. Following exposure to high intensity white light for 3 h (1,000 mumol quanta m(-2) s(-1)) expression of ELIP1/2 and APX2 was strongly induced and LHCB2.4 expression repressed in wild type. The cry1 and hy5 mutants showed specific misregulation of ELIP1/2, and we show that the induction of ELIP1/2 expression is mediated via CRY1 in a blue light intensity-dependent manner. Furthermore, using the Affymetrix Arabidopsis (Arabidopsis thaliana) 24 K Gene-Chip, we showed that 77 of the high light-responsive genes are regulated via CRY1, and 26 of those genes were also HY5 dependent. As a consequence of the misregulation of these genes, the cry1 mutant displayed a high irradiance-sensitive phenotype with significant photoinactivation of photosystem II, indicated by reduced maximal fluorescence ratio. Thus, we describe a novel function of CRY1 in mediating plant responses to high irradiances that is essential to the induction of photoprotective mechanisms. This indicates that high irradiance can be sensed in a chloroplast-independent manner by a cytosolic/nucleic component.
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Affiliation(s)
- Tatjana Kleine
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
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148
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Panagiotis M, Kritonas K, Irini NO, Kiriaki C, Nicolaos P, Athanasios T. Expression of the yeast cpd1 gene in tobacco confers resistance to the fungal toxin cercosporin. BIOMOLECULAR ENGINEERING 2007; 24:245-51. [PMID: 17317309 DOI: 10.1016/j.bioeng.2006.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Revised: 12/13/2006] [Accepted: 12/18/2006] [Indexed: 10/23/2022]
Abstract
Many phytopathogenic species of the fungus Cercospora produce cercosporin, a photoactivated perylenequinone toxin that belongs to a family of photosensitizers, which absorb light energy and produce extremely cytotoxic, reactive oxygen species. The cpd1 (cercosporin photosensitizer detoxification) gene of yeast (Saccharomyces cerevisiae), which encodes for a novel protein with significant similarity to the FAD-dependent pyridine nucleotide reductases, confers resistance to cercosporin when over-expressed in yeast. The aim of this work was to investigate the potential ability of cpd1 gene to confer resistance to cercosporin when expressed in tobacco plants (Nicotiana tabacum). Transgenic tobacco plants were produced using Agrobacterium tumefaciens, with cpd1 integrated as the gene of interest. We report here that expression of cpd1 gene in tobacco can mediate resistance to cercosporin. The involvement of cpd1 gene in the detoxification of the cercosporin reinforces previous observations, which suggested that resistance to cercosporin is mediated by a mechanism involving toxin reduction.
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Affiliation(s)
- Madesis Panagiotis
- Department of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki 54 124, Greece
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149
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Tambasco-Studart M, Tews I, Amrhein N, Fitzpatrick TB. Functional analysis of PDX2 from Arabidopsis, a glutaminase involved in vitamin B6 biosynthesis. PLANT PHYSIOLOGY 2007; 144:915-25. [PMID: 17468224 PMCID: PMC1914173 DOI: 10.1104/pp.107.096784] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Vitamin B6 is an essential metabolite in all organisms, being required as a cofactor for a wide variety of biochemical reactions. De novo biosynthesis of the vitamin occurs in microorganisms and plants, but animals must obtain it from their diet. Two distinct and mutually exclusive de novo pathways have been identified to date, namely deoxyxylulose 5-phosphate dependent, which is restricted to a subset of eubacteria, and deoxyxylulose 5-phosphate independent, present in archaea, fungi, plants, protista, and most eubacteria. In these organisms, pyridoxal 5'-phosphate (PLP) formation is catalyzed by a single glutamine amidotransferase (PLP synthase) composed of a glutaminase domain, PDX2, and a synthase domain, PDX1. Despite plants being an important source of vitamin B6, very little is known about its biosynthesis. Here, we provide information for Arabidopsis thaliana. The functionality of PDX2 is demonstrated, using both in vitro and in vivo analyses. The expression pattern of PDX2 is assessed at both the RNA and protein level, providing insight into the spatial and temporal pattern of vitamin B6 biosynthesis. We then provide a detailed biochemical analysis of the plant PLP synthase complex. While the active sites of PDX1 and PDX2 are remote from each other, coordination of catalysis is much more pronounced with the plant proteins than its bacterial counterpart, Bacillus subtilis. Based on a model of the PDX1/PDX2 complex, mutation of a single residue uncouples enzyme coordination and in turn provides tangible evidence for the existence of the recently proposed ammonia tunnel through the core of PDX1.
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Affiliation(s)
- Marina Tambasco-Studart
- Institute of Plant Sciences, Eidgenössische Technische Hochschule Zurich, 8092 Zurich, Switzerland
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150
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Matxain JM, Ristilä M, Strid A, Eriksson LA. Theoretical Study of the Reaction of Vitamin B6 with1O2. Chemistry 2007; 13:4636-42. [PMID: 17348056 DOI: 10.1002/chem.200700002] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Singlet oxygen is known to cause oxidative stress in cells, leading to severe damage (e.g., lipid peroxidation, membrane degradation, mutagenic alterations to DNA, protein misfunctionality). Recently, pyridoxine has been discovered to be capable of quenching singlet oxygen, however, the mechanism of this reaction remains essentially unknown. In this work, we have investigated four sets of reactions: 1) 1,3-addition to a double bond connected to a hydrogen-carrying group, resulting in the formation of allylic hydroperoxides; 2) [pi2+pi2] 1,2-cycloaddition to an isolated double bond, resulting in the formation of 1,2-peroxides; 3) 1,4-cycloaddition to a system containing at least two conjugated double bonds, resulting in the formation of the so-called 1,4-peroxides; 4) 1,4-addition to phenols and naphthols with the formation of hydroperoxide ketones. Thermodynamically, reaction 4 and the 6(9), 3(8), and 5(8) cases of reaction 1 are the most exergonic ones, with energies ranging from -16 to -18 kcal mol(-1). Furthermore, reaction 4 shows the lowest barrier through the reaction path, and is predicted to be the preferred mechanism for the pyridoxine + singlet-oxygen reaction, which is in agreement with previous experimental results.
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Affiliation(s)
- Jon M Matxain
- Department of Natural Sciences and Orebro Life Science Center, Orebro University, 70182 Orebro, Sweden.
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