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Ferik F, Ates D, Ercisli S, Erdogan A, Orhan E, Tanyolac MB. Genome-wide association links candidate genes to fruit firmness, fruit flesh color, flowering time, and soluble solid content in apricot (Prunus armeniaca L.). Mol Biol Rep 2021; 49:5283-5291. [PMID: 34741707 DOI: 10.1007/s11033-021-06856-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Apricots originated from China, Central Asia and the Near East and arrived in Anatolia, and particularly in their second homeland of Malatya province in Turkey. Apricots are outstanding summer fruits, with their beautiful attractive color, delicious sweet taste, aroma and high vitamin and mineral content. METHODS AND RESULTS In the current study, a total of 259 apricots genotypes from different geographical origins in Turkey were used. Significant variations were detected in fruit firmness (FF), fruit flesh color (FFC), flowering time (FT), and soluble solid content (SSC). A total of 11,532 SNPs based on DArT were developed and used in the analyses of population structure and association mapping (AM). According to the STRUCTURE (v.2.2) analysis, the apricot genotypes were divided into three groups. The mixed linear model with Q and K matrixes were used to detect the associations between the SNPs and four traits. A total of 131 SNPs were associated with FF, FFC and SSC. No SNP marker was detected associated with FT. CONCLUSION The results demonstrated that AM had high potential of revealing the markers associated with economically important traits in apricot. The SNPs identified in the study can be used in future breeding programs for marker-assisted selection in apricot.
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Affiliation(s)
- Filiz Ferik
- Engineering Faculty, Department of Bioengineering, Ege University, Bornova, 35040, Izmir, Turkey
| | - Duygu Ates
- Engineering Faculty, Department of Bioengineering, Ege University, Bornova, 35040, Izmir, Turkey
| | - Sezai Ercisli
- Agriculture Faculty, Department of Horticulture, Ataturk University, Yakutiye, 25030, Erzurum, Turkey
| | - Abdullah Erdogan
- Institute for Apricot Research of Malatya, 44090, Malatya, Turkey
| | - Emine Orhan
- Agriculture Faculty, Department of Horticulture, Ataturk University, Yakutiye, 25030, Erzurum, Turkey
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Webb ME, Marquet A, Mendel RR, Rébeillé F, Smith AG. Elucidating biosynthetic pathways for vitamins and cofactors. Nat Prod Rep 2007; 24:988-1008. [PMID: 17898894 DOI: 10.1039/b703105j] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The elucidation of the pathways to the water-soluble vitamins and cofactors has provided many biochemical and chemical challenges. This is a reflection both of their complex chemical nature, and the fact that they are often made in small amounts, making detection of the enzyme activities and intermediates difficult. Here we present an orthogonal review of how these challenges have been overcome using a combination of methods, which are often ingenious. We make particular reference to some recent developments in the study of biotin, pantothenate, folate, pyridoxol, cobalamin, thiamine, riboflavin and molybdopterin biosynthesis.
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Affiliation(s)
- Michael E Webb
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
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3
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Cabezas A, Costas MJ, Pinto RM, Couto A, Cameselle JC. Identification of human and rat FAD-AMP lyase (cyclic FMN forming) as ATP-dependent dihydroxyacetone kinases. Biochem Biophys Res Commun 2005; 338:1682-9. [PMID: 16289032 DOI: 10.1016/j.bbrc.2005.10.142] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2005] [Accepted: 10/24/2005] [Indexed: 10/25/2022]
Abstract
Rat liver FAD-AMP lyase or FMN cyclase is the only known enzymatic source of the unusual flavin nucleotide riboflavin 4',5'-cyclic phosphate. To determine its molecular identity, a peptide-mass fingerprint of the purified rat enzyme was obtained. It pointed to highly related, mammalian hypothetical proteins putatively classified as dihydroxyacetone (Dha) kinases due to weaker homologies to biochemically proven Dha kinases of plants, yeasts, and bacteria. The human protein LOC26007 cDNA was used to design PCR primers. The product amplified from human brain cDNA was cloned, sequenced (GenBank Accession No. ), and found to differ from protein LOC26007 cDNA by three SNPs. Its heterologous expression yielded a protein active both as FMN cyclase and ATP-dependent Dha kinase, each activity being inhibited by the substrate(s) of the other. Cyclase and kinase activities copurified from rat liver extracts. Evidence supports that a single protein sustains both activities, probably in a single active center. Putative Dha kinases from other mammals are likely to be FMN cyclases too. Future work will profit from the availability of the structure of Citrobacter freundii Dha kinase, which contains substrate-interacting residues conserved in human Dha kinase/FMN cyclase.
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Affiliation(s)
- Alicia Cabezas
- Unidad de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Extremadura, 06080 Badajoz, Spain
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4
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Bächler C, Flükiger-Brühwiler K, Schneider P, Bähler P, Erni B. From ATP as substrate to ADP as coenzyme: functional evolution of the nucleotide binding subunit of dihydroxyacetone kinases. J Biol Chem 2005; 280:18321-5. [PMID: 15753087 DOI: 10.1074/jbc.m500279200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dihydroxyacetone kinases are a family of sequence-related enzymes that utilize either ATP or a protein of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) as a source of high energy phosphate. The PTS is a multicomponent system involved in carbohydrate uptake and control of carbon metabolism in bacteria. Phylogenetic analysis suggests that the PTS-dependent dihydroxyacetone kinases evolved from an ATP-dependent ancestor. Their nucleotide binding subunit, an eight-helix barrel of regular up-down topology, retains ADP as phosphorylation site for the double displacement of phosphate from a phospho-histidine of the PTS protein to dihydroxyacetone. ADP is bound essentially irreversibly with a t((1/2)) of 100 min. Complexation with ADP increases the thermal unfolding temperature of dihydroxyacetone L from 40 (apo-form) to 65 degrees C (holoenzyme). ADP assumes the same role as histidines, cysteines, and aspartic acids in histidine kinases and PTS proteins. This conversion of a substrate binding site into a cofactor binding site reflects a remarkable instance of parsimonious evolution.
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Affiliation(s)
- Christoph Bächler
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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5
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Garcia-Alles LF, Siebold C, Nyffeler TL, Flükiger-Brühwiler K, Schneider P, Bürgi HB, Baumann U, Erni B. Phosphoenolpyruvate- and ATP-dependent dihydroxyacetone kinases: covalent substrate-binding and kinetic mechanism. Biochemistry 2004; 43:13037-45. [PMID: 15476397 DOI: 10.1021/bi048575m] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dihydroxyacetone (Dha) kinases are a sequence-conserved family of enzymes, which utilize two different phosphoryldonors, ATP in animals, plants, and some bacteria, and a multiphosphoprotein of the phosphoenolpyruvate carbohydrate phosphotransferase system (PTS) in most bacteria. Here, we compare the PTS-dependent kinase of Escherichia coli and the ATP-dependent kinase of Citrobacter freundii. They display 30% sequence identity. The binding constants of the E. coli kinase for eleven short-chain carbonyl compounds were determined by acetone precipitation of the enzyme-substrate complexes. They are 3.4 microM for Dha, 780 microM for Dha-phosphate (DhaP), 50 microM for D,L-glyceraldehyde (GA), and 90 microM for D,L-glyceraldehyde-3-phosphate. The k(cat) for Dha of the PTS-dependent kinase is 290 min(-1), and that of the ATP-dependent kinase is 1050 min(-1). The Km for Dha of both kinases is <6 microM. The X-ray structures of the enzyme-GA and the enzyme-DhaP complex show that substrates as well as products are bound in hemiaminal linkage to an active-site histidine. Quantum-mechanical calculations offer no indication for activation of the reacting hydroxyl group by the formation of the hemiaminal. However, the formation of the hemiaminal bond allows selection for short-chain carbonyl compounds and discrimination against structurally similar polyols. The Dha kinase remains fully active in the presence of 2 M glycerol, and phosphorylates trace impurities of carbonyl compounds present in glycerol.
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Affiliation(s)
- Luis F Garcia-Alles
- Department of Chemistry and Biochemistry and Laboratory for Chemical and Mineralogical Crystallography, University of Berne, CH-3012 Berne, Switzerland
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6
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Fischer M, Römisch W, Saller S, Illarionov B, Richter G, Rohdich F, Eisenreich W, Bacher A. Evolution of vitamin B2 biosynthesis: structural and functional similarity between pyrimidine deaminases of eubacterial and plant origin. J Biol Chem 2004; 279:36299-308. [PMID: 15208317 DOI: 10.1074/jbc.m404406200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Arabidopsis thaliana open reading frame At4g20960 predicts a protein whose N-terminal part is similar to the eubacterial 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate deaminase domain. A synthetic open reading frame specifying a pseudomature form of the plant enzyme directed the synthesis of a recombinant protein which was purified to apparent homogeneity and was shown by NMR spectroscopy to convert 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate into 5-amino-6-ribosylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate at a rate of 0.9 micromol mg(-1) min(-1). The substrate and product of the enzyme are both subject to spontaneous anomerization of the ribosyl side chain as shown by (13)C NMR spectroscopy. The protein contains 1 eq of Zn(2+)/subunit. The deaminase activity could be assigned to the N-terminal section of the plant protein. The deaminase domains of plants and eubacteria share a high degree of similarity, in contrast to deaminases from fungi. These data show that the riboflavin biosynthesis in plants proceeds by the same reaction steps as in eubacteria, whereas fungi use a different pathway.
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MESH Headings
- Amino Acid Sequence
- Arabidopsis/genetics
- Bacillus subtilis/metabolism
- Bacterial Proteins/chemistry
- Base Sequence
- Biochemical Phenomena
- Biochemistry
- Carrier Proteins/chemistry
- Cloning, Molecular
- DNA/metabolism
- DNA Restriction Enzymes/pharmacology
- DNA, Complementary/metabolism
- Electrophoresis, Polyacrylamide Gel
- Escherichia coli/metabolism
- Evolution, Molecular
- GTP Cyclohydrolase/chemistry
- Genetic Complementation Test
- Guanosine Triphosphate/chemistry
- Kinetics
- Magnetic Resonance Spectroscopy
- Maltose-Binding Proteins
- Models, Chemical
- Models, Genetic
- Molecular Sequence Data
- Mutation
- Nucleotide Deaminases/chemistry
- Nucleotide Deaminases/metabolism
- Oligonucleotides/chemistry
- Open Reading Frames
- Phylogeny
- Plasmids/metabolism
- Protein Structure, Tertiary
- Recombinant Proteins/chemistry
- Riboflavin/biosynthesis
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Spectrometry, Mass, Electrospray Ionization
- Spectrophotometry, Atomic
- Sugar Alcohol Dehydrogenases/chemistry
- Time Factors
- Zinc/chemistry
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Affiliation(s)
- Markus Fischer
- Lehrstuhl für Organische Chemie und Biochemie, Technische Universität München, Lichtenbergstrasse 4, Garching D-85747, Germany.
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7
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Siebold C, García-Alles LF, Erni B, Baumann U. A mechanism of covalent substrate binding in the x-ray structure of subunit K of the Escherichia coli dihydroxyacetone kinase. Proc Natl Acad Sci U S A 2003; 100:8188-92. [PMID: 12813127 PMCID: PMC166204 DOI: 10.1073/pnas.0932787100] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dihydroxyacetone (Dha) kinases are homologous proteins that use different phosphoryl donors, a multiphosphoryl protein of the phosphoenolpyruvate-dependent carbohydrate:phosphotransferase system in bacteria, ATP in animals, plants, and some bacteria. The Dha kinase of Escherichia coli consists of three subunits, DhaK and DhaL, which are colinear to the ATP-dependent Dha kinases of eukaryotes, and the multiphosphoryl protein DhaM. Here we show the crystal structure of the DhaK subunit in complex with Dha at 1.75 A resolution. DhaK is a homodimer with a fold consisting of two six-stranded mixed beta-sheets surrounded by nine alpha-helices and a beta-ribbon covering the exposed edge strand of one sheet. The core of the N-terminal domain has an alpha/beta fold common to subunits of carbohydrate transporters and transcription regulators of the phosphoenolpyruvate-dependent carbohydrate:phosphotransferase system. The core of the C-terminal domain has a fold similar to the C-terminal domain of the cell-division protein FtsZ. A molecule of Dha is covalently bound in hemiaminal linkage to the N epsilon 2 of His-230. The hemiaminal does not participate in covalent catalysis but is the chemical basis for discrimination between short-chain carbonyl compounds and polyols. Paralogs of Dha kinases occur in association with transcription regulators of the TetR/QacR and the SorC families, pointing to their biological role as sensors in signaling.
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Affiliation(s)
- Christian Siebold
- Departement für Chemie und Biochemie,
Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | | | - Bernhard Erni
- Departement für Chemie und Biochemie,
Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
- To whom correspondence may be addressed: E-mail:
or
| | - Ulrich Baumann
- Departement für Chemie und Biochemie,
Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
- To whom correspondence may be addressed: E-mail:
or
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Haase I, Mörtl S, Köhler P, Bacher A, Fischer M. Biosynthesis of riboflavin in archaea. 6,7-dimethyl-8-ribityllumazine synthase of Methanococcus jannaschii. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:1025-32. [PMID: 12603336 DOI: 10.1046/j.1432-1033.2003.03478.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Heterologous expression of the putative open reading frame MJ0303 of Methanococcus jannaschii provided a recombinant protein catalysing the formation of the riboflavin precursor, 6,7-dimethyl-8-ribityllumazine, by condensation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione and 3,4-dihydroxy-2-butanone 4-phosphate. Steady state kinetic analysis at 37 degrees C and pH 7.0 indicated a catalytic rate of 11 nmol.mg-1.min-1; Km values for 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione and 3,4-dihydroxybutanone 4-phosphate were 12.5 and 52 micro m, respectively. The enzyme sediments at an apparent velocity of about 12 S. Sedimentation equilibrium analysis indicated a molecular mass around 1 MDa but was hampered by nonideal solute behaviour. Negative-stained electron micrographs showed predominantly spherical particles with a diameter of about 150 A. The data suggest that the enzyme from M. jannaschii can form capsids with icosahedral 532 symmetry consisting of 60 subunits.
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Affiliation(s)
- Ilka Haase
- Lehrstuhl für Organische Chemie und Biochemie, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
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