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Šebela M, Rašková M. Polyamine-Derived Aminoaldehydes and Acrolein: Cytotoxicity, Reactivity and Analysis of the Induced Protein Modifications. Molecules 2023; 28:7429. [PMID: 37959847 PMCID: PMC10648994 DOI: 10.3390/molecules28217429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Polyamines participate in the processes of cell growth and development. The degradation branch of their metabolism involves amine oxidases. The oxidation of spermine, spermidine and putrescine releases hydrogen peroxide and the corresponding aminoaldehyde. Polyamine-derived aminoaldehydes have been found to be cytotoxic, and they represent the subject of this review. 3-aminopropanal disrupts the lysosomal membrane and triggers apoptosis or necrosis in the damaged cells. It is implicated in the pathogenesis of cerebral ischemia. Furthermore, 3-aminopropanal yields acrolein through the elimination of ammonia. This reactive aldehyde is also generated by the decomposition of aminoaldehydes produced in the reaction of serum amine oxidase with spermidine or spermine. In addition, acrolein is a common environmental pollutant. It causes covalent modifications of proteins, including carbonylation, the production of Michael-type adducts and cross-linking, and it has been associated with inflammation-related diseases. APAL and acrolein are detoxified by aldehyde dehydrogenases and other mechanisms. High-performance liquid chromatography, immunochemistry and mass spectrometry have been largely used to analyze the presence of polyamine-derived aminoaldehydes and protein modifications elicited by their effect. However, the main and still open challenge is to find clues for discovering clear linkages between aldehyde-induced modifications of specific proteins and the development of various diseases.
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Affiliation(s)
- Marek Šebela
- Department of Biochemistry, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
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2
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Fernández-Silva A, Juárez-Vázquez AL, González-Segura L, Juárez-Díaz JA, Muñoz-Clares RA. The uncharacterized Pseudomonas aeruginosa PA4189 is a novel and efficient aminoacetaldehyde dehydrogenase. Biochem J 2023; 480:259-281. [PMID: 36727473 DOI: 10.1042/bcj20220567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/03/2023]
Abstract
Neither the Pseudomonas aeruginosa aldehyde dehydrogenase encoded by the PA4189 gene nor its ortholog proteins have been biochemically or structurally characterized and their physiological function is unknown. We cloned the PA4189 gene, obtained the PA4189 recombinant protein, and studied its structure-function relationships. PA4189 is an NAD+-dependent aminoaldehyde dehydrogenase highly efficient with protonated aminoacetaldehyde and 3-aminopropionaldehyde, which are much more preferred to the non-protonated species as indicated by pH studies. Based on the higher activity with aminoacetaldehyde than with 3-aminopropionaldehyde, we propose that aminoacetaldehyde might be the PA4189 physiological substrate. Even though at the physiological pH of P. aeruginosa cells the non-protonated aminoacetaldehyde species will be predominant, and despite the competition of these species with the protonated ones, PA4189 would very efficiently oxidize ACTAL in vivo, producing glycine. To our knowledge, PA4189 is the first reported enzyme that might metabolize ACTAL, which is considered a dead-end metabolite because its consuming reactions are unknown. The PA4189 crystal structure reported here suggested that the charge and size of the active-site residue Glu457, which narrows the aldehyde-entrance tunnel, greatly define the specificity for small positively charged aldehydes, as confirmed by the kinetics of the E457G and E457Q variants. Glu457 and the residues that determine Glu457 conformation inside the active site are conserved in the PA4189 orthologs, which we only found in proteobacteria species. Also is conserved the PA4189 genomic neighborhood, which suggests that PA4189 participates in an uncharacterized metabolic pathway. Our results open the door to future efforts to characterize this pathway.
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Affiliation(s)
- Arline Fernández-Silva
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Ana L Juárez-Vázquez
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Lilian González-Segura
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Javier Andrés Juárez-Díaz
- Departamento de Biología Comparada, Facultad de Ciencias, Ciudad Universitaria, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Rosario A Muñoz-Clares
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
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3
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Glenn KC, Silvanovich A, Lee SG, Allen A, Park S, Dunn SE, Kessenich C, Meng C, Vicini JL, Jez JM. Biochemical and clinical studies of putative allergens to assess what distinguishes them from other non-allergenic proteins in the same family. Transgenic Res 2022; 31:507-524. [PMID: 35939227 PMCID: PMC9489553 DOI: 10.1007/s11248-022-00316-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 07/21/2022] [Indexed: 10/26/2022]
Abstract
Many protein families have numerous members listed in databases as allergens; however, some allergen database entries, herein called "orphan allergens", are members of large families of which all other members are not allergens. These orphan allergens provide an opportunity to assess whether specific structural features render a protein allergenic. Three orphan allergens [Cladosporium herbarum aldehyde dehydrogenase (ChALDH), Alternaria alternata ALDH (AaALDH), and C. herbarum mannitol dehydrogenase (ChMDH)] were recombinantly produced and purified for structure characterization and for clinical skin prick testing (SPT) in mold allergic participants. Examination of the X-ray crystal structures of ChALDH and ChMDH and a homology structure model of AaALDH did not identify any discernable epitopes that distinguish these putative orphan allergens from their non-allergenic protein relatives. SPT results were aligned with ChMDH being an allergen, 53% of the participants were SPT (+). AaALDH did not elicit SPT reactivity above control proteins not in allergen databases (i.e., Psedomonas syringae indole-3-acetaldehyde dehydrogenase and Zea mays ALDH). Although published results showed consequential human IgE reactivity with ChALDH, no SPT reactivity was observed in this study. With only one of these three orphan allergens, ChMDH, eliciting SPT(+) reactions consistent with the protein being included in allergen databases, this underscores the complicated nature of how bioinformatics is used to assess the potential allergenicity of food proteins that could be newly added to human diets and, when needed, the subsequent clinical testing of that bioinformatic assessment.Trial registration number and date of registration AAC-2017-0467, approved as WIRB protocol #20172536 on 07DEC2017 by WIRB-Copernicus (OHRP/FDA Registration #: IRB00000533, organization #: IORG0000432).
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Affiliation(s)
- Kevin C Glenn
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA
| | - Andre Silvanovich
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA
| | - Soon Goo Lee
- Department of Biology, Washington University, CB 1137, One Brookings Dr., St. Louis, MO, 63130, USA.,Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC, 28403, USA
| | - Aron Allen
- Department of Biology, Washington University, CB 1137, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Stephanie Park
- Allergy and Asthma Care of St. Louis, 8888 Ladue Road, Suite 105, St. Louis, MO, 63124, USA
| | - S Eliza Dunn
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA
| | - Colton Kessenich
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA
| | - Chen Meng
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA
| | - John L Vicini
- Bayer Crop Science, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA.
| | - Joseph M Jez
- Department of Biology, Washington University, CB 1137, One Brookings Dr., St. Louis, MO, 63130, USA
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CsCuAOs and CsAMADH1 Are Required for Putrescine-Derived γ-Aminobutyric Acid Accumulation in Tea. Foods 2022; 11:foods11091356. [PMID: 35564078 PMCID: PMC9100525 DOI: 10.3390/foods11091356] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/28/2022] [Accepted: 05/04/2022] [Indexed: 11/22/2022] Open
Abstract
Polyamines are a potential source of γ-aminobutyric acid (GABA) in plants under abiotic stress. However, studies on GABA enrichment in tea mostly focus on the GABA shunt, while the correlation between polyamine degradation and GABA formation in tea is largely unknown. In this study, tea plants responded to exogenous putrescine, resulting in a significant increase in GABA content, while the glutamate level did not change. At the same time, five copper-containing amine oxidase (CuAO) and eight aminoaldehyde dehydrogenase (AMADH) genes involved in the putrescine-derived GABA pathway were identified from the Tea Plant Information Archive. Expression analysis indicated that CsCuAO1, CsCuAO3 as well as CsAMADH1 were induced to play an important function in response to exogenous putrescine. Thus, the three genes were cloned and the catalytic efficiency of soluble recombinant proteins was determined. CsCuAOs and CsAMADH1 exhibited indispensable functions in the GABA production from putrescine in vitro. Subcellular localization assays indicated that CsAMADH1 was localized in plastid, while both CsCuAO1 and CsCuAO3 were localized in peroxisome. In addition, the synergistic effects of CsCuAOs and CsAMADH1 were investigated by a transient co-expression system in Nicotiana benthamiana. Our data suggest that these three genes regulate the accumulation of GABA in tea by participating in the polyamine degradation pathway and improve the content of GABA in tea to a certain extent. The results will greatly contribute to the production of GABA tea.
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Design of a Microbial Remediation Inoculation Program for Petroleum Hydrocarbon Contaminated Sites Based on Degradation Pathways. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18168794. [PMID: 34444543 PMCID: PMC8395025 DOI: 10.3390/ijerph18168794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 11/24/2022]
Abstract
This paper analyzed the degradation pathways of petroleum hydrocarbon degradation bacteria, screened the main degradation pathways, and found the petroleum hydrocarbon degradation enzymes corresponding to each step of the degradation pathway. Through the Copeland method, the best inoculation program of petroleum hydrocarbon degradation bacteria in a polluted site was selected as follows: single oxygenation path was dominated by Streptomyces avermitilis, hydroxylation path was dominated by Methylosinus trichosporium OB3b, secondary oxygenation path was dominated by Pseudomonas aeruginosa, secondary hydroxylation path was dominated by Methylococcus capsulatus, double oxygenation path was dominated by Acinetobacter baylyi ADP1, hydrolysis path was dominated by Rhodococcus erythropolis, and CoA path was dominated by Geobacter metallireducens GS-15 to repair petroleum hydrocarbon contaminated sites. The Copeland method score for this solution is 22, which is the highest among the 375 solutions designed in this paper, indicating that it has the best degradation effect. Meanwhile, we verified its effect by the Cdocker method, and the Cdocker energy of this solution is −285.811 kcal/mol, which has the highest absolute value. Among the inoculation programs of the top 13 petroleum hydrocarbon degradation bacteria, the effect of the best inoculation program of petroleum hydrocarbon degradation bacteria was 18% higher than that of the 13th group, verifying that this solution has the best overall degradation effect. The inoculation program of petroleum hydrocarbon degradation bacteria designed in this paper considered the main pathways of petroleum hydrocarbon pollutant degradation, especially highlighting the degradability of petroleum hydrocarbon intermediate degradation products, and enriching the theoretical program of microbial remediation of petroleum hydrocarbon contaminated sites.
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Tola AJ, Jaballi A, Germain H, Missihoun TD. Recent Development on Plant Aldehyde Dehydrogenase Enzymes and Their Functions in Plant Development and Stress Signaling. Genes (Basel) 2020; 12:genes12010051. [PMID: 33396326 PMCID: PMC7823795 DOI: 10.3390/genes12010051] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 12/15/2022] Open
Abstract
Abiotic and biotic stresses induce the formation of reactive oxygen species (ROS), which subsequently causes the excessive accumulation of aldehydes in cells. Stress-derived aldehydes are commonly designated as reactive electrophile species (RES) as a result of the presence of an electrophilic α, β-unsaturated carbonyl group. Aldehyde dehydrogenases (ALDHs) are NAD(P)+-dependent enzymes that metabolize a wide range of endogenous and exogenous aliphatic and aromatic aldehyde molecules by oxidizing them to their corresponding carboxylic acids. The ALDH enzymes are found in nearly all organisms, and plants contain fourteen ALDH protein families. In this review, we performed a critical analysis of the research reports over the last decade on plant ALDHs. Newly discovered roles for these enzymes in metabolism, signaling and development have been highlighted and discussed. We concluded with suggestions for future investigations to exploit the potential of these enzymes in biotechnology and to improve our current knowledge about these enzymes in gene signaling and plant development.
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7
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Lee SG, Harline K, Abar O, Akadri SO, Bastian AG, Chen HYS, Duan M, Focht CM, Groziak AR, Kao J, Kottapalli JS, Leong MC, Lin JJ, Liu R, Luo JE, Meyer CM, Mo AF, Pahng SH, Penna V, Raciti CD, Srinath A, Sudhakar S, Tang JD, Cox BR, Holland CK, Cascella B, Cruz W, McClerkin SA, Kunkel BN, Jez JM. The plant pathogen enzyme AldC is a long-chain aliphatic aldehyde dehydrogenase. J Biol Chem 2020; 295:13914-13926. [PMID: 32796031 DOI: 10.1074/jbc.ra120.014747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
Aldehyde dehydrogenases are versatile enzymes that serve a range of biochemical functions. Although traditionally considered metabolic housekeeping enzymes because of their ability to detoxify reactive aldehydes, like those generated from lipid peroxidation damage, the contributions of these enzymes to other biological processes are widespread. For example, the plant pathogen Pseudomonas syringae strain PtoDC3000 uses an indole-3-acetaldehyde dehydrogenase to synthesize the phytohormone indole-3-acetic acid to elude host responses. Here we investigate the biochemical function of AldC from PtoDC3000. Analysis of the substrate profile of AldC suggests that this enzyme functions as a long-chain aliphatic aldehyde dehydrogenase. The 2.5 Å resolution X-ray crystal of the AldC C291A mutant in a dead-end complex with octanal and NAD+ reveals an apolar binding site primed for aliphatic aldehyde substrate recognition. Functional characterization of site-directed mutants targeting the substrate- and NAD(H)-binding sites identifies key residues in the active site for ligand interactions, including those in the "aromatic box" that define the aldehyde-binding site. Overall, this study provides molecular insight for understanding the evolution of the prokaryotic aldehyde dehydrogenase superfamily and their diversity of function.
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Affiliation(s)
- Soon Goo Lee
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA; Department of Chemistry and Biochemistry, University of North Carolina-Wilmington, Wilmington, North Carolina, USA
| | - Kate Harline
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Orchid Abar
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Sakirat O Akadri
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Alexander G Bastian
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Hui-Yuan S Chen
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael Duan
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Caroline M Focht
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Amanda R Groziak
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jesse Kao
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | | | - Matthew C Leong
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Joy J Lin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Regina Liu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Joanna E Luo
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Christine M Meyer
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Albert F Mo
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Seong Ho Pahng
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Vinay Penna
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Chris D Raciti
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Abhinav Srinath
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Shwetha Sudhakar
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Joseph D Tang
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Brian R Cox
- Department of Chemistry and Biochemistry, University of North Carolina-Wilmington, Wilmington, North Carolina, USA
| | - Cynthia K Holland
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA; Department of Biology, Williams College, Williamstown, Massachusetts, USA
| | - Barrie Cascella
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Wilhelm Cruz
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Sheri A McClerkin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA; Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, USA
| | - Barbara N Kunkel
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA.
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Guo H, Wang Y, Zhang B, Li D, Chen J, Zong J, Li J, Liu J, Jiang Y. Association of candidate genes with drought tolerance traits in zoysiagrass germplasm. JOURNAL OF PLANT PHYSIOLOGY 2019; 237:61-71. [PMID: 31026777 DOI: 10.1016/j.jplph.2019.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
Drought stress negatively influences the growth and physiology of perennial grasses. The objective of this study was to identify associations of candidate genes with drought tolerance traits in 96 zoysiagrass (Zoysia Willd.) accessions. Germplasm varied largely in leaf wilting, canopy and air temperature difference (CAD), leaf water content (LWC), chlorophyll fluorescence (Fv/Fm), leaf dry weight (LDW), stolon dry weight (SDW), rhizome dry weight (RZW), and root dry weight (RDW) under drought stress across the two experiments in 2014 and 2015 in a greenhouse. The population exhibited three subgroups based on molecular marker analysis and had minimum relative kinship. Associations between single nucleotide polymorphisms (SNPs) in BADH encoding betaine aldehyde dehydrogenase, DREB1 encoding DREB-like protein 1, Ndhf encoding NADH dehydrogenase subunit F, CAT encoding catalase, and VP1 encoding H+-pyrophosphatase were analyzed with trait under drought stress (D) and relative values compared to the control (R). Twenty-seven mark and trait associations were detected in year 2014, 2015, and a two-year combination across four genes, including 13 associations in 7 SNP loci in BADH, 9 associations in 5 SNP loci in DREB1, 3 associations in one SNP locus in Ndhf, and 2 associations in one SNP locus in CAT. Of them, one SNP in BADH was associated with D-RDW or D-SDW, three SNPs in DREB1 were associated with D-RZW, D-RDW, R-LWC, and D-CAD, and one SNP in CAT was associated with D-SDW. Nucleotide changes in these SNP loci caused non-synonymous amino acid substitutions. The results indicated that allelic diversity in genes involved in antioxidant metabolism, osmotic homeostasis, and dehydration responsive transcription factor could contribute to growth and physiological variations in zoysiagrass under drought stress.
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Affiliation(s)
- Hailin Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Yi Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Bing Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Dandan Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Jingbo Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Junqing Zong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Jianjian Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA.
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Frömmel J, Končitíková R, Kopečný D, Soural M, Šebela M. Oxidation of imidazole- and pyrazole-derived aldehydes by plant aldehyde dehydrogenases from the family 2 and 10. Chem Biol Interact 2019; 304:194-201. [PMID: 30768969 DOI: 10.1016/j.cbi.2019.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/20/2018] [Accepted: 02/11/2019] [Indexed: 11/20/2022]
Abstract
Plant cytosolic aldehyde dehydrogenases from family 2 (ALDH2s, EC 1.2.1.3) are non-specific enzymes and participate for example in the metabolism of acetaldehyde or biosynthesis of phenylpropanoids. Plant aminoaldehyde dehydrogenases (AMADHs, ALDH10 family, EC 1.2.1.19) are broadly specific and play an important role in polyamine degradation or production of osmoprotectants. We have tested imidazole and pyrazole carbaldehydes and their alkyl-, allyl-, benzyl-, phenyl-, pyrimidinyl- or thienyl-derivatives as possible substrates of plant ALDH2 and ALDH10 enzymes. Imidazole represents a building block of histidine, histamine as well as certain alkaloids. It also appears in synthetic pharmaceuticals such as imidazole antifungals. Biological compounds containing pyrazole are rare (e.g. pyrazole-1-alanine and pyrazofurin antibiotics) but the ring is often found as a constituent of many synthetic drugs and pesticides. The aim was to evaluate whether aldehyde compounds based on azole heterocycles are oxidized by the enzymes, which would further support their expected role as detoxifying aldehyde scavengers. The analyzed imidazole and pyrazole carbaldehydes were only slowly converted by ALDH10s but well oxidized by cytosolic maize ALDH2 isoforms (particularly by ALDH2C1). In the latter case, the respective Km values were in the range of 10-2000 μmol l-1; the kcat values appeared mostly between 0.1 and 1.0 s-1. The carbaldehyde group at the position 4 of imidazole was oxidized faster than that at the position 2. Such a difference was not observed for pyrazole carbaldehydes. Aldehydes with an aromatic substituent on their heterocyclic ring were oxidized faster than those with an aliphatic substituent. The most efficient of the tested substrates were comparable to benzaldehyde and p-anisaldehyde known as the best aromatic aldehyde substrates of plant cytosolic ALDH2s in vitro.
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Affiliation(s)
- Jan Frömmel
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71, Olomouc, Czech Republic
| | - Radka Končitíková
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71, Olomouc, Czech Republic
| | - David Kopečný
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71, Olomouc, Czech Republic.
| | - Miroslav Soural
- Institute of Molecular and Translation Medicine, Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 5, 779 00, Olomouc, Czech Republic
| | - Marek Šebela
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71, Olomouc, Czech Republic.
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Muñoz-Clares RA, Casanova-Figueroa K. The importance of assessing aldehyde substrate inhibition for the correct determination of kinetic parameters and mechanisms: the case of the ALDH enzymes. Chem Biol Interact 2019; 305:86-97. [PMID: 30928398 DOI: 10.1016/j.cbi.2019.03.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/23/2019] [Accepted: 03/25/2019] [Indexed: 01/22/2023]
Abstract
Substrate inhibition by the aldehyde has been observed for decades in NAD(P)+-dependent aldehyde dehydrogenase (ALDH) enzymes, which follow a Bi Bi ordered steady-state kinetic mechanism. In this work, by using theoretical simulations of different possible substrate inhibition mechanisms in monosubstrate and Bi Bi ordered steady-state reactions, we explored the kind and extent of errors arising when estimating the kinetic parameters and determining the kinetic mechanisms if substrate inhibition is intentionally or unintentionally ignored. We found that, in every mechanism, fitting the initial velocity data of apparently non-inhibitory substrate concentrations to a rectangular hyperbola produces important errors, not only in the estimation of Vmax values, which were underestimated as expected, but, surprisingly, even more in the estimation of Km values, which led to overestimation of the Vmax/Km values. We show that the greater errors in Km arises from fitting data that do experience substrate inhibition, although it may not be evident, to a Michaelis-Menten equation, which causes overestimation of the data at low substrate concentrations. Similarly, we show that if substrate inhibition is not fully assessed when inhibitors are evaluated, the estimated inhibition constants will have significant errors, and the type of inhibition could be grossly mistaken. We exemplify these errors with experimental results obtained with the betaine aldehyde dehydrogenase from spinach showing the errors predicted by the theoretical simulations and that these errors are increased in the presence of NADH, which in this enzyme favors aldehyde substrate inhibition. Therefore, we strongly recommend assessing substrate inhibition by the aldehyde in every ALDH kinetic study, particularly when inhibitors are evaluated. The common practices of using an apparently non-inhibitory concentration range of the aldehyde or a single high concentration of the aldehyde or the coenzyme when varying the other to determine true kinetic parameters should be abandoned.
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Affiliation(s)
- Rosario A Muñoz-Clares
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico.
| | - Karla Casanova-Figueroa
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
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11
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Carrillo-Campos J, Riveros-Rosas H, Rodríguez-Sotres R, Muñoz-Clares RA. Bona fide choline monoxygenases evolved in Amaranthaceae plants from oxygenases of unknown function: Evidence from phylogenetics, homology modeling and docking studies. PLoS One 2018; 13:e0204711. [PMID: 30256846 PMCID: PMC6157903 DOI: 10.1371/journal.pone.0204711] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/12/2018] [Indexed: 12/25/2022] Open
Abstract
Few land plants can synthesize and accumulate the osmoprotectant glycine betaine (GB) even though this metabolic trait has major adaptive importance given the prevalence of drought, hypersaline soils or cold. GB is synthesized from choline in two reactions catalyzed by choline monooxygenases (CMOs) and enzymes of the family 10 of aldehyde dehydrogenases (ALDH10s) that gained betaine aldehyde dehydrogenase activity (BADH). Homolog genes encoding CMO and ALDH10 enzymes are present in all known land plant genomes, but since GB-non-accumulators plants lack the BADH-type ALDH10 isozyme, they would be expected to also lack the CMO activity to avoid accumulation of the toxic betaine aldehyde. To explore CMOs substrate specificity, we performed amino acid sequence alignments, phylogenetic analysis, homology modeling and docking simulations. We found that plant CMOs form a monophyletic subfamily within the Rieske/mononuclear non-heme oxygenases family with two clades: CMO1 and CMO2, the latter diverging from CMO1 after gene duplication. CMO1 enzymes are present in all plants; CMO2s only in the Amaranthaceae high-GB-accumulators plants. CMO2s, and particularly their mononuclear non-heme iron domain where the active site is located, evolved at a faster rate than CMO1s, which suggests positive selection. The homology model and docking simulations of the spinach CMO2 enzyme showed at the active site three aromatic residues forming a box with which the trimethylammonium group of choline could interact through cation-π interactions, and a glutamate, which also may interact with the trimethylammonium group through a charge-charge interaction. The aromatic box and the carboxylate have been shown to be critical for choline binding in other proteins. Interestingly, these residues are conserved in CMO2 proteins but not in CMO1 proteins, where two of these aromatic residues are leucine and the glutamate is asparagine. These findings reinforce our proposal that the CMO1s physiological substrate is not choline but a still unknown metabolite.
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Affiliation(s)
- Javier Carrillo-Campos
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Héctor Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rogelio Rodríguez-Sotres
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rosario A. Muñoz-Clares
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
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12
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Liu Y, Song Y, Zeng S, Patra B, Yuan L, Wang Y. Isolation and characterization of a salt stress-responsive betaine aldehyde dehydrogenase in Lycium ruthenicum Murr. PHYSIOLOGIA PLANTARUM 2018; 163:73-87. [PMID: 29297198 DOI: 10.1111/ppl.12669] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 10/10/2017] [Accepted: 10/14/2017] [Indexed: 05/02/2023]
Abstract
As compatible solute, glycine betaine (GB) plays a significant role in salinity tolerance in GB accumulating plants. Solanaceous crops such as tomato (Solanum lycopersicum) and tobacco (Nicotiana tabacum) are salt sensitive and naturally GB non-accumulators. In Solanaceae, only the Lycium genus has been recorded as halophytes in China, and several Lycium species have been reported as GB accumulators. The last biosynthetic step of GB is catalyzed by aminoaldehyde dehydrogenase (AMADH) with betaine aldehyde dehydrogenase (BADH) activities. Failure of GB synthesis in tomato and tobacco was attributed to lack of BADH activity. Here, by comparing the BADH functional residues of AMADHs between the Lycium genus and solanaceous crops, we predict that all studied AMADH1s have low BADH activities while only LbAMADH2 from L. barbarum has high BADH activity. For two AMADHs in L. ruthenicum, results from substrate enzyme assays confirmed low BADH activity of LrAMADH1 and no BADH activity of LrAMADH2. Despite the very low GB contents in L. ruthenicum seedlings (< 0.5 μmol g-1 fresh weight), GB contents in fruits are up to 150 μmol g-1 FW, inferring fruits of L. ruthenicum as good GB sources. In NaCl treated seedlings, accompanied by elevated GB accumulation, expression of LrAMADH1 was up-regulated, indicating response of LrAMADH1 to salt stress in L. ruthenicum. Virus-induced silence of LrAMADH1 leads to less GB accumulation than control, revealing that LrAMADH1 participates in GB synthesis in planta. Collectively, our results show that LrAMADH1 is the bona fide BADH, which responds to salt stress in L. ruthenicum.
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Affiliation(s)
- Yongliang Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- The Kentucky Tobacco Research and Development Center, Lexington, KY 40546, USA
| | - Yanli Song
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Shaohua Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Barunava Patra
- The Kentucky Tobacco Research and Development Center, Lexington, KY 40546, USA
| | - Ling Yuan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- The Kentucky Tobacco Research and Development Center, Lexington, KY 40546, USA
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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13
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Park YS, Choi UJ, Nam NH, Choi SJ, Nasir A, Lee SG, Kim KJ, Jung GY, Choi S, Shim JY, Park S, Yoo TH. Engineering an aldehyde dehydrogenase toward its substrates, 3-hydroxypropanal and NAD +, for enhancing the production of 3-hydroxypropionic acid. Sci Rep 2017; 7:17155. [PMID: 29214999 PMCID: PMC5719400 DOI: 10.1038/s41598-017-15400-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/25/2017] [Indexed: 11/09/2022] Open
Abstract
3-Hydroxypropionic acid (3-HP) can be produced via the biological route involving two enzymatic reactions: dehydration of glycerol to 3-hydroxypropanal (3-HPA) and then oxidation to 3-HP. However, commercial production of 3-HP using recombinant microorganisms has been hampered with several problems, some of which are associated with the toxicity of 3-HPA and the efficiency of NAD+ regeneration. We engineered α-ketoglutaric semialdehyde dehydrogenase (KGSADH) from Azospirillum brasilense for the second reaction to address these issues. The residues in the binding sites for the substrates, 3-HPA and NAD+, were randomized, and the resulting libraries were screened for higher activity. Isolated KGSADH variants had significantly lower Km values for both the substrates. The enzymes also showed higher substrate specificities for aldehyde and NAD+, less inhibition by NADH, and greater resistance to inactivation by 3-HPA than the wild-type enzyme. A recombinant Pseudomonas denitrificans strain with one of the engineered KGSADH variants exhibited less accumulation of 3-HPA, decreased levels of inactivation of the enzymes, and higher cell growth than that with the wild-type KGSADH. The flask culture of the P. denitrificans strain with the mutant KGSADH resulted in about 40% increase of 3-HP titer (53 mM) compared with that using the wild-type enzyme (37 mM).
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Affiliation(s)
- Ye Seop Park
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea
| | - Un Jong Choi
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea
| | - Nguyen Hoai Nam
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Sang Jin Choi
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea
| | - Abdul Nasir
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea
| | - Sun-Gu Lee
- Department of Chemical and Biomolecular Engineering, Pusan National University, Pusan, 46241, Korea
| | - Kyung Jin Kim
- School of Life Sciences, Kyungpook National University, Daegu, 41566, Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea
| | - Jeung Yeop Shim
- Bio R&D Center, Noroo Holdings Co., Ltd, Suwon, 16229, Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea.
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea.
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14
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Ruangnam S, Wanchana S, Phoka N, Saeansuk C, Mahatheeranont S, de Hoop SJ, Toojinda T, Vanavichit A, Arikit S. A deletion of the gene encoding amino aldehyde dehydrogenase enhances the "pandan-like" aroma of winter melon (Benincasa hispida) and is a functional marker for the development of the aroma. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2557-2565. [PMID: 28887587 DOI: 10.1007/s00122-017-2976-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 08/30/2017] [Indexed: 05/16/2023]
Abstract
The gene conferring a "pandan-like" aroma of winter melon was identified. The sequence variation (804-bp deletion) found in the gene was used as the target for functional marker development. Winter melon (Benincasa hispida), a member of the Cucurbitaceae family, is a commonly consumed vegetable in Asian countries that is popular for its nutritional and medicinal value. A "pandan-like" aroma, which is economically important in crops including rice and soybean, is rarely found in most commercial varieties of winter melon, but is present in some landraces. This aroma is a value-added potential trait in breeding winter melon with a higher economic value. In this study, we confirmed that the aroma of winter melon is due to the potent volatile compound 2-acetyl-1-pyrroline (2AP) as previously identified in other plants. Based on an analysis of public transcriptome data, BhAMADH encoding an aminoaldehyde dehydrogenase (AMADH) was identified as a candidate gene conferring aroma of winter melon. A sequence comparison of BhAMADH between the aromatic and non-aromatic accessions revealed an 804-bp deletion encompassing exons 11-13 in the aromatic accession. The deletion caused several premature stop codons and could result in a truncated protein with a length of only 208 amino acids compared with 503 amino acids in the normal protein. A functional marker was successfully developed based on the 804-bp deletion and validated in 237 F2 progenies. A perfect association of the marker genotypes and aroma phenotypes indicates that BhAMADH is the major gene conferring the aroma. The recently developed functional marker could be efficiently used in breeding programs for the aroma trait in winter melon.
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Affiliation(s)
- Saowalak Ruangnam
- Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
- Hortigenetics Research (S.E. Asia) Limited, Suphanburi, 72190, Thailand
| | - Samart Wanchana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand
| | - Nongnat Phoka
- King Mongkut's University of Technology Thonburi, Ratchaburi Campus, Ratchaburi, 70150, Thailand
| | - Chatree Saeansuk
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
- Interdisciplinary Graduate Program in Genetic Engineering, Kasetsart University, Bangkok, Thailand
| | - Sugunya Mahatheeranont
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Simon Jan de Hoop
- Hortigenetics Research (S.E. Asia) Limited, Suphanburi, 72190, Thailand
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand
| | - Apichart Vanavichit
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 7314, Thailand
| | - Siwaret Arikit
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 7314, Thailand.
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15
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Rousseau H, Rousseau-Gueutin M, Dauvergne X, Boutte J, Simon G, Marnet N, Bouchereau A, Guiheneuf S, Bazureau JP, Morice J, Ravanel S, Cabello-Hurtado F, Ainouche A, Salmon A, Wendel JF, Ainouche ML. Evolution of DMSP (dimethylsulfoniopropionate) biosynthesis pathway: Origin and phylogenetic distribution in polyploid Spartina (Poaceae, Chloridoideae). Mol Phylogenet Evol 2017; 114:401-414. [PMID: 28694102 DOI: 10.1016/j.ympev.2017.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/05/2017] [Accepted: 07/06/2017] [Indexed: 11/20/2022]
Abstract
DMSP (dimethylsulfoniopropionate) is an ecologically important sulfur metabolite commonly produced by marine algae and by some higher plant lineages, including the polyploid salt marsh genus Spartina (Poaceae). The molecular mechanisms and genes involved in the DMSP biosynthesis pathways are still unknown. In this study, we performed comparative analyses of DMSP amounts and molecular phylogenetic analyses to decipher the origin of DMSP in Spartina that represents one of the major source of terrestrial DMSP in coastal marshes. DMSP content was explored in 14 Spartina species using 1H Nuclear Magnetic Resonance (NMR) spectroscopy and Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS). Putative genes encoding the four enzymatic steps of the DMSP biosynthesis pathway in Spartina were examined and their evolutionary dynamics were studied. We found that the hexaploid lineage containing S. alterniflora, S. foliosa and S. maritima and their derived hybrids and allopolyploids are all able to produce DMSP, in contrast to species in the tetraploid clade. Thus, examination of DMSP synthesis in a phylogenetic context implicated a single origin of this physiological innovation, which occurred in the ancestor of the hexaploid Spartina lineage, 3-6MYA. Candidate genes specific to the Spartina DMSP biosynthesis pathway were also retrieved from Spartina transcriptomes, and provide a framework for future investigations to decipher the molecular mechanisms involved in this plant phenotypic novelty that has major ecological impacts in saltmarsh ecosystems.
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Affiliation(s)
- Hélène Rousseau
- UMR CNRS 6553 Ecobio, Université de Rennes 1, Campus de Beaulieu, 35 042 Rennes Cedex, France
| | - Mathieu Rousseau-Gueutin
- UMR IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, BP35327, F-35653 Le Rheu Cedex, France
| | - Xavier Dauvergne
- EA 2219 Géoarchitecture, Université de Bretagne Occidentale, 6 av. le Gorgeu - CS93837, 29238 Brest Cedex 3, France
| | - Julien Boutte
- UMR CNRS 6553 Ecobio, Université de Rennes 1, Campus de Beaulieu, 35 042 Rennes Cedex, France
| | - Gaëlle Simon
- Plateforme technologique de Résonance Magnétique Nucléaire, Résonance Paramagnétique Electronique et Spectrométrie de Masse, 6, av. Victor Le Gorgeu, CS93837, 29238 Brest Cedex 3, France
| | - Nathalie Marnet
- Plateau de Profilage Métabolique et Métabolomique (P2M2), Centre de Recherche Angers Nantes BIA, INRA de Rennes, F-35653 Le Rheu, France
| | - Alain Bouchereau
- UMR IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, BP35327, F-35653 Le Rheu Cedex, France
| | - Solène Guiheneuf
- UMR CNRS 6226, Groupe Ingénierie Chimique & Molécules pour le Vivant (ICMV), Sciences Chimiques de Rennes, Université de Rennes 1, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Jean-Pierre Bazureau
- UMR CNRS 6226, Groupe Ingénierie Chimique & Molécules pour le Vivant (ICMV), Sciences Chimiques de Rennes, Université de Rennes 1, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Jérôme Morice
- UMR IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, BP35327, F-35653 Le Rheu Cedex, France
| | - Stéphane Ravanel
- Laboratoire de Physiologie Cellulaire & Végétale, UMR 5168 CNRS-CEA-UMR 1417 INRA-Université Grenoble Alpes, Grenoble, France
| | | | - Abdelkader Ainouche
- UMR CNRS 6553 Ecobio, Université de Rennes 1, Campus de Beaulieu, 35 042 Rennes Cedex, France
| | - Armel Salmon
- UMR CNRS 6553 Ecobio, Université de Rennes 1, Campus de Beaulieu, 35 042 Rennes Cedex, France
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Malika L Ainouche
- UMR CNRS 6553 Ecobio, Université de Rennes 1, Campus de Beaulieu, 35 042 Rennes Cedex, France.
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16
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Cloning and molecular characterization of the betaine aldehyde dehydrogenase involved in the biosynthesis of glycine betaine in white shrimp (Litopenaeus vannamei). Chem Biol Interact 2017; 276:65-74. [PMID: 28212821 DOI: 10.1016/j.cbi.2017.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 01/09/2017] [Accepted: 02/13/2017] [Indexed: 11/21/2022]
Abstract
The enzyme betaine aldehyde dehydrogenase (BADH) catalyzes the irreversible oxidation of betaine aldehyde to glycine betaine (GB), a very efficient osmolyte accumulated during osmotic stress. In this study, we determined the nucleotide sequence of the cDNA for the BADH from the white shrimp Litopenaeus vannamei (LvBADH). The cDNA was 1882 bp long, with a complete open reading frame of 1524 bp, encoding 507 amino acids with a predicted molecular mass of 54.15 kDa and a pI of 5.4. The predicted LvBADH amino acid sequence shares a high degree of identity with marine invertebrate BADHs. Catalytic residues (C-298, E-264 and N-167) and the decapeptide VTLELGGKSP involved in nucleotide binding and highly conserved in BADHs were identified in the amino acid sequence. Phylogenetic analyses classified LvBADH in a clade that includes ALDH9 sequences from marine invertebrates. Molecular modeling of LvBADH revealed that the protein has amino acid residues and sequence motifs essential for the function of the ALDH9 family of enzymes. LvBADH modeling showed three potential monovalent cation binding sites, one site is located in an intra-subunit cavity; other in an inter-subunit cavity and a third in a central-cavity of the protein. The results show that LvBADH shares a high degree of identity with BADH sequences from marine invertebrates and enzymes that belong to the ALDH9 family. Our findings suggest that the LvBADH has molecular mechanisms of regulation similar to those of other BADHs belonging to the ALDH9 family, and that BADH might be playing a role in the osmoregulation capacity of L. vannamei.
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17
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Bhojane P, Duff MR, Bafna K, Rimmer GP, Agarwal PK, Howell EE. Aspects of Weak Interactions between Folate and Glycine Betaine. Biochemistry 2016; 55:6282-6294. [PMID: 27768285 PMCID: PMC5198541 DOI: 10.1021/acs.biochem.6b00873] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/19/2016] [Indexed: 01/22/2023]
Abstract
Folate, or vitamin B9, is an important compound in one-carbon metabolism. Previous studies have found weaker binding of dihydrofolate to dihydrofolate reductase in the presence of osmolytes. In other words, osmolytes are more difficult to remove from the dihydrofolate solvation shell than water; this shifts the equilibrium toward the free ligand and protein species. This study uses vapor-pressure osmometry to explore the interaction of folate with the model osmolyte, glycine betaine. This method yields a preferential interaction potential (μ23/RT value). This value is concentration-dependent as folate dimerizes. The μ23/RT value also tracks the deprotonation of folate's N3-O4 keto-enol group, yielding a pKa of 8.1. To determine which folate atoms interact most strongly with betaine, the interaction of heterocyclic aromatic compounds (as well as other small molecules) with betaine was monitored. Using an accessible surface area approach coupled with osmometry measurements, deconvolution of the μ23/RT values into α values for atom types was achieved. This allows prediction of μ23/RT values for larger molecules such as folate. Molecular dynamics simulations of folate show a variety of structures from extended to L-shaped. These conformers possess μ23/RT values from -0.18 to 0.09 m-1, where a negative value indicates a preference for solvation by betaine and a positive value indicates a preference for water. This range of values is consistent with values observed in osmometry and solubility experiments. As the average predicted folate μ23/RT value is near zero, this indicates folate interacts almost equally well with betaine and water. Specifically, the glutamate tail prefers to interact with water, while the aromatic rings prefer betaine. In general, the more protonated species in our small molecule survey interact better with betaine as they provide a source of hydrogens (betaine is not a hydrogen bond donor). Upon deprotonation of the small molecule, the preference swings toward water interaction because of its hydrogen bond donating capacities.
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Affiliation(s)
- Purva
P. Bhojane
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Michael R. Duff
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Khushboo Bafna
- Genome
Science and Technology Program, University
of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Gabriella P. Rimmer
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Pratul K. Agarwal
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
- Genome
Science and Technology Program, University
of Tennessee, Knoxville, Tennessee 37996-0840, United States
- Computer
Science and Mathematics Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Elizabeth E. Howell
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
- Genome
Science and Technology Program, University
of Tennessee, Knoxville, Tennessee 37996-0840, United States
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18
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Saensuk C, Wanchana S, Choowongkomon K, Wongpornchai S, Kraithong T, Imsabai W, Chaichoompu E, Ruanjaichon V, Toojinda T, Vanavichit A, Arikit S. De novo transcriptome assembly and identification of the gene conferring a "pandan-like" aroma in coconut (Cocos nucifera L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:324-334. [PMID: 27717469 DOI: 10.1016/j.plantsci.2016.08.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 08/26/2016] [Accepted: 08/27/2016] [Indexed: 06/06/2023]
Abstract
Thailand's aromatic coconut (Cocos nucifera L.) is a special type of green dwarf coconut, the liquid endosperm of which is characterized by a pleasant "pandan-like" aroma due to the presence of 2-acetyl-1-pyrroline (2AP). The aim of this study was to perform a de novo assembly of transriptome from C. nucifera endosperm and to identify the gene responsible for 2AP biosynthesis. CnAMADH2 was identified as an ortholog of the rice aromatic gene and a G-to-C substitution found in exon 14 was associated with 2AP content in the aromatic green dwarf coconut accessions. The base substitution caused an amino-acid change, alanine-to-proline, at position 442 (P442A). The presence of P at this position might alter the steric conformation at the loop region and subsequently result in an unstabilized dimer conformation that could lower AMADH enzyme activity. Among AMADH/BADH protein sequences in different plant species, the P442A mutation was found exclusively in aromatic coconut. The PCR marker developed based on this sequence variation can perfectly detect the aromatic and non-aromatic alleles of the gene. This study confirms the hypothesis that plants may share a mechanism of 2AP biosynthesis. This is the first identification of the gene associated with 2AP biosynthesis in a tree plant.
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Affiliation(s)
- Chatree Saensuk
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand; Interdisciplinary Graduate Program in Genetic Engineering, Kasetsart University, Bangkok, 10900, Thailand
| | - Samart Wanchana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Sugunya Wongpornchai
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Tippaya Kraithong
- Chumphon Horticultural Research Center, Department of Agriculture, Bangkok, 10900, Thailand
| | - Wachiraya Imsabai
- Department of Horticulture, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
| | - Ekawat Chaichoompu
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
| | - Vinitchan Ruanjaichon
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand
| | - Apichart Vanavichit
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand; Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
| | - Siwaret Arikit
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand; Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.
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Arabidopsis aldehyde dehydrogenase 10 family members confer salt tolerance through putrescine-derived 4-aminobutyrate (GABA) production. Sci Rep 2016; 6:35115. [PMID: 27725774 PMCID: PMC5057122 DOI: 10.1038/srep35115] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/26/2016] [Indexed: 11/26/2022] Open
Abstract
Polyamines represent a potential source of 4-aminobutyrate (GABA) in plants exposed to abiotic stress. Terminal catabolism of putrescine in Arabidopsis thaliana involves amine oxidase and the production of 4-aminobutanal, which is a substrate for NAD+-dependent aminoaldehyde dehydrogenase (AMADH). Here, two AMADH homologs were chosen (AtALDH10A8 and AtALDH10A9) as candidates for encoding 4-aminobutanal dehydrogenase activity for GABA synthesis. The two genes were cloned and soluble recombinant proteins were produced in Escherichia coli. The pH optima for activity and catalytic efficiency of recombinant AtALDH10A8 with 3-aminopropanal as substrate was 10.5 and 8.5, respectively, whereas the optima for AtALDH10A9 were approximately 9.5. Maximal activity and catalytic efficiency were obtained with NAD+ and 3-aminopropanal, followed by 4-aminobutanal; negligible activity was obtained with betaine aldehyde. NAD+ reduction was accompanied by the production of GABA and β-alanine, respectively, with 4-aminobutanal and 3-aminopropanal as substrates. Transient co-expression systems using Arabidopsis cell suspension protoplasts or onion epidermal cells and several organelle markers revealed that AtALDH10A9 was peroxisomal, but AtALDH10A8 was cytosolic, although the N-terminal 140 amino acid sequence of AtALDH10A8 localized to the plastid. Root growth of single loss-of-function mutants was more sensitive to salinity than wild-type plants, and this was accompanied by reduced GABA accumulation.
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20
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A betaine aldehyde dehydrogenase gene in quinoa (Chenopodium quinoa): structure, phylogeny, and expression pattern. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0445-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Reversible, partial inactivation of plant betaine aldehyde dehydrogenase by betaine aldehyde: mechanism and possible physiological implications. Biochem J 2016; 473:873-85. [DOI: 10.1042/bj20151084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/20/2016] [Indexed: 12/16/2022]
Abstract
The activity of plant BADH enzymes may be down-regulated in the short term by a novel and physiologically relevant mechanism, consisting of the reversible formation of a thiohemiacetal between a conserved non-essential cysteine residue and the substrate betaine aldehyde.
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22
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Yundaeng C, Somta P, Tangphatsornruang S, Chankaew S, Srinives P. A single base substitution in BADH/AMADH is responsible for fragrance in cucumber (Cucumis sativus L.), and development of SNAP markers for the fragrance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1881-92. [PMID: 26081947 DOI: 10.1007/s00122-015-2554-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 06/05/2015] [Indexed: 05/22/2023]
Abstract
Sequence analysis revealed that an SNP (A1855G) in CsBADH of cucumber accession PK2011T202 causes amino acid change in a highly conserved motif, Y163C. Gene mapping showed association between the SNP and the fragrance. Pandan-like fragrance is a value-added trait in several food crops such as rice, vegetable soybean and sorghum. The fragrance is caused by the volatile chemical 2-acetyl-1-pyrroline (2AP). Mutation(s) in betaine aldehyde dehydrogenase 2 (BADH2; also known as aminoaldehyde dehydrogenase 2) gene causes defective BADH2 and results in biosynthesis of 2AP. Recently, cucumber cultivars possessing pandan-like fragrance were discovered in Thailand. In this study, we report an association between CsBADH and the fragrance in cucumber accession "PK2011T202". Gene expression analysis of CsBADH in leaves of PK2011T202 and "301176" (non-fragrant) at various growth stages revealed that CsBADH was expressed in both accessions. Sequence comparison of CsBADH showed that PK2011T202 possesses a single base substitution (A1855G) in exon 5 which causes an amino acid change in a highly conserved motif of BADH, Y163C. Single nucleotide-amplified polymorphism markers were developed to detect the SNP polymorphism between the wild-type and fragrance alleles. Since CsBADH is located on chromosome 1, quantitative trait locus (QTL) mapping was conducted for this chromosome using an F2 and a backcross populations developed from the cross between PK2011T202 and 301176. QTL analysis in both populations showed that the major QTL for fragrance, qFgr, was co-localized with the CsBADH. We concluded that the defect function of CsBADH is responsible for fragrance in cucumber PK2011T202.
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Affiliation(s)
- Chutintorn Yundaeng
- Program in Plant Breeding, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand
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Zarei A, Trobacher CP, Shelp BJ. NAD(+)-aminoaldehyde dehydrogenase candidates for 4-aminobutyrate (GABA) and β-alanine production during terminal oxidation of polyamines in apple fruit. FEBS Lett 2015; 589:2695-700. [PMID: 26296314 DOI: 10.1016/j.febslet.2015.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 08/04/2015] [Accepted: 08/06/2015] [Indexed: 10/23/2022]
Abstract
The last step of polyamine catabolism involves the oxidation of 3-aminopropanal or 4-aminobutanal via aminoaldehyde dehydrogenase. In this study, two apple (Malus x domestica) AMADH genes were selected (MdAMADH1 and MdAMADH2) as candidates for encoding 4-aminobutanal dehydrogenase activity. Maximal activity and catalytic efficiency were obtained with NAD(+) and 3-aminopropanal, followed by 4-aminobutanal, at pH 9.8. NAD(+) reduction was accompanied by the production of GABA and β-alanine, respectively, when 4-aminobutanal and 3-aminopropanal were utilized as substrates. MdAMADH2 was peroxisomal and MdAMADH1 cytosolic. These findings shed light on the potential role of apple AMADHs in 4-aminobutyrate and β-alanine production.
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Affiliation(s)
- Adel Zarei
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
| | | | - Barry J Shelp
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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24
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Delgado-Gaytán MF, Hernández-Palomares MLE, Soñanez-Organis JG, Muhlia-Almazán A, Sánchez-Paz A, Stephens-Camacho NA, Valenzuela-Soto EM, Rosas-Rodríguez JA. Molecular characterization and organ-specific expression of the gene that encodes betaine aldehyde dehydrogenase from the white shrimp Litopenaeus vannamei in response to osmotic stress. Comp Biochem Physiol B Biochem Mol Biol 2015. [PMID: 26219579 DOI: 10.1016/j.cbpb.2015.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Crustaceans overcome osmotic disturbances by regulating their intracellular concentration of ions and osmolytes. Glycine betaine (GB), an osmolyte accumulated in response to hyperosmotic stress, is synthesized by betaine aldehyde dehydrogenase (BADH EC 1.2.1.8) through the oxidation of betaine aldehyde. A partial BADH cDNA sequence from the white shrimp Litopenaeus vannamei was obtained and its organ-specific expression during osmotic stress (low and high salinity) was evaluated. The partial BADH cDNA sequence (LvBADH) is 1103bp long and encodes an open reading frame for 217 protein residues. The amino acid sequence of LvBADH is related to that of other BADHs, TMABA-DH and ALDH9 from invertebrate and vertebrate homologues, and includes the essential domains of their function and regulation. LvBADH activity and mRNA expression were detected in the gills, hepatopancreas and muscle with the highest levels in the hepatopancreas. LvBADH mRNA expression increased 2-3-fold in the hepatopancreas and gills after 7days of osmotic variation (25 and 40ppt). In contrast, LvBADH mRNA expression in muscle decreased 4-fold and 15-fold after 7days at low and high salinity, respectively. The results indicate that LvBADH is ubiquitously expressed, but its levels are organ-specific and regulated by osmotic stress, and that LvBADH is involved in the cellular response of crustaceans to variations in environmental salinity.
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Affiliation(s)
- María F Delgado-Gaytán
- Centro de Investigación en Alimentación y Desarrollo AC, Apartado Postal 1735, Hermosillo 83000, Sonora, Mexico
| | - Magally L E Hernández-Palomares
- Universidad de Sonora, Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora Unidad Regional Sur, Apartado Postal 85390, Navojoa, Sonora, Mexico
| | - José G Soñanez-Organis
- Universidad de Sonora, Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora Unidad Regional Sur, Apartado Postal 85390, Navojoa, Sonora, Mexico
| | - Adriana Muhlia-Almazán
- Centro de Investigación en Alimentación y Desarrollo AC, Apartado Postal 1735, Hermosillo 83000, Sonora, Mexico
| | - Arturo Sánchez-Paz
- Centro de Investigaciones Biológicas del Noroeste S. C. (CIBNOR), Laboratorio de Referencia, Análisis y Diagnóstico en Sanidad Acuícola, Calle Hermosa 101, Col. Los Angeles, CP 83106, Hermosillo, Sonora, Mexico
| | - Norma A Stephens-Camacho
- Licenciatura en Nutrición Humana, Universidad Estatal de Sonora UAN, Periférico Sur y Carretera a Huatabampo, Navojoa, Sonora, Mexico
| | - Elisa M Valenzuela-Soto
- Centro de Investigación en Alimentación y Desarrollo AC, Apartado Postal 1735, Hermosillo 83000, Sonora, Mexico
| | - Jesús A Rosas-Rodríguez
- Universidad de Sonora, Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora Unidad Regional Sur, Apartado Postal 85390, Navojoa, Sonora, Mexico.
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25
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Muñoz-Clares RA, González-Segura L, Riveros-Rosas H, Julián-Sánchez A. Amino acid residues that affect the basicity of the catalytic glutamate of the hydrolytic aldehyde dehydrogenases. Chem Biol Interact 2015; 234:45-58. [DOI: 10.1016/j.cbi.2015.01.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/21/2014] [Accepted: 01/15/2015] [Indexed: 11/26/2022]
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26
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Functional and expression analyses of two kinds of betaine aldehyde dehydrogenases in a glycinebetaine-hyperaccumulating graminaceous halophyte, Leymus chinensis. SPRINGERPLUS 2015; 4:202. [PMID: 25992309 PMCID: PMC4431990 DOI: 10.1186/s40064-015-0997-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/23/2015] [Indexed: 01/24/2023]
Abstract
Glycinebetaine (GB) is an important compatible solute for salinity tolerance in many plants. In this study, we analyzed the enzymatic activity and the expression level of betaine aldehyde dehydrogenase (BADH), an important enzyme that catalyzes the last step in the GB synthesis in Leymus chinensis, a GB-hyperaccumulating graminaceous halophyte, and compared with those of barley, a graminaceous glycophyte. We have isolated cDNAs for two BADH genes, LcBADH1 and LcBADH2. LcBADH1 has a putative peroxisomal signal peptide (PTS1) at its C-terminus, while LcBADH2 does not have any typical signal peptide. Using immunofluorescent labeling, we showed that BADH proteins were localized to the cytosol and dot-shaped organelles in the mesophyll and bundle sheath cells of L.chinensis leaves. The affinity of recombinant LcBADH2 for betaine aldehyde was comparable to other plant BADHs, whereas recombinant LcBADH1 showed extremely low affinity for betaine aldehyde, indicating that LcBADH2 plays a major role in GB synthesis in L. chinensis. In addition, the recombinant LcBADH2 protein was tolerant to NaCl whereas LcBADH1 wasn't. The kinetics, subcellular and tissue localization of BADH proteins were comparable between L. chinensis and barley. The activity and expression level of BADH proteins were higher in L. chinensis compared with barley under both normal and salinized conditions, which may be related to the significant difference in the amount of GB accumulation between two plants.
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Halavaty AS, Rich RL, Chen C, Joo JC, Minasov G, Dubrovska I, Winsor JR, Myszka DG, Duban M, Shuvalova L, Yakunin AF, Anderson WF. Structural and functional analysis of betaine aldehyde dehydrogenase from Staphylococcus aureus. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1159-75. [PMID: 25945581 PMCID: PMC4427200 DOI: 10.1107/s1399004715004228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/01/2015] [Indexed: 02/02/2023]
Abstract
When exposed to high osmolarity, methicillin-resistant Staphylococcus aureus (MRSA) restores its growth and establishes a new steady state by accumulating the osmoprotectant metabolite betaine. Effective osmoregulation has also been implicated in the acquirement of a profound antibiotic resistance by MRSA. Betaine can be obtained from the bacterial habitat or produced intracellularly from choline via the toxic betaine aldehyde (BA) employing the choline dehydrogenase and betaine aldehyde dehydrogenase (BADH) enzymes. Here, it is shown that the putative betaine aldehyde dehydrogenase SACOL2628 from the early MRSA isolate COL (SaBADH) utilizes betaine aldehyde as the primary substrate and nicotinamide adenine dinucleotide (NAD(+)) as the cofactor. Surface plasmon resonance experiments revealed that the affinity of NAD(+), NADH and BA for SaBADH is affected by temperature, pH and buffer composition. Five crystal structures of the wild type and three structures of the Gly234Ser mutant of SaBADH in the apo and holo forms provide details of the molecular mechanisms of activity and substrate specificity/inhibition of this enzyme.
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Affiliation(s)
- Andrei S. Halavaty
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | | | - Chao Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Jeong Chan Joo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - George Minasov
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - Ievgeniia Dubrovska
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - James R. Winsor
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | | | - Mark Duban
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - Ludmilla Shuvalova
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Wayne F. Anderson
- Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
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Frömmel J, Šebela M, Demo G, Lenobel R, Pospíšil T, Soural M, Kopečný D. N-acyl-ω-aminoaldehydes are efficient substrates of plant aminoaldehyde dehydrogenases. Amino Acids 2015; 47:175-87. [PMID: 25344796 DOI: 10.1007/s00726-014-1853-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 10/07/2014] [Indexed: 11/29/2022]
Abstract
Plant aminoaldehyde dehydrogenases (AMADHs, EC 1.2.1.19) belong to the family 10 of aldehyde dehydrogenases and participate in the metabolism of compounds related to amino acids such as polyamines or osmoprotectants. Their broad specificity covers ω-aminoaldehydes, aliphatic and aromatic aldehydes as well as nitrogen-containing heterocyclic aldehydes. The substrate preference of plant AMADHs is determined by the presence of aspartic acid and aromatic residues in the substrate channel. In this work, 15 new N-acyl derivates of 3-aminopropanal (APAL) and 4-aminobutanal (ABAL) were synthesized and confirmed as substrates of two pea AMADH isoenzymes (PsAMADH 1 and 2). The compounds were designed considering the previously demonstrated conversion of N-acetyl derivatives as well as substrate channel dimensions (5-8 Å × 14 Å). The acyl chain length and its branching were found less significant for substrate properties than the length of the initial natural substrate. In general, APAL derivatives were found more efficient than the corresponding ABAL derivatives because of the prevailing higher conversion rates and lower K m values. Differences in enzymatic performance between the two isoenzymes corresponded in part to their preferences to APAL to ABAL. The higher PsAMADH2 affinity to substrates correlated with more frequent occurrence of an excess substrate inhibition. Molecular docking indicated the possible auxiliary role of Tyr163, Ser295 and Gln451 in binding of the new substrates. The only derivative carrying a free carboxyl group (N-adipoyl APAL) was surprisingly better substrate than ABAL in PsAMADH2 reaction indicating that also negatively charged aldehydes might be good substrates for ALDH10 family.
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Affiliation(s)
- Jan Frömmel
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71, Olomouc, Czech Republic
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29
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Nagy GN, Marton L, Contet A, Ozohanics O, Ardelean LM, Révész Á, Vékey K, Irimie FD, Vial H, Cerdan R, Vértessy BG. Composite Aromatic Boxes for Enzymatic Transformations of Quaternary Ammonium Substrates. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Nagy GN, Marton L, Contet A, Ozohanics O, Ardelean LM, Révész A, Vékey K, Irimie FD, Vial H, Cerdan R, Vértessy BG. Composite aromatic boxes for enzymatic transformations of quaternary ammonium substrates. Angew Chem Int Ed Engl 2014; 53:13471-6. [PMID: 25283789 DOI: 10.1002/anie.201408246] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Indexed: 11/07/2022]
Abstract
Cation-π interactions to cognate ligands in enzymes have key roles in ligand binding and enzymatic catalysis. We have deciphered the key functional role of both charged and aromatic residues within the choline binding subsite of CTP:phosphocholine cytidylyltransferase and choline kinase from Plasmodium falciparum. Comparison of quaternary ammonium binding site structures revealed a general composite aromatic box pattern of enzyme recognition sites, well distinguished from the aromatic box recognition site of receptors.
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Affiliation(s)
- Gergely N Nagy
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, 1111 Budapest (Hungary); Institute of Enzymology, Research Centre of National Sciences, HAS, 1117 Budapest (Hungary).
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31
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Yu HQ, Wang YG, Yong TM, She YH, Fu FL, Li WC. Heterologous expression of betaine aldehyde dehydrogenase gene from Ammopiptanthus nanus confers high salt and heat tolerance to Escherichia coli. Gene 2014; 549:77-84. [PMID: 25046139 DOI: 10.1016/j.gene.2014.07.049] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 06/17/2014] [Accepted: 07/17/2014] [Indexed: 11/25/2022]
Abstract
Betaine aldehyde dehydrogenase (BADH) catalyzes the synthesis of glycine betaine, a regulator of osmosis, and therefore BADH is considered to play a significant role in response of plants to abiotic stresses. Here, based on the conserved residues of the deduced amino acid sequences of the homologous BADH genes, we cloned the AnBADH gene from the xerophytic leguminous plant Ammopiptanthus nanus by using reverse transcription PCR and rapid amplification of cDNA ends. The full-length cDNA is 1,868 bp long without intron, and contains an open reading frame of 1512 bp, and 3'- and 5'-untranslated regions of 294 and 62 bp. It encodes a 54.71 kDa protein of 503 amino acids. The deduced amino acid sequence shares high homology, conserved amino acid residues and sequence motifs crucial for the function with the BADHs in other leguminous species. The sequence of the open reading frame was used to construct a prokaryotic expression vector pET32a-AnBADH, and transform Escherichia coli. The transformants expressed the heterologous AnBADH gene under the induction of isopropyl β-D-thiogalactopyranoside, and demonstrated significant enhancement of salt and heat tolerance under the stress conditions of 700 mmol L(-1) NaCl and 55°C high temperature. This result suggests that the AnBADH gene might play a crucial role in adaption of A. nanus to the abiotic stresses, and have the potential to be applied to transgenic operations of commercially important crops for improvement of abiotic tolerance.
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Affiliation(s)
- Hao-Qiang Yu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Ying-Ge Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Tai-Ming Yong
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Yue-Hui She
- Agronomy Faculty, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Feng-Ling Fu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China.
| | - Wan-Chen Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China.
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Muñoz-Clares RA, Riveros-Rosas H, Garza-Ramos G, González-Segura L, Mújica-Jiménez C, Julián-Sánchez A. Exploring the evolutionary route of the acquisition of betaine aldehyde dehydrogenase activity by plant ALDH10 enzymes: implications for the synthesis of the osmoprotectant glycine betaine. BMC PLANT BIOLOGY 2014; 14:149. [PMID: 24884441 PMCID: PMC4046141 DOI: 10.1186/1471-2229-14-149] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/22/2014] [Indexed: 05/10/2023]
Abstract
BACKGROUND Plant ALDH10 enzymes are aminoaldehyde dehydrogenases (AMADHs) that oxidize different ω-amino or trimethylammonium aldehydes, but only some of them have betaine aldehyde dehydrogenase (BADH) activity and produce the osmoprotectant glycine betaine (GB). The latter enzymes possess alanine or cysteine at position 441 (numbering of the spinach enzyme, SoBADH), while those ALDH10s that cannot oxidize betaine aldehyde (BAL) have isoleucine at this position. Only the plants that contain A441- or C441-type ALDH10 isoenzymes accumulate GB in response to osmotic stress. In this work we explored the evolutionary history of the acquisition of BAL specificity by plant ALDH10s. RESULTS We performed extensive phylogenetic analyses and constructed and characterized, kinetically and structurally, four SoBADH variants that simulate the parsimonious intermediates in the evolutionary pathway from I441-type to A441- or C441-type enzymes. All mutants had a correct folding, average thermal stabilities and similar activity with aminopropionaldehyde, but whereas A441S and A441T exhibited significant activity with BAL, A441V and A441F did not. The kinetics of the mutants were consistent with their predicted structural features obtained by modeling, and confirmed the importance of position 441 for BAL specificity. The acquisition of BADH activity could have happened through any of these intermediates without detriment of the original function or protein stability. Phylogenetic studies showed that this event occurred independently several times during angiosperms evolution when an ALDH10 gene duplicate changed the critical Ile residue for Ala or Cys in two consecutive single mutations. ALDH10 isoenzymes frequently group in two clades within a plant family: one includes peroxisomal I441-type, the other peroxisomal and non-peroxisomal I441-, A441- or C441-type. Interestingly, high GB-accumulators plants have non-peroxisomal A441- or C441-type isoenzymes, while low-GB accumulators have the peroxisomal C441-type, suggesting some limitations in the peroxisomal GB synthesis. CONCLUSION Our findings shed light on the evolution of the synthesis of GB in plants, a metabolic trait of most ecological and physiological relevance for their tolerance to drought, hypersaline soils and cold. Together, our results are consistent with smooth evolutionary pathways for the acquisition of the BADH function from ancestral I441-type AMADHs, thus explaining the relatively high occurrence of this event.
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Affiliation(s)
- Rosario A Muñoz-Clares
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, México D.F., México
| | - Héctor Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., México
| | - Georgina Garza-Ramos
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., México
| | - Lilian González-Segura
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, México D.F., México
| | - Carlos Mújica-Jiménez
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, México D.F., México
| | - Adriana Julián-Sánchez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., México
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Structure-based mutational studies of substrate inhibition of betaine aldehyde dehydrogenase BetB from Staphylococcus aureus. Appl Environ Microbiol 2014; 80:3992-4002. [PMID: 24747910 DOI: 10.1128/aem.00215-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Inhibition of enzyme activity by high concentrations of substrate and/or cofactor is a general phenomenon demonstrated in many enzymes, including aldehyde dehydrogenases. Here we show that the uncharacterized protein BetB (SA2613) from Staphylococcus aureus is a highly specific betaine aldehyde dehydrogenase, which exhibits substrate inhibition at concentrations of betaine aldehyde as low as 0.15 mM. In contrast, the aldehyde dehydrogenase YdcW from Escherichia coli, which is also active against betaine aldehyde, shows no inhibition by this substrate. Using the crystal structures of BetB and YdcW, we performed a structure-based mutational analysis of BetB and introduced the YdcW residues into the BetB active site. From a total of 32 mutations, those in five residues located in the substrate binding pocket (Val288, Ser290, His448, Tyr450, and Trp456) greatly reduced the substrate inhibition of BetB, whereas the double mutant protein H448F/Y450L demonstrated a complete loss of substrate inhibition. Substrate inhibition was also reduced by mutations of the semiconserved Gly234 (to Ser, Thr, or Ala) located in the BetB NAD(+) binding site, suggesting some cooperativity between the cofactor and substrate binding sites. Substrate docking analysis of the BetB and YdcW active sites revealed that the wild-type BetB can bind betaine aldehyde in both productive and nonproductive conformations, whereas only the productive binding mode can be modeled in the active sites of YdcW and the BetB mutant proteins with reduced substrate inhibition. Thus, our results suggest that the molecular mechanism of substrate inhibition of BetB is associated with the nonproductive binding of betaine aldehyde.
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Stiti N, Podgórska K, Bartels D. Aldehyde dehydrogenase enzyme ALDH3H1 from Arabidopsis thaliana: Identification of amino acid residues critical for cofactor specificity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:681-93. [DOI: 10.1016/j.bbapap.2014.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 01/09/2014] [Accepted: 01/13/2014] [Indexed: 11/27/2022]
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Partial purification, characterization and cDNA cloning of aminoaldehyde dehydrogenase in germinated soybean (Glycine max L.). Eur Food Res Technol 2013. [DOI: 10.1007/s00217-013-2043-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Kopečny D, Končitíková R, Tylichová M, Vigouroux A, Moskalíková H, Soural M, Šebela M, Moréra S. Plant ALDH10 family: identifying critical residues for substrate specificity and trapping a thiohemiacetal intermediate. J Biol Chem 2013; 288:9491-507. [PMID: 23408433 DOI: 10.1074/jbc.m112.443952] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plant ALDH10 family members are aminoaldehyde dehydrogenases (AMADHs), which oxidize ω-aminoaldehydes to the corresponding acids. They have been linked to polyamine catabolism, osmoprotection, secondary metabolism (fragrance), and carnitine biosynthesis. Plants commonly contain two AMADH isoenzymes. We previously studied the substrate specificity of two AMADH isoforms from peas (PsAMADHs). Here, two isoenzymes from tomato (Solanum lycopersicum), SlAMADHs, and three AMADHs from maize (Zea mays), ZmAMADHs, were kinetically investigated to obtain further clues to the catalytic mechanism and the substrate specificity. We also solved the high resolution crystal structures of SlAMADH1 and ZmAMADH1a because these enzymes stand out from the others regarding their activity. From the structural and kinetic analysis, we can state that five residues at positions 163, 288, 289, 444, and 454 (PsAMADHs numbering) can, directly or not, significantly modulate AMADH substrate specificity. In the SlAMADH1 structure, a PEG aldehyde derived from the precipitant forms a thiohemiacetal intermediate, never observed so far. Its absence in the SlAMADH1-E260A structure suggests that Glu-260 can activate the catalytic cysteine as a nucleophile. We show that the five AMADHs studied here are capable of oxidizing 3-dimethylsulfoniopropionaldehyde to the cryo- and osmoprotectant 3-dimethylsulfoniopropionate. For the first time, we also show that 3-acetamidopropionaldehyde, the third aminoaldehyde besides 3-aminopropionaldehyde and 4-aminobutyraldehyde, is generally oxidized by AMADHs, meaning that these enzymes are unique in metabolizing and detoxifying aldehyde products of polyamine degradation to nontoxic amino acids. Finally, gene expression profiles in maize indicate that AMADHs might be important for controlling ω-aminoaldehyde levels during early stages of the seed development.
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Affiliation(s)
- David Kopečny
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
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Garza-Ramos G, Mújica-Jiménez C, Muñoz-Clares RA. Potassium and ionic strength effects on the conformational and thermal stability of two aldehyde dehydrogenases reveal structural and functional roles of K⁺-binding sites. PLoS One 2013; 8:e54899. [PMID: 23365686 PMCID: PMC3554688 DOI: 10.1371/journal.pone.0054899] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 12/17/2012] [Indexed: 11/18/2022] Open
Abstract
Many aldehyde dehydrogenases (ALDHs) have potential potassium-binding sites of as yet unknown structural or functional roles. To explore possible K(+)-specific effects, we performed comparative structural studies on the tetrameric betaine aldehyde dehydrogenase from Pseudomonas aeruginosa (PaBADH) and on the dimeric BADH from spinach (SoBADH), whose activities are K(+)-dependent and K(+)-independent, respectively, although both enzymes contain potassium-binding sites. Size exclusion chromatography, dynamic light scattering, far- and near-UV circular dichroism, and extrinsic fluorescence results indicated that in the absence of K(+) ions and at very low ionic strength, PaBADH remained tetrameric but its tertiary structure was significantly altered, accounting for its inactivation, whereas SoBADH formed tetramers that maintained the native tertiary structure. The recovery of PaBADH native tertiary-structure was hyperbolically dependent on KCl concentration, indicating potassium-specific structuring effects probably arising from binding to a central-cavity site present in PaBADH but not in SoBADH. K(+) ions stabilized the native structure of both enzymes against thermal denaturation more than did tetraethylammonium (TEA(+)) ions. This indicated specific effects of potassium on both enzymes, particularly on PaBADH whose apparent T(m) values showed hyperbolical dependence on potassium concentration, similar to that observed with the tertiary structure changes. Interestingly, we also found that thermal denaturation of both enzymes performed in low ionic-strength buffers led to formation of heat-resistant, inactive soluble aggregates that retain 80% secondary structure, have increased β-sheet content and bind thioflavin T. These structured aggregates underwent further thermal-induced aggregation and precipitation when the concentrations of KCl or TEACl were raised. Given that PaBADH and SoBADH belong to different ALDH families and differ not only in amino acid composition but also in association state and surface electrostatic potential, the formation of this kind of β-sheet pre-fibrillar aggregates, not described before for any ALDH enzyme, appear to be a property of the ALDH fold.
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Affiliation(s)
- Georgina Garza-Ramos
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México, Distrito Federal, México
| | - Carlos Mújica-Jiménez
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, México, Distrito Federal, México
| | - Rosario A. Muñoz-Clares
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, México, Distrito Federal, México
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González-Segura L, Riveros-Rosas H, Díaz-Sánchez AG, Julián-Sánchez A, Muñoz-Clares RA. Potential monovalent cation-binding sites in aldehyde dehydrogenases. Chem Biol Interact 2013; 202:41-50. [PMID: 23295228 DOI: 10.1016/j.cbi.2012.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 12/12/2012] [Accepted: 12/18/2012] [Indexed: 10/27/2022]
Abstract
Potassium ions are non-essential activators of several aldehyde dehydrogenases (ALDHs), whereas a few others require the cation for activity. Two kinds of cation-binding sites, which we named intra-subunit and inter-subunit, have been observed in crystal structures of ALDHs, and based on reported crystallographic data, we here propose the existence of a third kind located in the central cavity of some tetrameric ALDHs. Given the high structural similarity between these enzymes, cation-binding sites may be present in many other members of this superfamily. To explore the prevalence of these sites, we compared 37 known crystal structures from 13 different ALDH families and evaluated the possible existence of a cation on the basis of the number, distance and geometry of its potential interactions, as well as of B-factor values of modeled cations obtained in new refinements of some reported crystal structures. Also, by performing multiple alignments of 855 non-redundant amino acid sequences, we assessed the degree of conservation in their respective families of the amino acid residues putatively relevant for cation binding. Among the ALDH enzymes studied, and according to our analyses, potential intra-subunit cation-binding sites seem to be present in most members of ALDH2, ALDH1L, ALDH4, ALDH5, ALDH7, ALDH10, and ALDH25 families, as well as in the bacterial and fungal members of the ALDH9 family and in a few ALDH1, ALDH6, ALDH11 and ALDH26 enzymes; potential inter-subunit sites in members of ALDH1L, ALDH3, ALDH4 from bacillales, ALDH5, ALDH7, ALDH9, ALDH10, ALDH11 and ALDH25 families; and potential central-cavity sites only in some bacterial and animal ALDH9s and in most members of the ALDH1L family. Because potassium is the most abundant intracellular cation, we propose that these are potassium-binding sites, but the specific structural and/or functional roles of the cation bound to these different sites remain to be investigated.
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Affiliation(s)
- Lilian González-Segura
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, México, DF 04510, Mexico
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Riveros-Rosas H, González-Segura L, Julián-Sánchez A, Díaz-Sánchez AG, Muñoz-Clares RA. Structural determinants of substrate specificity in aldehyde dehydrogenases. Chem Biol Interact 2012; 202:51-61. [PMID: 23219887 DOI: 10.1016/j.cbi.2012.11.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 11/24/2012] [Accepted: 11/27/2012] [Indexed: 12/28/2022]
Abstract
Within the aldehyde dehydrogenase (ALDH) superfamily, proteins belonging to the ALDH9, ALDH10, ALDH25, ALDH26 and ALDH27 families display activity as ω-aminoaldehyde dehydrogenases (AMADHs). These enzymes participate in polyamine, choline and arginine catabolism, as well as in synthesis of several osmoprotectants and carnitine. Active site aromatic and acidic residues are involved in binding the ω-aminoaldehydes in plant ALDH10 enzymes. In order to ascertain the degree of conservation of these residues among AMADHs and to evaluate their possible relevance in determining the aminoaldehyde specificity, we compared the known amino acid sequences of every ALDH family that have at least one member with known crystal structure, as well as the electrostatic potential surface of the aldehyde binding sites of these structures. Our analyses showed that four or three aromatic residues form a similar "aromatic box" in the active site of the AMADH enzymes, being the equivalents to Phe170 and Trp177 (human ALDH2 numbering) strictly conserved in all of them, which supports their relevance in binding the aminoaldehyde by cation-π interactions. In addition, all AMADHs exhibit a negative electrostatic potential surface in the aldehyde-entrance tunnel, due to side-chain carboxyl and hydroxyl groups or main-chain carbonyl groups. In contrast, ALDHs that have non-polar or negatively charged substrates exhibit neutral or positive electrostatic potential surfaces, respectively. Finally, our comparative sequence analyses revealed that the residues equivalent to Asp121 and Phe170 are highly conserved in many ALDH families irrespective of their substrate specificity-suggesting that they perform a role in catalysis additional or different to binding of the substrate-and that the positions Met124, Cys301, and Cys303 are hot spots changed during evolution to confer aldehyde specificity to several ALDH families.
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Affiliation(s)
- Héctor Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 México, DF, Mexico
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Mahadevi AS, Sastry GN. Cation-π interaction: its role and relevance in chemistry, biology, and material science. Chem Rev 2012; 113:2100-38. [PMID: 23145968 DOI: 10.1021/cr300222d] [Citation(s) in RCA: 719] [Impact Index Per Article: 59.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- A Subha Mahadevi
- Molecular Modeling Group, CSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad 500 607, Andhra Pradesh, India
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