101
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Mu H, Sun J, Heras H, Chu KH, Qiu JW. An integrated proteomic and transcriptomic analysis of perivitelline fluid proteins in a freshwater gastropod laying aerial eggs. J Proteomics 2017; 155:22-30. [PMID: 28095328 DOI: 10.1016/j.jprot.2017.01.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 01/04/2017] [Accepted: 01/08/2017] [Indexed: 11/27/2022]
Abstract
Proteins of the egg perivitelline fluid (PVF) that surrounds the embryo are critical for embryonic development in many animals, but little is known about their identities. Using an integrated proteomic and transcriptomic approach, we identified 64 proteins from the PVF of Pomacea maculata, a freshwater snail adopting aerial oviposition. Proteins were classified into eight functional groups: major multifunctional perivitellin subunits, immune response, energy metabolism, protein degradation, oxidation-reduction, signaling and binding, transcription and translation, and others. Comparison of gene expression levels between tissues showed that 22 PVF genes were exclusively expressed in albumen gland, the female organ that secretes PVF. Base substitution analysis of PVF and housekeeping genes between P. maculata and its closely related species Pomacea canaliculata showed that the reproductive proteins had a higher mean evolutionary rate. Predicted 3D structures of selected PVF proteins showed that some nonsynonymous substitutions are located at or near the binding regions that may affect protein function. The proteome and sequence divergence analysis revealed a substantial amount of maternal investment in embryonic nutrition and defense, and higher adaptive selective pressure on PVF protein-coding genes when compared with housekeeping genes, providing insight into the adaptations associated with the unusual reproductive strategy in these mollusks. SIGNIFICANCE There has been great interest in studying reproduction-related proteins as such studies may not only answer fundamental questions about speciation and evolution, but also solve practical problems of animal infertility and pest outbreak. Our study has demonstrated the effectiveness of an integrated proteomic and transcriptomic approach in understanding the heavy maternal investment of proteins in the eggs of a non-model snail, and how the reproductive proteins may have evolved during the transition from laying underwater eggs to aerial eggs.
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Affiliation(s)
- Huawei Mu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Jin Sun
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Horacio Heras
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), Universidad Nacional de La Plata (UNLP)-CONICET CCT-La Plata, La Plata, Argentina; Cátedra de Química Biológica, Facultad de Ciencias Naturales y Museo, UNLP, Argentina
| | - Ka Hou Chu
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
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102
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Fu Y, Wang MX, Zhang D, Hou YW, Gao S, Zhao LX, Ye F. Design, synthesis, and herbicidal activity of pyrazole benzophenone derivatives. RSC Adv 2017. [DOI: 10.1039/c7ra09858h] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Design of pyrazole benzophenones as potent HPPD inhibitors with excellent herbicidal activities.
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Affiliation(s)
- Ying Fu
- Department of Applied Chemistry
- College of Science
- Northeast Agricultural University
- Harbin
- P. R. China
| | - Meng-Xia Wang
- Department of Applied Chemistry
- College of Science
- Northeast Agricultural University
- Harbin
- P. R. China
| | - Dong Zhang
- Department of Applied Chemistry
- College of Science
- Northeast Agricultural University
- Harbin
- P. R. China
| | - Yu-Wen Hou
- Department of Applied Chemistry
- College of Science
- Northeast Agricultural University
- Harbin
- P. R. China
| | - Shuang Gao
- Department of Applied Chemistry
- College of Science
- Northeast Agricultural University
- Harbin
- P. R. China
| | - Li-Xia Zhao
- Department of Applied Chemistry
- College of Science
- Northeast Agricultural University
- Harbin
- P. R. China
| | - Fei Ye
- Department of Applied Chemistry
- College of Science
- Northeast Agricultural University
- Harbin
- P. R. China
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103
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Wang M, Toda K, Maeda HA. Biochemical properties and subcellular localization of tyrosine aminotransferases in Arabidopsis thaliana. PHYTOCHEMISTRY 2016; 132:16-25. [PMID: 27726859 DOI: 10.1016/j.phytochem.2016.09.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/02/2016] [Accepted: 09/12/2016] [Indexed: 05/05/2023]
Abstract
Plants produce various L-tyrosine (Tyr)-derived compounds that are of pharmaceutical or nutritional importance to humans. Tyr aminotransferase (TAT) catalyzes the reversible transamination between Tyr and 4-hydroxyphenylpyruvate (HPP), the initial step in the biosynthesis of many Tyr-derived plant natural products. Herein reported is the biochemical characterization and subcellular localization of TAT enzymes from the model plant Arabidopsis thaliana. Phylogenetic analysis showed that Arabidopsis has at least two homologous TAT genes, At5g53970 (AtTAT1) and At5g36160 (AtTAT2). Their recombinant enzymes showed distinct biochemical properties: AtTAT1 had the highest activity towards Tyr, while AtTAT2 exhibited a broad substrate specificity for both amino and keto acid substrates. Also, AtTAT1 favored the direction of Tyr deamination to HPP, whereas AtTAT2 preferred transamination of HPP to Tyr. Subcellular localization analysis using GFP-fusion proteins and confocal microscopy showed that AtTAT1, AtTAT2, and HPP dioxygenase (HPPD), which catalyzes the subsequent step of TAT, are localized in the cytosol, unlike plastid-localized Tyr and tocopherol biosynthetic enzymes. Furthermore, subcellular fractionation indicated that, while HPPD activity is restricted to the cytosol, TAT activity is detected in both cytosolic and plastidic fractions of Arabidopsis leaf tissue, suggesting that an unknown aminotransferase(s) having TAT activity is also present in the plastids. Biochemical and cellular analyses of Arabidopsis TATs provide a fundamental basis for future in vivo studies and metabolic engineering for enhanced production of Tyr-derived phytochemicals in plants.
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Affiliation(s)
- Minmin Wang
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Kyoko Toda
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA; Institute of Crop Science, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA.
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104
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Gomez-Ospina N, Scott AI, Oh GJ, Potter D, Goel VV, Destino L, Baugh N, Enns GM, Niemi AK, Cowan TM. Expanding the phenotype of hawkinsinuria: new insights from response to N-acetyl-L-cysteine. J Inherit Metab Dis 2016; 39:821-829. [PMID: 27488560 DOI: 10.1007/s10545-016-9963-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/19/2016] [Accepted: 07/04/2016] [Indexed: 10/21/2022]
Abstract
Hawkinsinuria is a rare disorder of tyrosine metabolism that can manifest with metabolic acidosis and growth arrest around the time of weaning off breast milk, typically followed by spontaneous resolution of symptoms around 1 year of age. The urinary metabolites hawkinsin, quinolacetic acid, and pyroglutamic acid can aid in identifying this condition, although their relationship to the clinical manifestations is not known. Herein we describe clinical and laboratory findings in two fraternal twins with hawkinsinuria who presented with failure to thrive and metabolic acidosis. Close clinical follow-up and laboratory testing revealed previously unrecognized hypoglycemia, hypophosphatemia, combined hyperlipidemia, and anemia, along with the characteristic urinary metabolites, including massive pyroglutamic aciduria. Treatment with N-acetyl-L-cysteine (NAC) restored normal growth and normalized or improved most biochemical parameters. The dramatic response to NAC therapy supports the idea that glutathione depletion plays a key role in the pathogenesis of hawkinsinuria.
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Affiliation(s)
- Natalia Gomez-Ospina
- Department of Pediatrics, Stanford University School of Medicine, 300 Pasteur Drive, H 315, Stanford, CA, 94305-5208, USA.
| | - Anna I Scott
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gia J Oh
- Department of Pediatrics, Stanford University School of Medicine, 300 Pasteur Drive, H 315, Stanford, CA, 94305-5208, USA
| | - Donald Potter
- Department of Pediatrics, Stanford University School of Medicine, 300 Pasteur Drive, H 315, Stanford, CA, 94305-5208, USA
| | - Veena V Goel
- Department of Pediatrics, Stanford University School of Medicine, 300 Pasteur Drive, H 315, Stanford, CA, 94305-5208, USA
| | - Lauren Destino
- Department of Pediatrics, Stanford University School of Medicine, 300 Pasteur Drive, H 315, Stanford, CA, 94305-5208, USA
| | - Nancy Baugh
- Department of Pediatrics, Stanford University School of Medicine, 300 Pasteur Drive, H 315, Stanford, CA, 94305-5208, USA
| | - Gregory M Enns
- Department of Pediatrics, Stanford University School of Medicine, 300 Pasteur Drive, H 315, Stanford, CA, 94305-5208, USA
| | - Anna-Kaisa Niemi
- Department of Pediatrics, Stanford University School of Medicine, 300 Pasteur Drive, H 315, Stanford, CA, 94305-5208, USA
| | - Tina M Cowan
- Department of Pediatrics, Stanford University School of Medicine, 300 Pasteur Drive, H 315, Stanford, CA, 94305-5208, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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105
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Rokob TA. Pathways for Arene Oxidation in Non-Heme Diiron Enzymes: Lessons from Computational Studies on Benzoyl Coenzyme A Epoxidase. J Am Chem Soc 2016; 138:14623-14638. [PMID: 27682344 DOI: 10.1021/jacs.6b06987] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oxygenation of aromatic rings using O2 is catalyzed by several non-heme carboxylate-bridged diiron enzymes. In order to provide a general mechanistic description for these reactions, computational studies were carried out at the ONIOM(B3LYP/BP86/Amber) level on the non-heme diiron enzyme benzoyl coenzyme A epoxidase, BoxB. The calculations revealed four possible pathways for attacking the aromatic ring: (a) electrophilic (2e-) attack by a bis(μ-oxo)-diiron(IV) species (Q pathway); (b) electrophilic (2e-) attack via the σ* orbital of a μ-η2:η2-peroxo-diiron(III) intermediate (Pσ* pathway); (c) radical (1e-) attack via the π*-orbital of a superoxo-diiron(II,III) species (Pπ* pathway); (d) radical (1e-) attack of a partially quenched bis(μ-oxo)-diiron(IV) intermediate (Q' pathway). The results allowed earlier work of de Visser on olefin epoxidation by diiron complexes and QM-cluster studies of Liao and Siegbahn on BoxB to be put into a broader perspective. Parallels with epoxidation using organic peracids were also examined. Specifically for the BoxB enzyme, the Q pathway was found to be the most preferred, but the corresponding bis(μ-oxo)-diiron(IV) species is significantly destabilized and not expected to be directly observable. Epoxidation via the Pσ* pathway represents an energetically somewhat higher lying alternative; possible strategies for experimental discrimination are discussed. The selectivity toward epoxidation is shown to stem from a combination of inherent electronic properties of the thioacyl substituent and enzymatic constraints. Possible implications of the results for toluene monooxygenases are considered as well.
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Affiliation(s)
- Tibor András Rokob
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar Tudósok körútja 2, 1117 Budapest, Hungary
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106
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Péden R, Rocher B, Chan P, Vaudry D, Poret A, Olivier S, Le Foll F, Bultelle F. Consequences of acclimation on the resistance to acute thermal stress: Proteomic focus on mussels from pristine site. MARINE ENVIRONMENTAL RESEARCH 2016; 121:64-73. [PMID: 26972988 DOI: 10.1016/j.marenvres.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 02/10/2016] [Accepted: 02/14/2016] [Indexed: 06/05/2023]
Abstract
Climate change constitutes an additional threat for intertidal species that already have to cope with a challenging environment. The present study focuses on the blue mussel Mytilus edulis and aims at investigating the importance of thermal acclimation in heat stress response. Microcosm exposures were performed with mussels submitted to an identical acute thermal stress following two thermal summer acclimations standing for present or future temperature conditions. Gill proteomes were analyzed by 2DE and 96 differentially expressed proteoforms were identified. Our results show that cell integrity appears to be maintained by the rise in molecular protective systems (i.e. Heat Shock Proteins), and by the reallocation of energy production via a switch to anaerobic metabolism and the setting up of alternative energy pathways. Finally, our results indicate that the response of mussels to acute thermal stress is conditioned by the acclimation temperature with an improved response in organisms acclimated to higher temperatures.
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Affiliation(s)
- Romain Péden
- Laboratory of Ecotoxicology, UMR-I 02 SEBIO, Le Havre University, Normandy University, France.
| | - Béatrice Rocher
- Laboratory of Ecotoxicology, UMR-I 02 SEBIO, Le Havre University, Normandy University, France
| | - Philippe Chan
- Platform in Proteomics PISSARO IRIB, Rouen University, Normandy University, France
| | - David Vaudry
- Platform in Proteomics PISSARO IRIB, Rouen University, Normandy University, France; Laboratory of Neuronal and Neuroendocrine Differenciation and Communication, INSERM U982, Rouen University, Normandy University, France
| | - Agnès Poret
- Laboratory of Ecotoxicology, UMR-I 02 SEBIO, Le Havre University, Normandy University, France
| | - Stéphanie Olivier
- Laboratory of Ecotoxicology, UMR-I 02 SEBIO, Le Havre University, Normandy University, France
| | - Frank Le Foll
- Laboratory of Ecotoxicology, UMR-I 02 SEBIO, Le Havre University, Normandy University, France
| | - Florence Bultelle
- Laboratory of Ecotoxicology, UMR-I 02 SEBIO, Le Havre University, Normandy University, France
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107
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Ahmad S, Lee SY, Kong HG, Jo EJ, Choi HK, Khan R, Lee SW. Genetic Determinants for Pyomelanin Production and Its Protective Effect against Oxidative Stress in Ralstonia solanacearum. PLoS One 2016; 11:e0160845. [PMID: 27513990 PMCID: PMC4981395 DOI: 10.1371/journal.pone.0160845] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/26/2016] [Indexed: 11/18/2022] Open
Abstract
Ralstonia solanacearum is a soil-borne plant pathogen that infects more than 200 plant species. Its broad host range and long-term survival under different environmental stress conditions suggest that it uses a variety of mechanisms to protect itself against various types of biotic and abiotic stress. R. solanacearum produces a melanin-like brown pigment in the stationary phase when grown in minimal medium containing tyrosine. To gain deeper insight into the genetic determinants involved in melanin production, transposon-inserted mutants of R. solanacearum strain SL341 were screened for strains with defective melanin-producing capability. In addition to one mutant already known to be involved in pyomelanin production (viz., strain SL341D, with disruption of the hydroxphenylpyruvate dioxygenase gene), we identified three other mutants with disruption in the regulatory genes rpoS, hrpG, and oxyR, respectively. Wild-type SL341 produced pyomelanin in minimal medium containing tyrosine whereas the mutant strains did not. Likewise, homogentisate, a major precursor of pyomelanin, was detected in the culture filtrate of the wild-type strain but not in those of the mutant strains. A gene encoding hydroxyphenylpyruvate dioxygenase exhibited a significant high expression in wild type SL341 compared to other mutant strains, suggesting that pyomelanin production is regulated by three different regulatory proteins. However, analysis of the gene encoding homogentisate dioxygenase revealed no significant difference in its relative expression over time in the wild-type SL341 and mutant strains, except for SL341D, at 72 h incubation. The pigmented SL341 strain also exhibited a high tolerance to hydrogen peroxide stress compared with the non-pigmented SL341D strain. Our study suggests that pyomelanin production is controlled by several regulatory factors in R. solanacearum to confer protection under oxidative stress.
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Affiliation(s)
- Shabir Ahmad
- Department of Applied Biosciences, Dong-A University, Busan, 49315, Republic of Korea
| | - Seung Yeup Lee
- Department of Applied Biosciences, Dong-A University, Busan, 49315, Republic of Korea
| | - Hyun Gi Kong
- Department of Applied Biosciences, Dong-A University, Busan, 49315, Republic of Korea
| | - Eun Jeong Jo
- Department of Applied Biosciences, Dong-A University, Busan, 49315, Republic of Korea
| | - Hye Kyung Choi
- Department of Applied Biosciences, Dong-A University, Busan, 49315, Republic of Korea
| | - Raees Khan
- Department of Applied Biosciences, Dong-A University, Busan, 49315, Republic of Korea
| | - Seon-Woo Lee
- Department of Applied Biosciences, Dong-A University, Busan, 49315, Republic of Korea
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108
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Žunec S, Kašuba V, Pavičić I, Marjanović AM, Tariba B, Milić M, Kopjar N, Pizent A, Vrdoljak AL, Rozgaj R, Želježić D. Assessment of oxidative stress responses and the cytotoxic and genotoxic potential of the herbicide tembotrione in HepG2 cells. Food Chem Toxicol 2016; 94:64-74. [DOI: 10.1016/j.fct.2016.05.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/09/2016] [Accepted: 05/26/2016] [Indexed: 12/22/2022]
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109
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Kopáček P, Perner J. Vector Biology: Tyrosine Degradation Protects Blood Feeders from Death via La Grande Bouffe. Curr Biol 2016; 26:R763-5. [DOI: 10.1016/j.cub.2016.06.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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110
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Strenkert D, Limso CA, Fatihi A, Schmollinger S, Basset GJ, Merchant SS. Genetically Programmed Changes in Photosynthetic Cofactor Metabolism in Copper-deficient Chlamydomonas. J Biol Chem 2016; 291:19118-31. [PMID: 27440043 DOI: 10.1074/jbc.m116.717413] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Indexed: 01/08/2023] Open
Abstract
Genetic and genomic studies indicate that copper deficiency triggers changes in the expression of genes encoding key enzymes in various chloroplast-localized lipid/pigment biosynthetic pathways. Among these are CGL78 involved in chlorophyll biosynthesis and HPPD1, encoding 4-hydroxyphenylpyruvate dioxygenase catalyzing the committed step of plastoquinone and tocopherol biosyntheses. Copper deficiency in wild-type cells does not change the chlorophyll content, but a survey of chlorophyll protein accumulation in this situation revealed increased accumulation of LHCSR3, which is blocked at the level of mRNA accumulation when either CGL78 expression is reduced or in the crd1 mutant, which has a copper-nutrition conditional defect at the same step in chlorophyll biosynthesis. Again, like copper-deficient crd1 strains, cgl78 knock-down lines also have reduced chlorophyll content concomitant with loss of PSI-LHCI super-complexes and reduced abundance of a chlorophyll binding subunit of PSI, PSAK, which connects LHCI to PSI. For HPPD1, increased mRNA results in increased abundance of the corresponding protein in copper-deficient cells concomitant with CRR1-dependent increased accumulation of γ-tocopherols, but not plastoquinone-9 nor total tocopherols. In crr1 mutants, where increased HPPD1 expression is blocked, plastochromanol-8, derived from plastoquinone-9 and purported to also have an antioxidant function, is found instead. Although not previously found in algae, this metabolite may occur only in stress conditions.
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Affiliation(s)
- Daniela Strenkert
- From the Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, the Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - Clariss Ann Limso
- the Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - Abdelhak Fatihi
- the Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, 78026 Versailles Cedex, France, and
| | - Stefan Schmollinger
- From the Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, the Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - Gilles J Basset
- the Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Sabeeha S Merchant
- From the Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, the Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095,
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111
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Romdhane S, Devers-Lamrani M, Barthelmebs L, Calvayrac C, Bertrand C, Cooper JF, Dayan FE, Martin-Laurent F. Ecotoxicological Impact of the Bioherbicide Leptospermone on the Microbial Community of Two Arable Soils. Front Microbiol 2016; 7:775. [PMID: 27252691 PMCID: PMC4877392 DOI: 10.3389/fmicb.2016.00775] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/09/2016] [Indexed: 11/13/2022] Open
Abstract
The ecotoxicological impact of leptospermone, a β-triketone bioherbicide, on the bacterial community of two arable soils was investigated. Soil microcosms were exposed to 0 × (control), 1 × or 10 × recommended dose of leptospermone. The β-triketone was moderately adsorbed to both soils (i.e.,: Kfa ~ 1.2 and Koc ~ 140 mL g−1). Its dissipation was lower in sterilized than in unsterilized soils suggesting that it was mainly influenced by biotic factors. Within 45 days, leptospermone disappeared almost entirely from one of the two soils (i.e., DT50 < 10 days), while 25% remained in the other. The composition of the microbial community assessed by qPCR targeting 11 microbial groups was found to be significantly modified in soil microcosms exposed to leptospermone. Pyrosequencing of 16S rRNA gene amplicons showed a shift in the bacterial community structure and a significant impact of leptospermone on the diversity of the soil bacterial community. Changes in the composition, and in the α- and β-diversity of microbial community were transient in the soil able to fully dissipate the leptospermone, but were persistent in the soil where β-triketone remained. To conclude the bacterial community of the two soils was sensitive to leptospermone and its resilience was observed only when leptospermone was fully dissipated.
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Affiliation(s)
- Sana Romdhane
- Biocapteurs Analyse Environnement, EA 4218, University of Perpignan via DomitiaPerpignan, France; Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, University of Perpignan via DomitiaPerpignan, France; Institut National de la Recherche Agronomique, UMR 1347 Agroécologie, EcolDurDijon, France
| | - Marion Devers-Lamrani
- Institut National de la Recherche Agronomique, UMR 1347 Agroécologie, EcolDur Dijon, France
| | - Lise Barthelmebs
- Biocapteurs Analyse Environnement, EA 4218, University of Perpignan via Domitia Perpignan, France
| | - Christophe Calvayrac
- Biocapteurs Analyse Environnement, EA 4218, University of Perpignan via Domitia Perpignan, France
| | - Cédric Bertrand
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, University of Perpignan via Domitia Perpignan, France
| | - Jean-François Cooper
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, University of Perpignan via Domitia Perpignan, France
| | - Franck E Dayan
- Bioagricultural Sciences and Pest Management Department, Colorado State University Fort Collins, CO, USA
| | - Fabrice Martin-Laurent
- Institut National de la Recherche Agronomique, UMR 1347 Agroécologie, EcolDur Dijon, France
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112
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Evaluation of toxicological biomarkers in secreted proteins of HepG2 cells exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin and their expressions in the plasma of rats and incineration workers. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:584-93. [DOI: 10.1016/j.bbapap.2016.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 02/16/2016] [Accepted: 02/22/2016] [Indexed: 11/21/2022]
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113
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The different catalytic roles of the metal-binding ligands in human 4-hydroxyphenylpyruvate dioxygenase. Biochem J 2016; 473:1179-89. [PMID: 26936969 DOI: 10.1042/bcj20160146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/02/2016] [Indexed: 11/17/2022]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a non-haem iron(II)-dependent oxygenase that catalyses the conversion of 4-hydroxyphenylpyruvate (HPP) to homogentisate (HG). In the active site, a strictly conserved 2-His-1-Glu facial triad co-ordinates the iron ready for catalysis. Substitution of these residues resulted in about a 10-fold decrease in the metal binding affinity, as measured by isothermal titration calorimetry, and a large reduction in enzyme catalytic efficiencies. The present study revealed the vital role of the ligand Glu(349) in enzyme function. Replacing this residue with alanine resulted in loss of activity. The E349G variant retained 5% activity for the coupled reaction, suggesting that co-ordinating water may be able to support activation of the trans-bound dioxygen upon substrate binding. The reaction catalysed by the H183A variant was fully uncoupled. H183A variant catalytic activity resulted in protein cleavage between Ile(267) and Ala(268) and the production of an N-terminal fragment. The H266A variant was able to produce 4-hydroxyphenylacetate (HPA), demonstrating that decarboxylation had occurred but that there was no subsequent product formation. Structural modelling of the variant enzyme with bound dioxygen revealed the rearrangement of the co-ordination environment and the dynamic behaviour of bound dioxygen in the H266A and H183A variants respectively. These models suggest that the residues regulate the geometry of the reactive oxygen intermediate during the oxidation reaction. The mutagenesis and structural simulation studies demonstrate the critical and unique role of each ligand in the function of HPPD, and which correlates with their respective co-ordination position.
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114
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Pharmacological targeting of the HIF hydroxylases--A new field in medicine development. Mol Aspects Med 2016; 47-48:54-75. [PMID: 26791432 DOI: 10.1016/j.mam.2016.01.001] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/11/2015] [Accepted: 01/04/2016] [Indexed: 12/13/2022]
Abstract
In human cells oxygen levels are 'sensed' by a set of ferrous iron and 2-oxoglutarate dependent dioxygenases. These enzymes regulate a broad range of cellular and systemic responses to hypoxia by catalysing the post-translational hydroxylation of specific residues in the alpha subunits of hypoxia inducible factor (HIF) transcriptional complexes. The HIF hydroxylases are now the subject of pharmaceutical targeting by small molecule inhibitors that aim to activate or augment the endogenous HIF transcriptional response for the treatment of anaemia and other hypoxic human diseases. Here we consider the rationale for this therapeutic strategy from the biochemical, biological and medical perspectives. We outline structural and mechanistic considerations that are relevant to the design of HIF hydroxylase inhibitors, including likely determinants of specificity, and review published reports on their activity in pre-clinical models and clinical trials.
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115
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Quesne MG, Borowski T, de Visser SP. Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs. Chemistry 2015; 22:2562-81. [PMID: 26696271 DOI: 10.1002/chem.201503802] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Indexed: 11/08/2022]
Abstract
Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black-box method that is easily applied, but requires careful set-up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work-protocols developed in our groups for running successful QM/MM calculations.
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Affiliation(s)
- Matthew G Quesne
- Jerzy Haber Institute of Catalysis and Surface Chemistry of the, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland. .,Manchester Institute of Biotechnology and, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry of the, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland.
| | - Sam P de Visser
- Manchester Institute of Biotechnology and, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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Szymanska E, Sredzinska M, Ciara E, Piekutowska-Abramczuk D, Ploski R, Rokicki D, Tylki-Szymanska A. Tyrosinemia type III in an asymptomatic girl. Mol Genet Metab Rep 2015. [PMID: 28649543 PMCID: PMC5471395 DOI: 10.1016/j.ymgmr.2015.10.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Tyrosinemia type 3 (HT3) is a rare inborn error of tyrosine metabolism caused by mutations in the HPD gene encoding 4-hydroxyphenyl-pyruvate dioxygenase, which is transmitted in an autosomal recessive trait. The disorder is characterized by tyrosine accumulation in body fluids and massive excretion of tyrosine derivatives into urine (www.orpha.net). Since it is the least frequent form of tyrosinemia, only few cases with the variable but rather mild clinical features have been described so far. We report an 11 year old girl presenting with no clinical symptoms and with normal mental development who has been diagnosed with HT3 through metabolic screening on the basis of elevated serum level of tyrosine ranging from 425 to 535 μmol/L (normal values: 29–86 μmol/L), and elevated urinary excretion of p-hydroxyphenyl derivatives confirmed genetically with the homozygous c.479A > G (p.Tyr160Cys) missense change in the HPD gene. The girl has been only presenting with recurrent proteinuria of unknown etiology. A phenylalanine- and tyrosine-restricted diet has never been administered. Presented case may suggest that high tyrosine concentration itself does not participate directly in neuronal damage described in patients with tyrosinemia type 3.
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Affiliation(s)
- Edyta Szymanska
- Department of Pediatrics, Nutrition and Metabolic Disorders, The Children's Memorial Health Institute, Warsaw, Poland
| | - Malgorzata Sredzinska
- Department of Pediatrics, Nutrition and Metabolic Disorders, The Children's Memorial Health Institute, Warsaw, Poland
| | - Elzbieta Ciara
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | | | - Rafal Ploski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Dariusz Rokicki
- Department of Pediatrics, Nutrition and Metabolic Disorders, The Children's Memorial Health Institute, Warsaw, Poland
| | - Anna Tylki-Szymanska
- Department of Pediatrics, Nutrition and Metabolic Disorders, The Children's Memorial Health Institute, Warsaw, Poland
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Rocaboy-Faquet E, Barthelmebs L, Calas-Blanchard C, Noguer T. A novel amperometric biosensor for ß-triketone herbicides based on hydroxyphenylpyruvate dioxygenase inhibition: A case study for sulcotrione. Talanta 2015; 146:510-6. [PMID: 26695298 DOI: 10.1016/j.talanta.2015.09.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/09/2015] [Accepted: 09/11/2015] [Indexed: 11/28/2022]
Abstract
An amperometric biosensor was designed for the determination of sulcotrione, a β-triketone herbicide, based on inhibition of hydroxyphenylpyruvate dioxygenase (HPPD), an enzyme allowing the oxidation of hydroxyphenylpyruvate (HPP) in homogentisic acid (HGA). HPPD was produced by cloning the hppd gene from Arabidopsis thaliana in E. coli, followed by overexpression and purification by nickel-histidine affinity. The electrochemical detection of HPPD activity was based on the electrochemical oxidation of HGA at +0.1 V vs. Ag/AgCl, using a poly(3,4-ethylenedioxythiophene) polystyrene sulfonate-modified screen-printed electrode. Assays were performed at 25°C in 0.1 M phosphate buffer pH 8 containing 0.1M KCl. The purified HPPD was shown to display a maximum velocity of 0.51 µM(HGA) min(-1), and an apparent K(M) of 22.6 µM for HPP. HPPD inhibition assays in presence of sulcotrione confirmed a competitive inhibition of HPPD, the calculated inhibition constant K(I) was 1.11.10(-8) M. The dynamic range for sulcotrione extended from 5.10(-10) M to 5.10(-6) M and the limit of detection (LOD), estimated as the concentration inducing 20% of inhibition, was 1.4.10(-10) M.
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Affiliation(s)
- Emilie Rocaboy-Faquet
- Laboratoire BAE, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan cedex 9, France
| | - Lise Barthelmebs
- Laboratoire BAE, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan cedex 9, France
| | - Carole Calas-Blanchard
- Laboratoire BAE, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan cedex 9, France
| | - Thierry Noguer
- Laboratoire BAE, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan cedex 9, France.
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118
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Ibarra-Laclette E, Zamudio-Hernández F, Pérez-Torres CA, Albert VA, Ramírez-Chávez E, Molina-Torres J, Fernández-Cortes A, Calderón-Vázquez C, Olivares-Romero JL, Herrera-Estrella A, Herrera-Estrella L. De novo sequencing and analysis of Lophophora williamsii transcriptome, and searching for putative genes involved in mescaline biosynthesis. BMC Genomics 2015; 16:657. [PMID: 26330142 PMCID: PMC4557841 DOI: 10.1186/s12864-015-1821-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 08/07/2015] [Indexed: 12/04/2022] Open
Abstract
Background Lophophora williamsii (commonly named peyote) is a small, spineless cactus with psychoactive alkaloids, particularly mescaline. Peyote utilizes crassulacean acid metabolism (CAM), an alternative form of photosynthesis that exists in succulents such as cacti and other desert plants. Therefore, its transcriptome can be considered an important resource for future research focused on understanding how these plants make more efficient use of water in marginal environments and also for research focused on better understanding of the overall mechanisms leading to production of plant natural products and secondary metabolites. Results In this study, two cDNA libraries were generated from L. williamsii. These libraries, representing buttons (tops of stems) and roots were sequenced using different sequencing platforms (GS-FLX, GS-Junior and PGM, respectively). A total of 5,541,550 raw reads were generated, which were assembled into 63,704 unigenes with an average length of 564.04 bp. A total of 25,149 unigenes (62.19 %) was annotated using public databases. 681 unigenes were found to be differentially expressed when comparing the two libraries, where 400 were preferentially expressed in buttons and 281 in roots. Some of the major alkaloids, including mescaline, were identified by GC-MS and relevant metabolic pathways were reconstructed using the Kyoto encyclopedia of genes and genomes database (KEGG). Subsequently, the expression patterns of preferentially expressed genes putatively involved in mescaline production were examined and validated by qRT-PCR. Conclusions High throughput transcriptome sequencing (RNA-seq) analysis allowed us to efficiently identify candidate genes involved in mescaline biosynthetic pathway in L. williamsii; these included tyrosine/DOPA decarboxylase, hydroxylases, and O-methyltransferases. This study sets the theoretical foundation for bioassay design directed at confirming the participation of these genes in mescaline production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1821-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Enrique Ibarra-Laclette
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México. .,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, México.
| | - Flor Zamudio-Hernández
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
| | - Claudia Anahí Pérez-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México. .,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, México. .,Investigador Cátedra CONACyT, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, México.
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, 14260, USA.
| | - Enrique Ramírez-Chávez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36821, Irapuato, Guanajuato, México.
| | - Jorge Molina-Torres
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36821, Irapuato, Guanajuato, México.
| | - Araceli Fernández-Cortes
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
| | - Carlos Calderón-Vázquez
- Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Instituto Politécnico Nacional, 81000, Guasave, Sinaloa, México.
| | | | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
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Silva TC, dos Santos Pires M, de Castro AA, da Cunha EFF, Caetano MS, Ramalho TC. Molecular insight into the inhibition mechanism of plant and rat 4-hydroxyphenylpyruvate dioxygenase by molecular docking and DFT calculations. Med Chem Res 2015. [DOI: 10.1007/s00044-015-1436-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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120
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Determinants of tolerance to inhibitors in hardwood spent sulfite liquor in genome shuffled Pachysolen tannophilus strains. Antonie van Leeuwenhoek 2015; 108:811-34. [PMID: 26231071 DOI: 10.1007/s10482-015-0537-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 07/15/2015] [Indexed: 01/05/2023]
Abstract
Genome shuffling was used to obtain Pachysolen tannophilus mutants with improved tolerance to inhibitors in hardwood spent sulfite liquor (HW SSL). Genome shuffled strains (GHW301, GHW302 and GHW303) grew at higher concentrations of HW SSL (80 % v/v) compared to the HW SSL UV mutant (70 % v/v) and the wild-type (WT) strain (50 % v/v). In defined media containing acetic acid (0.70-0.90 % w/v), GHW301, GHW302 and GHW303 exhibited a shorter lag compared to the acetic acid UV mutant, while the WT did not grow. Genome shuffled strains produced more ethanol than the WT at higher concentrations of HW SSL and an aspen hydrolysate. To identify the genetic basis of inhibitor tolerance, whole genome sequencing was carried out on GHW301, GHW302 and GHW303 and compared to the WT strain. Sixty single nucleotide variations were identified that were common to all three genome shuffled strains. Of these, 40 were in gene sequences and 20 were within 5 bp-1 kb either up or downstream of protein encoding genes. Based on the mutated gene products, mutations were grouped into functional categories and affected a variety of cellular functions, demonstrating the complexity of inhibitor tolerance in yeast. Sequence analysis of UV mutants (UAA302 and UHW303) from which GHW301, GHW302 and GHW303 were derived, confirmed the success of our cross-mating based genome shuffling strategy. Whole-genome sequencing analysis allowed identification of potential gene targets for tolerance to inhibitors in lignocellulosic hydrolysates.
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Wang DW, Lin HY, Cao RJ, Chen T, Wu FX, Hao GF, Chen Q, Yang WC, Yang GF. Synthesis and Herbicidal Activity of Triketone-Quinoline Hybrids as Novel 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:5587-5596. [PMID: 26006257 DOI: 10.1021/acs.jafc.5b01530] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27, HPPD) is one of the most important targets for herbicide discovery. In the search for new HPPD inhibitors with novel scaffolds, triketone-quinoline hybrids were designed and subsequently optimized on the basis of the structure-activity relationship (SAR) studies. Most of the synthesized compounds displayed potent inhibition of Arabidopsis thaliana HPPD (AtHPPD), and some of them exhibited broad-spectrum and promising herbicidal activity at the rate of 150 g ai/ha by postemergence application. Most promisingly, compound III-l, 3-hydroxy-2-(2-methoxy-7-(methylthio)quinoline-3-carbonyl)cyclohex-2-enone (Ki = 0.009 μM, AtHPPD), had broader spectrum of weed control than mesotrione. Furthermore, compound III-l was much safer to maize at the rate of 150 g ai/ha than mesotrione, demonstrating its great potential as herbicide for weed control in maize fields. Therefore, triketone-quinoline hybrids may serve as new lead structures for novel herbicide discovery.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Guang-Fu Yang
- ‡Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 30071, People's Republic of China
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Osteoarticular cells tolerate short-term exposure to nitisinone—implications in alkaptonuria. Clin Rheumatol 2015; 35:513-6. [DOI: 10.1007/s10067-015-2983-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 05/19/2015] [Accepted: 05/23/2015] [Indexed: 11/25/2022]
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123
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Abstract
Nitisinone 2-(2-nitro-4-trifluoromethylbenzoyl)cyclohexane-1,3-dione (NTBC), an effective herbicide, is the licensed treatment for the human condition, hereditary tyrosinaemia type 1 (HT-1). Its mode of action interrupts tyrosine metabolism through inhibition of 4-hydroxyphenylpyruvate dioxygenase (HPPD). Nitisinone is a remarkable safe drug to use with few side effects reported. Therefore, we propose that it should be investigated as a potential treatment for other disorders of tyrosine metabolism. These include alkaptonuria (AKU), a rare disease resulting is severe, early-onset osteoarthritis. We present a case study from the disease, and attempts to use the drug both off-label and in clinical research through the DevelopAKUre consortium.
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Transcriptome and Proteome Expression Analysis of the Metabolism of Amino Acids by the Fungus Aspergillus oryzae in Fermented Soy Sauce. BIOMED RESEARCH INTERNATIONAL 2015; 2015:456802. [PMID: 25945335 PMCID: PMC4405012 DOI: 10.1155/2015/456802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/07/2015] [Accepted: 01/18/2015] [Indexed: 11/17/2022]
Abstract
Amino acids comprise the majority of the flavor compounds in soy sauce. A portion of these amino acids are formed from the biosynthesis and metabolism of the fungus Aspergillus oryzae; however, the metabolic pathways leading to the formation of these amino acids in A. oryzae remain largely unknown. We sequenced the transcriptomes of A. oryzae 100-8 and A. oryzae 3.042 under similar soy sauce fermentation conditions. 2D gel electrophoresis was also used to find some differences in protein expression. We found that many amino acid hydrolases (endopeptidases, aminopeptidases, and X-pro-dipeptidyl aminopeptidase) were expressed at much higher levels (mostly greater than double) in A. oryzae 100-8 than in A. oryzae 3.042. Our results indicated that glutamate dehydrogenase may activate the metabolism of amino acids. We also found that the expression levels of some genes changed simultaneously in the metabolic pathways of tyrosine and leucine and that these conserved genes may modulate the function of the metabolic pathway. Such variation in the metabolic pathways of amino acids is important as it can significantly alter the flavor of fermented soy sauce.
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125
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Takeshige Y, Egami Y, Wakimoto T, Abe I. Production of indole antibiotics induced by exogenous gene derived from sponge metagenomes. MOLECULAR BIOSYSTEMS 2015; 11:1290-4. [PMID: 25828760 DOI: 10.1039/c5mb00131e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sponge metagenomes are accessible genetic sources containing genes and gene clusters responsible for the biosynthesis of sponge-derived bioactive natural products. In this study, we obtained the clone pDC112, producing turbomycin A and 2,2-di(3-indolyl)-3-indolone, based on the functional screening of the metagenome library derived from the marine sponge Discodermia calyx. The subcloning experiment identified ORF 25, which is homologous to inosine 5'-monophosphate dehydrogenase and required for the production of 2,2-di(3-indolyl)-3-indolone in Escherichia coli.
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Affiliation(s)
- Yuya Takeshige
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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Identification and molecular characterization of the homogentisate pathway responsible for pyomelanin production, the major melanin constituents in Aeromonas media WS. PLoS One 2015; 10:e0120923. [PMID: 25793756 PMCID: PMC4368426 DOI: 10.1371/journal.pone.0120923] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/27/2015] [Indexed: 11/19/2022] Open
Abstract
The pigmentation of many Aeromonas species has been thought to be due to the production of a L-DOPA (L-3,4-dihydroxyphenylalanine) based melanin. However, in this study we found that although L-DOPA synthesis occurs in the high-melanin-yielding Aeromonas media strain WS, it plays a minor, if any, role in pigmentation. Instead, the pigmentation of A. media strain WS is due to the production of pyomelanin through HGA (homogentisate). Gene products of phhA (encodes phenylalanine hydroxylase), tyrB and aspC (both encode aromatic amino acid aminotransferase), and hppD (encodes 4-hydroxyphenylpyruvate dioxygenase) constitute a linear pathway of converting phenylalanine to HGA and disruption of any one of these genes impairs or blocks pigmentation of A. media strain WS. This HGA biosynthesis pathway is widely distributed in Aeromonas, but HGA is only detectable in the cultures of pigmented Aeromonas species. Heterologous expression of HppD from both pigmented and non-pigmented Aeromonas species in E. coli leads to the production of pyomelanin and thus pigmentation, suggesting that most Aeromonas species have the critical enzymes to produce pyomelanin through HGA. Taken together, we have identified a widely conserved biosynthesis pathway of HGA based pyomelanin in Aeromonas that may be responsible for pigmentation of many Aeromonas species.
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Synthesis and bioevaluation of pyrazole-benzimidazolone hybrids as novel human 4-Hydroxyphenylpyruvate dioxygenase inhibitors. Eur J Med Chem 2015; 92:427-38. [DOI: 10.1016/j.ejmech.2015.01.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/09/2015] [Accepted: 01/09/2015] [Indexed: 11/19/2022]
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128
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Salerno C, Zicari A, Mari E, D'Eufemia P. Scavenging properties of neutrophil 4-hydroxyphenylpyruvate dioxygenase are based on a hypothesis that does not stand up to scrutiny. Biomed Pharmacother 2014; 68:1045-8. [PMID: 25443415 DOI: 10.1016/j.biopha.2014.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 09/09/2014] [Indexed: 11/28/2022] Open
Abstract
It was previously reported by D'Eufemia et al. [9] that neutrophil preparations from a patient with tyrosinemia type III, i.e. with inherited deficiency of 4-hydroxyphenylpyruvate dioxygenase (HPPD), exhibited a far higher NO release than controls, when NO was estimated in terms of nitrite content in the suspending media. It was hypothesized that HPPD might participate to NO sequestration in neutrophils and that excessive NO release might reflect the lack of the scavenging action in defective cells. In recent control experiments, we found that HPPD activity in neutrophils preparations from healthy subjects is below the detection limit of the enzymatic assay (less than 3nmol product/h per mg protein). This indicates that HPPD concentration in neutrophils is very low, if any, confirming what was already suggested in literature, and rules out the possibility of a prominent role of HPPD as NO scavenger in these cells. Moreover, we found that 500μM l-tyrosine increases nitrite release and accumulation in suspending media of U-937 cells, a human monoblast-like lymphoma cell line which displays many characteristics of macrophages, including the expression of inducible and endothelial nitric oxide synthases. We hypothesize that the increase of nitrite release by patient's neutrophils might be related to the presence of high l-tyrosine concentrations in the blood samples (426μmol/L instead of 52.1±10.9μmol/L as healthy subjects), rather than to HPPD deficiency of in these cells.
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Affiliation(s)
- Costantino Salerno
- Department of Biochemical Sciences, University of Roma La Sapienza, 00161 Rome, Italy.
| | - Alessandra Zicari
- Department of Experimental Medicine, University of Roma La Sapienza, 00161 Rome, Italy
| | - Emanuela Mari
- Department of Experimental Medicine, University of Roma La Sapienza, 00161 Rome, Italy
| | - Patrizia D'Eufemia
- Department of Pediatrics, University of Roma La Sapienza, 00161 Rome, Italy
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Efficient synthesis of fused bicyclic ethers and their application in herbicide chemistry. Bioorg Med Chem Lett 2014; 24:4643-4649. [DOI: 10.1016/j.bmcl.2014.08.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/14/2014] [Accepted: 08/20/2014] [Indexed: 11/19/2022]
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130
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Wójcik A, Broclawik E, Siegbahn PEM, Lundberg M, Moran G, Borowski T. Role of Substrate Positioning in the Catalytic Reaction of 4-Hydroxyphenylpyruvate Dioxygenase—A QM/MM Study. J Am Chem Soc 2014; 136:14472-85. [DOI: 10.1021/ja506378u] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anna Wójcik
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland
- Department
of Computational Biophysics and Bioinformatics, Faculty of Biochemistry,
Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Cracow, Poland
| | - Ewa Broclawik
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland
| | - Per E. M. Siegbahn
- Department
of Organic Chemistry, Stockholm University, S-106 91, Stockholm, Sweden
| | - Marcus Lundberg
- Ångstrom
Laboratory, Department of Chemistry, Uppsala University, Box 518, SE-751 20 Uppsala, Sweden
| | - Graham Moran
- Department
of Chemistry and Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211-3209, United States
| | - Tomasz Borowski
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland
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Xu YL, Lin HY, Cao RJ, Ming ZZ, Yang WC, Yang GF. Pyrazolone-quinazolone hybrids: a novel class of human 4-hydroxyphenylpyruvate dioxygenase inhibitors. Bioorg Med Chem 2014; 22:5194-211. [PMID: 25182962 DOI: 10.1016/j.bmc.2014.08.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 08/07/2014] [Accepted: 08/08/2014] [Indexed: 10/24/2022]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD), converting 4-hydroxyphenylpyruvate acid to homogentisate, is an important target for treating type I tyrosinemia and alkaptonuria due to its significant role in tyrosine catabolism. However, only one commercial drug, NTBC, also known as nitisinone, has been available for clinical use so far. Herein, we have elucidated the structure-based design of a series of pyrazolone-quinazolone hybrids that are novel potent human HPPD inhibitors through the successful integration of various techniques including computational simulations, organic synthesis, and biochemical characterization. Most of the new compounds displayed potent inhibitory activity against the recombinant human HPPD in nanomolar range. Compounds 3h and 3u were identified as the most potent candidates with Ki values of around 10 nM against human HPPD, about three-fold more potent than NTBC. Molecular modeling indicated that the interaction between the pyrazolone ring and ferrous ion, and the hydrophobic interaction of quinazolone with its surrounding residues, such as Phe347 and Phe364, contributed greatly to the high potency of these inhibitors. Therefore, compounds 3h and 3u could be potentially useful for the treatment of type I tyrosinemia and other diseases with defects in tyrosine degradation.
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Affiliation(s)
- Yu-Ling Xu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Hong-Yan Lin
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Run-Jie Cao
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Ze-Zhong Ming
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Wen-Chao Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China.
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 30071, PR China.
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132
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Ma HJ, Zhang JH, Xia XD, Xu MH, Ning J, Li JH. Design, synthesis and herbicidal activities of novel 4-(1H-pyrazol-1-yl)-6-(alkynyloxy)-pyrimidine derivatives as potential pigment biosynthesis inhibitors. PEST MANAGEMENT SCIENCE 2014; 70:946-952. [PMID: 23966363 DOI: 10.1002/ps.3633] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 07/18/2013] [Accepted: 08/21/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND With the objective of finding novel valuable herbicidal candidates, a series of novel 4-(1H-pyrazol-1-yl)-6-(alkynyloxy)-pyrimidine derivatives were synthesised and their herbicide activities were evaluated in vivo. RESULTS The results showed that many target compounds expressed bleaching activities. Among these, compound 5 h showed the best bleaching activity to gramineous weeds, being able to produce the highest inhibition of chlorophyll level in seedlings of Pennisetum alopecuroides L. (IC50 = 3.48 mg L(-1) ). Moreover, compound 5 h expressed good selective toxicity between gramineous P. alopecuroides L. and broadleaf plant Brassica campestris L. CONCLUSIONS The present work demonstrates that pyrimidine derivatives containing pyrazole can be used as potential lead compounds for developing novel pigment biosynthesis inhibitors.
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Affiliation(s)
- Hong-Ju Ma
- Department of Plant Protection, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
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133
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Zou XW, Liu YC, Hsu NS, Huang CJ, Lyu SY, Chan HC, Chang CY, Yeh HW, Lin KH, Wu CJ, Tsai MD, Li TL. Structure and mechanism of a nonhaem-iron SAM-dependent C-methyltransferase and its engineering to a hydratase and an O-methyltransferase. ACTA ACUST UNITED AC 2014; 70:1549-60. [PMID: 24914966 DOI: 10.1107/s1399004714005239] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/06/2014] [Indexed: 12/16/2022]
Abstract
In biological systems, methylation is most commonly performed by methyltransferases (MTs) using the electrophilic methyl source S-adenosyl-L-methionine (SAM) via the S(N)2 mechanism. (2S,3S)-β-Methylphenylalanine, a nonproteinogenic amino acid, is a building unit of the glycopeptide antibiotic mannopeptimycin. The gene product of mppJ from the mannopeptimycin-biosynthetic gene cluster is the MT that methylates the benzylic C atom of phenylpyruvate (Ppy) to give βMePpy. Although the benzylic C atom of Ppy is acidic, how its nucleophilicity is further enhanced to become an acceptor for C-methylation has not conclusively been determined. Here, a structural approach is used to address the mechanism of MppJ and to engineer it for new functions. The purified MppJ displays a turquoise colour, implying the presence of a metal ion. The crystal structures reveal MppJ to be the first ferric ion SAM-dependent MT. An additional four structures of binary and ternary complexes illustrate the molecular mechanism for the metal ion-dependent methyltransfer reaction. Overall, MppJ has a nonhaem iron centre that bind, orients and activates the α-ketoacid substrate and has developed a sandwiched bi-water device to avoid the formation of the unwanted reactive oxo-iron(IV) species during the C-methylation reaction. This discovery further prompted the conversion of the MT into a structurally/functionally unrelated new enzyme. Through stepwise mutagenesis and manipulation of coordination chemistry, MppJ was engineered to perform both Lewis acid-assisted hydration and/or O-methyltransfer reactions to give stereospecific new compounds. This process was validated by six crystal structures. The results reported in this study will facilitate the development and design of new biocatalysts for difficult-to-synthesize biochemicals.
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Affiliation(s)
- Xiao-Wei Zou
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Chen Liu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ning-Shian Hsu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | | | - Syue-Yi Lyu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsiu-Chien Chan
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chin-Yuan Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsien-Wei Yeh
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chang-Jer Wu
- Department of Food Science, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Ming-Daw Tsai
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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134
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Rocaboy-Faquet E, Noguer T, Romdhane S, Bertrand C, Dayan FE, Barthelmebs L. Novel bacterial bioassay for a high-throughput screening of 4-hydroxyphenylpyruvate dioxygenase inhibitors. Appl Microbiol Biotechnol 2014; 98:7243-52. [PMID: 24816780 DOI: 10.1007/s00253-014-5793-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/11/2014] [Accepted: 04/23/2014] [Indexed: 10/25/2022]
Abstract
Plant 4-hydroxyphenylpyruvate dioxygenase (HPPD) is the molecular target of a range of synthetic β-triketone herbicides that are currently used commercially. Their mode of action is based on an irreversible inhibition of HPPD. Therefore, this inhibitory capacity was used to develop a whole-cell colorimetric bioassay with a recombinant Escherichia coli expressing a plant HPPD for the herbicide analysis of β-triketones. The principle of the bioassay is based on the ability of the recombinant E. coli clone to produce a soluble melanin-like pigment, from tyrosine catabolism through p-hydroxyphenylpyruvate and homogentisate. The addition of sulcotrione, a HPPD inhibitor, decreased the pigment production. With the aim to optimize the assay, the E. coli recombinant clone was immobilized in sol-gel or agarose matrix in a 96-well microplate format. The limit of detection for mesotrione, tembotrione, sulcotrione, and leptospermone was 0.069, 0.051, 0.038, and 20 μM, respectively, allowing to validate the whole-cell colorimetric bioassay as a simple and cost-effective alternative tool for laboratory use. The bioassay results from sulcotrione-spiked soil samples were confirmed with high-performance liquid chromatography.
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Affiliation(s)
- Emilie Rocaboy-Faquet
- Institut de Modélisation et d'Analyse en Géo-Environnement et Santé, Université Perpignan Via Domitia, EA 4218, 66860, Perpignan, France
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135
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Structural and functional characterization of 4-hydroxyphenylpyruvate dioxygenase from the thermoacidophilic archaeon Picrophilus torridus. Extremophiles 2014; 18:641-51. [PMID: 24794033 DOI: 10.1007/s00792-014-0645-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 04/13/2014] [Indexed: 10/25/2022]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (Hpd, EC 1.13.11.27) catalyzes the conversion of 4-hydroxyphenylpyruvate into homogentisate in the second step of oxidative tyrosine catabolism. This pathway is known from bacteria and eukaryotes, but so far no archaeal Hpd has been described. Here, we report the biochemical characterization of an Hpd from the extremophilic archaeon Picrophilus torridus (Pt_Hpd), together with its three-dimensional structure at a resolution of 2.6 Å. Two pH optima were observed at 50 °C: pH 4.0 (close to native conditions) and pH 7.0. The enzyme showed only moderate thermostability and was inactivated with a half-life of ~1.5 h even under optimal reaction conditions. At the ideal physiological growth conditions of P. torridus, Pt_Hpd was inactive after 1 h, showing that the enzyme is protected in vivo from denaturation and/or is only partially adapted to the harsh environmental conditions in the cytosol of P. torridus. The influence of different additives on the activity was investigated. Pt_Hpd exhibited a turnover number k(cat) of 9.9 ± 0.6 s(-1) and a substrate binding affinity K(m) of 142 ± 23 µM. In addition, substrate inhibition with a binding affinity K(i) of 1.9 ± 0.3 mM was observed. Pt_Hpd is compared with isoenzymes from other species and the putative bacterial origin of the gene is discussed.
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136
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Kramer CM, Launis KL, Traber MG, Ward DP. Vitamin E levels in soybean (Glycine max (L.) Merr.) expressing a p-hydroxyphenylpyruvate gene from oat (Avena sativa L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:3453-7. [PMID: 24684596 DOI: 10.1021/jf4048995] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The enzyme p-hydroxyphenylpyruvate dioxygenase (HPPD) is ubiquitous in plants and functions in the tyrosine catabolic pathway, resulting in the formation of homogentisate. Homogentisate is the aromatic precursor of all plastoquinones and tocochromanols, including tocopherols and tocotrienols. Soybean (Glycine max (L.) Merr.) has been genetically modified to express the gene avhppd-03 that encodes the protein AvHPPD-03 derived from oat (Avena sativa L.). The AvHPPD-03 isozyme has an inherent reduced binding affinity for mesotrione, a herbicide that inhibits the wild-type soybean HPPD enzyme. Expression of avhppd-03 in soybean plants confers a mesotrione-tolerant phenotype. Seeds from three different avhppd-03-expressing soybean events were quantitatively assessed for content of eight vitamin E isoforms. Although increased levels of two tocopherol isoforms were identified for each of the three soybean events, they were within, or not substantially different from, the ranges of these isoforms found in nontransgenic soybean varieties. The increases of these tocopherols in the avhppd-03-expressing soybean events may have a slight benefit with regard to vitamin E nutrition but, given the commercial processing of soybeans, are unlikely to have a material impact on human nutrition with regard to vitamin E concentrations in soybean oil.
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Affiliation(s)
- Catherine M Kramer
- Syngenta Crop Protection, LLC, 3054 Cornwallis Road, Research Triangle Park, North Carolina 27709, United States
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137
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Karlsen OA, Sheehan D, Goksøyr A. Alterations in the Atlantic cod (Gadus morhua) hepatic thiol-proteome after methylmercury exposure. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2014; 77:650-662. [PMID: 24754398 DOI: 10.1080/15287394.2014.887427] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Proteomic studies in general have demonstrated that the most effective and thorough analysis of biological samples requires subfractionation and/or enrichment prior to downstream processing. In the present study, Atlantic cod (Gadus morhua) liver samples were fractionated using activated thiol sepharose to isolate hepatic proteins containing free/reactive cysteines. This subset of proteins is of special interest when studying the physiological effects attributed to methylmercury (MeHg) exposure. Methylmercury is a persistent environmental contaminant that has a potent affinity toward thiol groups, and can directly bind proteins via available cysteine residues. Further, alterations in the cod thiol-proteome following MeHg exposure (2 mg/kg body weight) were explored with two-dimensional gel electrophoresis combined with downstream mass spectrometry analyses for protein identifications. Thirty-five protein spots were found to respond to MeHg exposure, and 13 of these were identified when searching cod-specific databases with acquired mass spectrometry data. Among the identified thiol-containing proteins, some are known to respond to MeHg treatment, including constituents of the cytoskeleton, and proteins involved in oxidative stress responses, protein synthesis, protein folding, and energy metabolism. Methylmercury also appeared to affect cod heme metabolism/turnover, producing significantly altered levels of hemoglobin and hemopexin in liver following metal exposure. The latter finding suggests that MeHg may also affect the hematological system in Atlantic cod.
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Affiliation(s)
- O A Karlsen
- a Department of Biology , University of Bergen , Bergen , Norway
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138
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Borowski T, Broclawik E. Bioinorganic Reaction Mechanisms – Quantum Chemistry Approach. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/978-3-642-28554-7_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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139
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Carbon-flux distribution within Streptomyces coelicolor metabolism: a comparison between the actinorhodin-producing strain M145 and its non-producing derivative M1146. PLoS One 2013; 8:e84151. [PMID: 24376790 PMCID: PMC3871631 DOI: 10.1371/journal.pone.0084151] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 11/19/2013] [Indexed: 01/12/2023] Open
Abstract
Metabolic Flux Analysis is now viewed as essential to elucidate the metabolic pattern of cells and to design appropriate genetic engineering strategies to improve strain performance and production processes. Here, we investigated carbon flux distribution in two Streptomyces coelicolor A3 (2) strains: the wild type M145 and its derivative mutant M1146, in which gene clusters encoding the four main antibiotic biosynthetic pathways were deleted. Metabolic Flux Analysis and (13)C-labeling allowed us to reconstruct a flux map under steady-state conditions for both strains. The mutant strain M1146 showed a higher growth rate, a higher flux through the pentose phosphate pathway and a higher flux through the anaplerotic phosphoenolpyruvate carboxylase. In that strain, glucose uptake and the flux through the Krebs cycle were lower than in M145. The enhanced flux through the pentose phosphate pathway in M1146 is thought to generate NADPH enough to face higher needs for biomass biosynthesis and other processes. In both strains, the production of NADPH was higher than NADPH needs, suggesting a key role for nicotinamide nucleotide transhydrogenase for redox homeostasis. ATP production is also likely to exceed metabolic ATP needs, indicating that ATP consumption for maintenance is substantial.Our results further suggest a possible competition between actinorhodin and triacylglycerol biosynthetic pathways for their common precursor, acetyl-CoA. These findings may be instrumental in developing new strategies exploiting S. coelicolor as a platform for the production of bio-based products of industrial interest.
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140
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Chaudhary N, Khurana P. Cloning, functional characterisation and transgenic manipulation of vitamin E biosynthesis genes of wheat. FUNCTIONAL PLANT BIOLOGY : FPB 2013; 40:1129-1136. [PMID: 32481180 DOI: 10.1071/fp12265] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 05/20/2013] [Indexed: 06/11/2023]
Abstract
Tocochromanols are an important group of plastidic lipophilic antioxidants that form an essential part of human diet and play important functions in photosynthetic organisms by protecting them from photo-oxidation, lipid peroxidation and membrane damage. Molecular genetics and genomics-based approaches have revealed the genes required for synthesis of these compounds in model organisms like rice, Arabidopsis and Synechocystis. To create a positive impact on human nutrition and health, the levels of total and specific tocochromanols have been altered in various agricultural crops by metabolic engineering. To understand the mechanisms involved in higher tocochromanol levels of wheat seeds and its germ, the tocochromanol biosynthesis pathway was investigated in wheat. The focus of this research was towards isolation of genes involved in wheat tocochromanol biosynthesis, and homologous and heterologous transgenic manipulation to alter their content and composition. Functional characterisation of TaHydroxyphenylpyruvate dioxygenase and Taγ-Tocopherol methyltransferase-overexpressing transgenic Arabidopsis plants revealed alterations in tocochromanol content and composition, which suggests better growth of these plants in the presence of sorbitol. TaHydroxyphenylpyruvate dioxygenase-overexpressing transgenic wheat, Triticum aestivum L. plants also showed 2.4-fold increase in tocochromanol content, which may have nutritional as well as antioxidative roles. Further characterisation and field trials of these transgenic lines can provide us more insight about the antioxidative roles of tocochromanols.
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Affiliation(s)
- Neetu Chaudhary
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi-110021, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi-110021, India
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141
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Oliveira MVD, Oliveira ACDF, Shida CS, Oliveira RCD, Nunes LR. Gene expression modulation by paraquat-induced oxidative stress conditions in Paracoccidioides brasiliensis. Fungal Genet Biol 2013; 60:101-9. [DOI: 10.1016/j.fgb.2013.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 04/29/2013] [Accepted: 05/18/2013] [Indexed: 01/06/2023]
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142
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Lin JF, Sheih YL, Chang TC, Chang NY, Chang CW, Shen CP, Lee HJ. The interactions in the carboxyl terminus of human 4-hydroxyphenylpyruvate dioxygenase are critical to mediate the conformation of the final helix and the tail to shield the active site for catalysis. PLoS One 2013; 8:e69733. [PMID: 23950902 PMCID: PMC3739788 DOI: 10.1371/journal.pone.0069733] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 06/12/2013] [Indexed: 11/18/2022] Open
Abstract
4-Hydroxylphenylpyruvate dioxygenase (4-HPPD) is an important enzyme for tyrosine catabolism, which catalyzes the conversion of 4-hydroxylphenylpyruvate (4-HPP) to homogentisate. In the present study, human 4-HPPD was cloned and expressed in E. coli. The kinetic parameters for 4-HPP conversion were: k cat=2.2 ± 0.1 s(-1); and K m=0.08 ± 0.02 mM. Sequence alignments show that human 4-HPPD possesses an extended C-terminus compared to other 4-HPPD enzymes. Successive truncation of the disordered tail which follows the final α-helix resulted in no changes in the K m value for 4-HPP substrate but the k cat values were significantly reduced. The results suggest that this disordered C-terminal tail plays an important role in catalysis. For inspection the effect of terminal truncation on protein structure, mutant models were built. These models suggest that the different conformation of E254, R378 and Q375 in the final helix might be the cause of the activity loss. In the structure E254 interacts with R378, the end residue in the final helix; mutation of either one of these residues causes a ca. 95% reductions in k cat values. Q375 provides bifurcate interactions to fix the tail and the final helix in position. The model of the Q375N mutant shows that a solvent accessible channel opens to the putative substrate binding site, suggesting this is responsible for the complete loss of activity. These results highlight the critical role of Q375 in orientating the tail and ensuring the conformation of the terminal α-helix to maintain the integrity of the active site for catalysis.
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Affiliation(s)
- Jang-Foung Lin
- Department of Biochemistry, National Defense Medical Center, Neihu, Taipei, Taiwan
| | - Yung-Lin Sheih
- Department of Biochemistry, National Defense Medical Center, Neihu, Taipei, Taiwan
| | - Tsu-Chung Chang
- Department of Biochemistry, National Defense Medical Center, Neihu, Taipei, Taiwan
| | - Ni-Yuan Chang
- Department of Biochemistry, National Defense Medical Center, Neihu, Taipei, Taiwan
| | - Chiung-Wen Chang
- Department of Biochemistry, National Defense Medical Center, Neihu, Taipei, Taiwan
| | - Chia-Pei Shen
- Department of Biochemistry, National Defense Medical Center, Neihu, Taipei, Taiwan
| | - Hwei-Jen Lee
- Department of Biochemistry, National Defense Medical Center, Neihu, Taipei, Taiwan
- * E-mail:
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143
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Gene expression in human fungal pathogen Coccidioides immitis changes as arthroconidia differentiate into spherules and mature. BMC Microbiol 2013; 13:121. [PMID: 23714098 PMCID: PMC3693894 DOI: 10.1186/1471-2180-13-121] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 05/20/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coccidioides immitis is a dimorphic fungus that causes disease in mammals, including human beings. It grows as a mycelium containing arthroconidia in the soil and in the host arthroconidia differentiates into a unique structure called a spherule. We used a custom open reading frame oligonucleotide microarray to compare the transcriptome of C. immitis mycelia with early (day 2) and late stage (day 8) spherules grown in vitro. All hybridizations were done in quadruplicate and stringent criteria were used to identify significantly differentially expressed genes. RESULTS 22% of C. immitis genes were differentially expressed in either day 2 or day 8 spherules compared to mycelia, and about 12% of genes were differentially expressed comparing the two spherule time points. Oxireductases, including an extracellular superoxide dismutase, were upregulated in spherules and they may be important for defense against oxidative stress. Many signal transduction molecules, including pleckstrin domain proteins, protein kinases and transcription factors were downregulated in day 2 spherules. Several genes involved in sulfur metabolism were downregulated in day 8 spherules compared to day 2 spherules. Transcription of amylase and α (1,3) glucan synthase was upregulated in spherules; these genes have been found to be important for differentiation to yeast in Histoplasma. There were two homologs of 4-hydroxyphenylpyruvate dioxygenase (4-HPPD); transcription of one was up- and the other downregulated. We tested the effect of a 4-HPPD inhibitor, nitisinone, on mycelial and spherule growth and found that it inhibited mycelial but not spherule growth. CONCLUSIONS Transcription of many genes was differentially expressed in the process of arthroconidia to spherule conversion and spherule maturation, as would be expected given the magnitude of the morphologic change. The transcription profile of early stage (day 2) spherules was different than late stage (day 8) endosporulating spherules. In addition, very few genes that are important for spore to yeast conversion in other dimorphic fungi are differentially expressed in C. immitis mycelia and spherules suggesting that dimorphic fungi may have evolved different mechanisms to differentiate from mycelia to tissue invasive forms.
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144
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Lundberg M, Borowski T. Oxoferryl species in mononuclear non-heme iron enzymes: Biosynthesis, properties and reactivity from a theoretical perspective. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.03.047] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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145
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Wójcik A, Broclawik E, Siegbahn PEM, Borowski T. Mechanism of benzylic hydroxylation by 4-hydroxymandelate synthase. A computational study. Biochemistry 2012; 51:9570-80. [PMID: 23126679 DOI: 10.1021/bi3010957] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxymandelate synthase (HMS) and 4-hydroxyphenylpyruvate dioxygenase (HPPD) are highly related enzymes using the same substrates but catalyzing hydroxylation reactions yielding different products. The first steps of the HMS and HPPD catalytic reactions are believed to proceed in the same way and lead to an Fe(IV)═O-hydroxyphenylacetate (HPA) intermediate. Further down the catalytic cycles, HMS uses Fe(IV)═O to perform hydroxylation of the benzylic carbon, whereas in HPPD, the reactive oxoferryl intermediate attacks the aromatic ring of HPA. This study focuses on this part of the HMS catalytic cycle that starts from the oxoferryl intermediate and aims to identify interactions within the active site that are responsible for enzyme specificity. To this end, a HMS-Fe(IV)═O-HPA complex was modeled with molecular dynamics simulations. On the basis of the molecular dynamics-equilibrated structure, an active site model suitable for quantum chemical investigations was constructed and used for density functional theory (B3LYP) calculations of the mechanism of the native reaction of HMS, i.e., benzylic hydroxylation, and the alternative electrophilic attack on the ring, which is a step of the HPPD catalytic cycle. The most important result of this study is the finding that the conformation of the Ser201 side chain in the second coordination shell has a key role in directing the reaction of Fe(IV)═O into either the HMS or the HPPD channel.
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Affiliation(s)
- Anna Wójcik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland
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146
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Effects of maternal worm infections and anthelminthic treatment during pregnancy on infant motor and neurocognitive functioning. J Int Neuropsychol Soc 2012; 18:1019-30. [PMID: 23158229 PMCID: PMC3948080 DOI: 10.1017/s1355617712000768] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We tested the hypothesis that maternal worm infections in pregnancy affect infant motor and neurocognitive development, and that anthelminthic treatment during pregnancy can reverse these effects. We used measures which examine infant motor, cognitive and executive function, including inhibition. We assessed 983 Ugandan infants aged 15 months, using locally appropriate measures within the Entebbe Mother and Baby Study, a trial of anthelminthic treatment during pregnancy. Key exposures were maternal worm infections and anthelminthic treatment during pregnancy. Effects of other health and social factors were controlled for statistically. Of the five major worm species found in the pregnant women, two had influences on the developmental measures: Maternal Mansonella perstans and Strongyloides stercoralis infections showed negative associations with the A-not B-task, and Language, respectively. Performance on other psychomotor and cognitive measures was associated with illnesses during infancy and infants' behavior during assessment, but not with maternal worm infections. There were no positive effects of maternal anthelminthic treatment on infant abilities. Mansonella perstans and Strongyloides stercoralis infection during pregnancy seem associated with impaired early executive function and language, respectively, but single-dose anthelminthic treatment during pregnancy was not beneficial. The biological mechanisms that could underlie these neurocognitive effects are discussed.
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147
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Fan L, Reynolds D, Liu M, Stark M, Kjelleberg S, Webster NS, Thomas T. Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts. Proc Natl Acad Sci U S A 2012; 109:E1878-87. [PMID: 22699508 PMCID: PMC3390844 DOI: 10.1073/pnas.1203287109] [Citation(s) in RCA: 236] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Microorganisms often form symbiotic relationships with eukaryotes, and the complexity of these relationships can range from those with one single dominant symbiont to associations with hundreds of symbiont species. Microbial symbionts occupying equivalent niches in different eukaryotic hosts may share functional aspects, and convergent genome evolution has been reported for simple symbiont systems in insects. However, for complex symbiont communities, it is largely unknown how prevalent functional equivalence is and whether equivalent functions are conducted by evolutionarily convergent mechanisms. Sponges represent an evolutionarily divergent group of species with common physiological and ecological traits. They also host complex communities of microbial symbionts and thus are the ideal model to test whether functional equivalence and evolutionary convergence exist in complex symbiont communities across phylogenetically divergent hosts. Here we use a sampling design to determine the phylogenetic and functional profiles of microbial communities associated with six sponge species. We identify common functions in the six microbiomes, demonstrating the existence of functional equivalence. These core functions are consistent with our current understanding of the biological and ecological roles of sponge-associated microorganisms and also provide insight into symbiont functions. Importantly, core functions also are provided in each sponge species by analogous enzymes and biosynthetic pathways. Moreover, the abundance of elements involved in horizontal gene transfer suggests their key roles in the genomic evolution of symbionts. Our data thus demonstrate evolutionary convergence in complex symbiont communities and reveal the details and mechanisms that underpin the process.
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Affiliation(s)
- Lu Fan
- School of Biotechnology and Biomolecular Sciences and
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - David Reynolds
- School of Biotechnology and Biomolecular Sciences and
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Michael Liu
- School of Biotechnology and Biomolecular Sciences and
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Manuel Stark
- Institute of Molecular Life Sciences and
- Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Staffan Kjelleberg
- School of Biotechnology and Biomolecular Sciences and
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, New South Wales 2052, Australia
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Republic of Singapore; and
| | - Nicole S. Webster
- Australian Institute of Marine Science, Townsville, Queensland 4810, Australia
| | - Torsten Thomas
- School of Biotechnology and Biomolecular Sciences and
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, New South Wales 2052, Australia
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148
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Zhao G, Hou L, Yao Y, Wang C, Cao X. Comparative proteome analysis of Aspergillus oryzae 3.042 and A. oryzae 100–8 strains: Towards the production of different soy sauce flavors. J Proteomics 2012; 75:3914-24. [DOI: 10.1016/j.jprot.2012.04.056] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 04/28/2012] [Accepted: 04/28/2012] [Indexed: 01/08/2023]
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149
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Li T, Huo L, Pulley C, Liu A. Decarboxylation mechanisms in biological system. Bioorg Chem 2012; 43:2-14. [PMID: 22534166 DOI: 10.1016/j.bioorg.2012.03.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 03/04/2012] [Accepted: 03/19/2012] [Indexed: 11/30/2022]
Abstract
This review examines the mechanisms propelling cofactor-independent, organic cofactor-dependent and metal-dependent decarboxylase chemistry. Decarboxylation, the removal of carbon dioxide from organic acids, is a fundamentally important reaction in biology. Numerous decarboxylase enzymes serve as key components of aerobic and anaerobic carbohydrate metabolism and amino acid conversion. In the past decade, our knowledge of the mechanisms enabling these crucial decarboxylase reactions has continued to expand and inspire. This review focuses on the organic cofactors biotin, flavin, NAD, pyridoxal 5'-phosphate, pyruvoyl, and thiamin pyrophosphate as catalytic centers. Significant attention is also placed on the metal-dependent decarboxylase mechanisms.
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Affiliation(s)
- Tingfeng Li
- Department of Biochemistry, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA
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150
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Kastner S, Müller S, Natesan L, König GM, Guthke R, Nett M. 4-Hydroxyphenylglycine biosynthesis in Herpetosiphon aurantiacus: a case of gene duplication and catalytic divergence. Arch Microbiol 2012; 194:557-66. [DOI: 10.1007/s00203-012-0789-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 12/09/2011] [Accepted: 12/22/2011] [Indexed: 12/25/2022]
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