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Kamoshita M, Kumar R, Anteghini M, Kunze M, Islinger M, Martins dos Santos V, Schrader M. Insights Into the Peroxisomal Protein Inventory of Zebrafish. Front Physiol 2022; 13:822509. [PMID: 35295584 PMCID: PMC8919083 DOI: 10.3389/fphys.2022.822509] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/07/2022] [Indexed: 12/19/2022] Open
Abstract
Peroxisomes are ubiquitous, oxidative subcellular organelles with important functions in cellular lipid metabolism and redox homeostasis. Loss of peroxisomal functions causes severe disorders with developmental and neurological abnormalities. Zebrafish are emerging as an attractive vertebrate model to study peroxisomal disorders as well as cellular lipid metabolism. Here, we combined bioinformatics analyses with molecular cell biology and reveal the first comprehensive inventory of Danio rerio peroxisomal proteins, which we systematically compared with those of human peroxisomes. Through bioinformatics analysis of all PTS1-carrying proteins, we demonstrate that D. rerio lacks two well-known mammalian peroxisomal proteins (BAAT and ZADH2/PTGR3), but possesses a putative peroxisomal malate synthase (Mlsl) and verified differences in the presence of purine degrading enzymes. Furthermore, we revealed novel candidate peroxisomal proteins in D. rerio, whose function and localisation is discussed. Our findings confirm the suitability of zebrafish as a vertebrate model for peroxisome research and open possibilities for the study of novel peroxisomal candidate proteins in zebrafish and humans.
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Affiliation(s)
- Maki Kamoshita
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Rechal Kumar
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Marco Anteghini
- LifeGlimmer GmbH, Berlin, Germany
- Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Markus Kunze
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Markus Islinger
- Institute of Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Vítor Martins dos Santos
- LifeGlimmer GmbH, Berlin, Germany
- Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
- *Correspondence: Michael Schrader,
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2
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Lin S, Zhang T, Zhu L, Pang K, Lu S, Liao X, Ying S, Zhu L, Xu X, Wu J, Wang X. Characteristic dysbiosis in gout and the impact of a uric acid-lowering treatment, febuxostat on the gut microbiota. J Genet Genomics 2021; 48:781-791. [PMID: 34509383 DOI: 10.1016/j.jgg.2021.06.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022]
Abstract
Gut dysbiosis is suggested to play a critical role in the pathogenesis of gout. The aim of our study was to identify the characteristic dysbiosis of the gut microbiota in gout patients and the impact of a commonly used uric acid-lowering treatment, febuxostat on gut microbiota in gout. 16S ribosomal RNA sequencing and metagenomic shotgun sequencing was performed on fecal DNA isolated from 38 untreated gout patients, 38 gout patients treated with febuxostat, and 26 healthy controls. A restriction of gut microbiota biodiversity was detected in the untreated gout patients, and the alteration was partly restored by febuxostat. Biochemical metabolic indexes involved in liver and kidney metabolism were significantly associated with the gut microbiota composition in gout patients. Functional analysis revealed that the gut microbiome of gout patients had an enriched function on carbohydrate metabolism but a lower potential for purine metabolism, which was comparatively enhanced in the febuxostat treated gout patients. A classification microbial model obtained a high mean area under the curve up to 0.973. Therefore, gut dysbiosis characterizings gout could potentially serve as a noninvasive diagnostic tool for gout and may be a promising target of future preventive interventions.
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Affiliation(s)
- Suxian Lin
- Rheumatology Department, Wenzhou People's Hospital, Wenzhou, Zhejiang 325000, China
| | - Tao Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Lingxiao Zhu
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Kun Pang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Saisai Lu
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Xin Liao
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Senhong Ying
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Lixia Zhu
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Xin Xu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325000, China.
| | - Xiaobing Wang
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China; Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China.
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3
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Najjari A, Shahbazmohammadi H, Omidinia E. Lactose inducible fermentation in Escherichia coli for improved production of recombinant urate oxidase: Optimization by statistical experimental designs. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.101943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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4
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Mirzaeinia S, Pazhang M, Imani M, Chaparzadeh N, Amani-Ghadim AR. Improving the stability of uricase from Aspergillus flavus by osmolytes: Use of response surface methodology for optimization of the enzyme stability. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.04.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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5
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Xiong XY, Liang J, Guo SY, Dai MZ, Zhou JL, Zhang Y, Liu Y. A natural complex product Yaocha reduces uric acid level in a live zebrafish model. J Pharmacol Toxicol Methods 2020; 102:106681. [DOI: 10.1016/j.vascn.2020.106681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 08/08/2019] [Accepted: 02/07/2020] [Indexed: 12/22/2022]
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6
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Crystal structure of cis-aconitate decarboxylase reveals the impact of naturally occurring human mutations on itaconate synthesis. Proc Natl Acad Sci U S A 2019; 116:20644-20654. [PMID: 31548418 PMCID: PMC6789909 DOI: 10.1073/pnas.1908770116] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
cis-Aconitate decarboxylase (CAD, also known as ACOD1 or Irg1) converts cis-aconitate to itaconate and plays central roles in linking innate immunity with metabolism and in the biotechnological production of itaconic acid by Aspergillus terreus We have elucidated the crystal structures of human and murine CADs and compared their enzymological properties to CAD from A. terreus Recombinant CAD is fully active in vitro without a cofactor. Murine CAD has the highest catalytic activity, whereas Aspergillus CAD is best adapted to a more acidic pH. CAD is not homologous to any known decarboxylase and appears to have evolved from prokaryotic enzymes that bind negatively charged substrates. CADs are homodimers, the active center is located in the interface between 2 distinct subdomains, and structural modeling revealed conservation in zebrafish and Aspergillus We identified 8 active-site residues critical for CAD function and rare naturally occurring human mutations in the active site that abolished CAD activity, as well as a variant (Asn152Ser) that increased CAD activity and is common (allele frequency 20%) in African ethnicity. These results open the way for 1) assessing the potential impact of human CAD variants on disease risk at the population level, 2) developing therapeutic interventions to modify CAD activity, and 3) improving CAD efficiency for biotechnological production of itaconic acid.
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7
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Wang X, Li ZM, Li Q, Shi M, Bao L, Xu D, Li Z. Purification and biochemical characterization of FrsA protein from Vibrio vulnificus as an esterase. PLoS One 2019; 14:e0215084. [PMID: 30951551 PMCID: PMC6450606 DOI: 10.1371/journal.pone.0215084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/26/2019] [Indexed: 11/19/2022] Open
Abstract
Fermentation-respiration switch protein (FrsA) was thought to play an important role in controlling the metabolic flux between respiration and fermentation pathways, whereas the biochemical function of FrsA was unclear yet. A gene coding for FrsA protein from Vibrio vulnificus was chemically synthesized. The recombinant VvFrsA was expressed as a soluble protein and purified by Ni-NTA affinity chromatography. The protein had a subunit molecular weight of ca. 45 kDa by SDS-PAGE and preferred short-chain esters when p-nitrophenyl alkanoate esters were used as substrates. Optimum condition for VvFrsA was found to be at pH 9.0 and 50 °C. The protein retained high esterase activity at alkaline condition and would denature slowly at over 50 °C. With p-nitrophenyl acetate as the substrate, the Km and kcat were determined to be 18.6 mM and 0.67 s-1, respectively, by steady-state kinetic assay. Molecular dynamics simulation and docking model structure revealed that p-nitrophenyl acetate could be the substrate of VvFrsA. In conclusion our results demonstrated that the protein was able to catalyze the hydrolysis of esters, especially p-nitrophenyl acetate, for the first time.
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Affiliation(s)
- Xiaoqin Wang
- College of Bioscience and Bioengineering, Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Zhi-Min Li
- College of Science, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Qingyue Li
- College of Chemistry, Sichuan University, Chengdu, Sichuan, China
| | - Mingsong Shi
- College of Chemistry, Sichuan University, Chengdu, Sichuan, China
| | - Lingling Bao
- College of Bioscience and Bioengineering, Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Dingguo Xu
- College of Chemistry, Sichuan University, Chengdu, Sichuan, China
| | - Zhimin Li
- College of Bioscience and Bioengineering, Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables in Jiangxi Province, Nanchang, Jiangxi, China
- * E-mail:
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8
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Oh J, Liuzzi A, Ronda L, Marchetti M, Corsini R, Folli C, Bettati S, Rhee S, Percudani R. Diatom Allantoin Synthase Provides Structural Insights into Natural Fusion Protein Therapeutics. ACS Chem Biol 2018; 13:2237-2246. [PMID: 29874034 DOI: 10.1021/acschembio.8b00404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Humans have lost the ability to convert urate into the more soluble allantoin with the evolutionary inactivation of three enzymes of the uricolytic pathway. Restoration of this function through enzyme replacement therapy can treat severe hyperuricemia and Lesch-Nyhan disease. Through a genomic exploration of natural gene fusions, we found that plants and diatoms independently evolved a fusion protein (allantoin synthase) complementing two human pseudogenes. The 1.85-Å-resolution crystal structure of allantoin synthase from the diatom Phaeodactylum tricornutum provides a rationale for the domain combinations observed in the metabolic pathway, suggesting that quaternary structure is key to the evolutionary success of protein domain fusions. Polyethylene glycol (PEG) conjugation experiments indicate that a PEG-modified form of the natural fusion protein provides advantages over separate enzymes in terms of activity maintenance and manufacturing of the bioconjugate. These results suggest that the combination of different activities in a single molecular unit can simplify the production and chemical modification of recombinant proteins for multifunctional enzyme therapy.
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Affiliation(s)
- Juntaek Oh
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Anastasia Liuzzi
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, 43124, Parma, Italy
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124, Parma, Italy
| | - Marialaura Marchetti
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124, Parma, Italy
| | - Romina Corsini
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Claudia Folli
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, 43124, Parma, Italy
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124, Parma, Italy
- National Institute of Biostructures and Biosystems, 00136, Rome, Italy
| | - Sangkee Rhee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124, Parma, Italy
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9
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Palmer M, Steenkamp ET, Coetzee MPA, Blom J, Venter SN. Genome-Based Characterization of Biological Processes That Differentiate Closely Related Bacteria. Front Microbiol 2018; 9:113. [PMID: 29467735 PMCID: PMC5808187 DOI: 10.3389/fmicb.2018.00113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/17/2018] [Indexed: 12/21/2022] Open
Abstract
Bacteriologists have strived toward attaining a natural classification system based on evolutionary relationships for nearly 100 years. In the early twentieth century it was accepted that a phylogeny-based system would be the most appropriate, but in the absence of molecular data, this approach proved exceedingly difficult. Subsequent technical advances and the increasing availability of genome sequencing have allowed for the generation of robust phylogenies at all taxonomic levels. In this study, we explored the possibility of linking biological characters to higher-level taxonomic groups in bacteria by making use of whole genome sequence information. For this purpose, we specifically targeted the genus Pantoea and its four main lineages. The shared gene sets were determined for Pantoea, the four lineages within the genus, as well as its sister-genus Tatumella. This was followed by functional characterization of the gene sets using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In comparison to Tatumella, various traits involved in nutrient cycling were identified within Pantoea, providing evidence for increased efficacy in recycling of metabolites within the genus. Additionally, a number of traits associated with pathogenicity were identified within species often associated with opportunistic infections, with some support for adaptation toward overcoming host defenses. Some traits were also only conserved within specific lineages, potentially acquired in an ancestor to the lineage and subsequently maintained. It was also observed that the species isolated from the most diverse sources were generally the most versatile in their carbon metabolism. By investigating evolution, based on the more variable genomic regions, it may be possible to detect biologically relevant differences associated with the course of evolution and speciation.
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Affiliation(s)
- Marike Palmer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Emma T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Martin P A Coetzee
- Department of Genetic, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Stephanus N Venter
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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10
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Ronda L, Marchetti M, Piano R, Liuzzi A, Corsini R, Percudani R, Bettati S. A Trivalent Enzymatic System for Uricolytic Therapy of HPRT Deficiency and Lesch-Nyhan Disease. Pharm Res 2017; 34:1477-1490. [PMID: 28508122 PMCID: PMC5445154 DOI: 10.1007/s11095-017-2167-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/25/2017] [Indexed: 12/21/2022]
Abstract
PURPOSE Because of the evolutionary loss of the uricolytic pathway, humans accumulate poorly soluble urate as the final product of purine catabolism. Restoration of uricolysis through enzyme therapy is a promising treatment for severe hyperuricemia caused by deficiency of hypoxanthine-guanine phosphoribosyltransferase (HPRT). To this end, we studied the effect of PEG conjugation on the activity and stability of the enzymatic complement required for conversion of urate into the more soluble (S)-allantoin. METHODS We produced in recombinant form three zebrafish enzymes required in the uricolytic pathway. We carried out a systematic study of the effect of PEGylation on the function and stability of the three enzymes by varying PEG length, chemistry and degree of conjugation. We assayed in vitro the uricolytic activity of the PEGylated enzymatic triad. RESULTS We defined conditions that allow PEGylated enzymes to retain native-like enzymatic activity even after lyophilization or prolonged storage. A combination of the three enzymes in an appropriate ratio allowed efficient conversion of urate to (S)-allantoin with no accumulation of intermediate metabolites. CONCLUSIONS Pharmaceutical restoration of the uricolytic pathway is a viable approach for the treatment of severe hyperuricemia.
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Affiliation(s)
- Luca Ronda
- Department of Medicine and Surgery,, University of Parma, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - Marialaura Marchetti
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma,, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - Riccardo Piano
- Department of Medicine and Surgery,, University of Parma, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - Anastasia Liuzzi
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma,, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - Romina Corsini
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma,, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma,, Parco Area delle Scienze 23/A, 43124, Parma, Italy.
| | - Stefano Bettati
- Department of Medicine and Surgery,, University of Parma, Parco Area delle Scienze 23/A, 43124, Parma, Italy. .,National Institute of Biostructures and Biosystems, Viale Medaglie d'Oro 305, 00136, Rome, Italy.
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11
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Talbot NC, Sparks WO, Phillips CE, Ealy AD, Powell AM, Caperna TJ, Garrett WM, Donovan DM, Blomberg LA. Bovine trophectoderm cells induced from bovine fibroblasts with induced pluripotent stem cell reprogramming factors. Mol Reprod Dev 2017; 84:468-485. [PMID: 28332752 DOI: 10.1002/mrd.22797] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/08/2017] [Indexed: 12/17/2022]
Abstract
Thirteen independent induced bovine trophectroderm (iBT) cell lines were established by reprogramming bovine fetal liver-derived fibroblasts after viral-vector transduction with either six or eight factors, including POU5F1 (OCT4), KLF4, SOX2, MYC, NANOG, LIN28, SV40 large T antigen, and hTERT. Light- and electron-microscopy analysis showed that the iBT cells had epithelial cell morphology typical of bovine trophectoderm cells. Reverse-transcription-PCR assays indicated that all of the cell lines expressed interferon-tau (IFNT) at passages 1 or 2. At later passages (≥ passage 8), however, immunoblot and antiviral activity assays revealed that more than half of the iBT cell lines had stopped expressing IFNT. Messenger RNAs specific to trophectoderm differentiation and function were found in the iBT cell lines, and 2-dimensional-gel analysis for cellular proteins showed an expression pattern similar to that of trophectoderm cell lines derived from bovine blastocysts. Integration of some of the human reprogramming factors, including POU5F1, KLF4, SOX2, MYC, NANOG, and LIN28, were detected by PCR, but their transcription was mostly absent in the iBT cell lines. Gene expression assessment of endogenous bovine reprogramming factor orthologs revealed endogenous bLIN28 and bMYC transcripts in all; bSOX2 and bNANOG in none; and bKLF4 and bPOU5F1 in less than half of the iBT cell lines. These results demonstrate that bovine trophectoderm can be induced via reprogramming factor expression from bovine liver-derived fibroblasts, although other fibroblast populations-e.g., derived from fetal thigh tissue-may produce similar results, albeit at lower frequencies.
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Affiliation(s)
- Neil C Talbot
- U.S. Department of Agriculture, Agricultural Research Service, Animal Biosciences and Biotechnology Laboratory, Beltsville, Maryland
| | - Wendy O Sparks
- U.S. Department of Agriculture, Agricultural Research Service, Animal Biosciences and Biotechnology Laboratory, Beltsville, Maryland
| | - Caitlin E Phillips
- U.S. Department of Agriculture, Agricultural Research Service, Animal Biosciences and Biotechnology Laboratory, Beltsville, Maryland
| | - Alan D Ealy
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia
| | - Anne M Powell
- U.S. Department of Agriculture, Agricultural Research Service, Animal Biosciences and Biotechnology Laboratory, Beltsville, Maryland
| | - Thomas J Caperna
- U.S. Department of Agriculture, Agricultural Research Service, Animal Biosciences and Biotechnology Laboratory, Beltsville, Maryland
| | - Wesley M Garrett
- U.S. Department of Agriculture, Agricultural Research Service, Animal Biosciences and Biotechnology Laboratory, Beltsville, Maryland
| | - David M Donovan
- U.S. Department of Agriculture, Agricultural Research Service, Animal Biosciences and Biotechnology Laboratory, Beltsville, Maryland
| | - Le Ann Blomberg
- U.S. Department of Agriculture, Agricultural Research Service, Animal Biosciences and Biotechnology Laboratory, Beltsville, Maryland
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12
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Marchetti M, Liuzzi A, Fermi B, Corsini R, Folli C, Speranzini V, Gandolfi F, Bettati S, Ronda L, Cendron L, Berni R, Zanotti G, Percudani R. Catalysis and Structure of Zebrafish Urate Oxidase Provide Insights into the Origin of Hyperuricemia in Hominoids. Sci Rep 2016; 6:38302. [PMID: 27922051 PMCID: PMC5138847 DOI: 10.1038/srep38302] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/03/2016] [Indexed: 01/24/2023] Open
Abstract
Urate oxidase (Uox) catalyses the first reaction of oxidative uricolysis, a three-step enzymatic pathway that allows some animals to eliminate purine nitrogen through a water-soluble compound. Inactivation of the pathway in hominoids leads to elevated levels of sparingly soluble urate and puts humans at risk of hyperuricemia and gout. The uricolytic activities lost during evolution can be replaced by enzyme therapy. Here we report on the functional and structural characterization of Uox from zebrafish and the effects on the enzyme of the missense mutation (F216S) that preceded Uox pseudogenization in hominoids. Using a kinetic assay based on the enzymatic suppression of the spectroscopic interference of the Uox reaction product, we found that the F216S mutant has the same turnover number of the wild-type enzyme but a much-reduced affinity for the urate substrate and xanthine inhibitor. Our results indicate that the last functioning Uox in hominoid evolution had an increased Michaelis constant, possibly near to upper end of the normal range of urate in the human serum (~300 μM). Changes in the renal handling of urate during primate evolution can explain the genetic modification of uricolytic activities in the hominoid lineage without the need of assuming fixation of deleterious mutations.
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Affiliation(s)
| | - Anastasia Liuzzi
- Department of Life Sciences, University of Parma, 43124, Parma, Italy
| | - Beatrice Fermi
- Department of Life Sciences, University of Parma, 43124, Parma, Italy
| | - Romina Corsini
- Department of Life Sciences, University of Parma, 43124, Parma, Italy
| | - Claudia Folli
- Department of Food Science University of Parma, 43124, Parma, Italy
| | | | | | - Stefano Bettati
- Department of Neurosciences, University of Parma, 43124, Parma, Italy
| | - Luca Ronda
- Department of Neurosciences, University of Parma, 43124, Parma, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Rodolfo Berni
- Department of Life Sciences, University of Parma, 43124, Parma, Italy
| | - Giuseppe Zanotti
- Department of Biology, University of Padova, 35121, Padova, Italy
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13
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Cendron L, Ramazzina I, Puggioni V, Maccacaro E, Liuzzi A, Secchi A, Zanotti G, Percudani R. The Structure and Function of a Microbial Allantoin Racemase Reveal the Origin and Conservation of a Catalytic Mechanism. Biochemistry 2016; 55:6421-6432. [DOI: 10.1021/acs.biochem.6b00881] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Laura Cendron
- Department
of Biomedical Sciences, University of Padova, Padova, Italy
| | | | | | | | | | - Andrea Secchi
- Department
of Chemistry, University of Parma, Parma, Italy
| | - Giuseppe Zanotti
- Department
of Biomedical Sciences, University of Padova, Padova, Italy
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14
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Zhuang CB, Zheng QC. QM/MM calculations and MD simulations of acetolactate decarboxylase to reveal substrate R/S-acetolactate binding mode and stereoselective catalytic mechansim. RSC Adv 2016. [DOI: 10.1039/c6ra19346c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Acetolactate decarboxylase (ALDC) catalyzesR/S-acetolactate to make the same product, (R)-acetoin, with different processes.
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Affiliation(s)
- Can-Bo Zhuang
- Laboratory of Theoretical and Computational Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130023
- People's Republic of China
| | - Qing-Chuan Zheng
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education
- Jilin University
- Changchun 130023
- People's Republic of China
- Laboratory of Theoretical and Computational Chemistry
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15
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Barelier S, Sterling T, O’Meara MJ, Shoichet BK. The Recognition of Identical Ligands by Unrelated Proteins. ACS Chem Biol 2015; 10:2772-84. [PMID: 26421501 DOI: 10.1021/acschembio.5b00683] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The binding of drugs and reagents to off-targets is well-known. Whereas many off-targets are related to the primary target by sequence and fold, many ligands bind to unrelated pairs of proteins, and these are harder to anticipate. If the binding site in the off-target can be related to that of the primary target, this challenge resolves into aligning the two pockets. However, other cases are possible: the ligand might interact with entirely different residues and environments in the off-target, or wholly different ligand atoms may be implicated in the two complexes. To investigate these scenarios at atomic resolution, the structures of 59 ligands in 116 complexes (62 pairs in total), where the protein pairs were unrelated by fold but bound an identical ligand, were examined. In almost half of the pairs, the ligand interacted with unrelated residues in the two proteins (29 pairs), and in 14 of the pairs wholly different ligand moieties were implicated in each complex. Even in those 19 pairs of complexes that presented similar environments to the ligand, ligand superposition rarely resulted in the overlap of related residues. There appears to be no single pattern-matching "code" for identifying binding sites in unrelated proteins that bind identical ligands, though modeling suggests that there might be a limited number of different patterns that suffice to recognize different ligand functional groups.
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Affiliation(s)
- Sarah Barelier
- Department of Pharmaceutical
Chemistry, University of California San Francisco, 1700 Fourth
Street, Byers Hall, San Francisco, California 94158, United States
| | - Teague Sterling
- Department of Pharmaceutical
Chemistry, University of California San Francisco, 1700 Fourth
Street, Byers Hall, San Francisco, California 94158, United States
| | - Matthew J. O’Meara
- Department of Pharmaceutical
Chemistry, University of California San Francisco, 1700 Fourth
Street, Byers Hall, San Francisco, California 94158, United States
| | - Brian K. Shoichet
- Department of Pharmaceutical
Chemistry, University of California San Francisco, 1700 Fourth
Street, Byers Hall, San Francisco, California 94158, United States
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16
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Jankowska DA, Trautwein-Schult A, Cordes A, Bode R, Baronian K, Kunze G. A novel enzymatic approach in the production of food with low purine content using Arxula adeninivorans endogenous and recombinant purine degradative enzymes. Bioengineered 2015; 6:20-5. [PMID: 25513995 DOI: 10.4161/21655979.2014.991667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The purine degradation pathway in humans ends with uric acid, which has low water solubility. When the production of uric acid is increased either by elevated purine intake or by impaired kidney function, uric acid will accumulate in the blood (hyperuricemia). This increases the risk of gout, a disease described in humans for at least 1000 years. Many lower organisms, such as the yeast Arxula adeninivorans, possess the enzyme, urate oxidase that converts uric acid to 5-hydroxyisourate, thus preventing uric acid accumulation. We have examined the complete purine degradation pathway in A. adeninivorans and analyzed enzymes involved. Recombinant adenine deaminase, guanine deaminase, urate oxidase and endogenous xanthine oxidoreductase have been investigated as potential additives to degrade purines in the food. Here, we review the current model of the purine degradation pathway of A. adeninivorans and present an overview of proposed enzyme system with perspectives for its further development.
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Affiliation(s)
- Dagmara A Jankowska
- a Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) ; Gatersleben , Germany
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17
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Miller EB, Murrett CS, Zhu K, Zhao S, Goldfeld DA, Bylund JH, Friesner RA. Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program. J Chem Theory Comput 2013; 9:1846-4864. [PMID: 23814507 DOI: 10.1021/ct301083q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Robust homology modeling to atomic-level accuracy requires in the general case successful prediction of protein loops containing small segments of secondary structure. Further, as loop prediction advances to success with larger loops, the exclusion of loops containing secondary structure becomes awkward. Here, we extend the applicability of the Protein Local Optimization Program (PLOP) to loops up to 17 residues in length that contain either helical or hairpin segments. In general, PLOP hierarchically samples conformational space and ranks candidate loops with a high-quality molecular mechanics force field. For loops identified to possess α-helical segments, we employ an alternative dihedral library composed of (ϕ,ψ) angles commonly found in helices. The alternative library is searched over a user-specified range of residues that define the helical bounds. The source of these helical bounds can be from popular secondary structure prediction software or from analysis of past loop predictions where a propensity to form a helix is observed. Due to the maturity of our energy model, the lowest energy loop across all experiments can be selected with an accuracy of sub-Ångström RMSD in 80% of cases, 1.0 to 1.5 Å RMSD in 14% of cases, and poorer than 1.5 Å RMSD in 6% of cases. The effectiveness of our current methods in predicting hairpin-containing loops is explored with hairpins up to 13 residues in length and again reaching an accuracy of sub-Ångström RMSD in 83% of cases, 1.0 to 1.5 Å RMSD in 10% of cases, and poorer than 1.5 Å RMSD in 7% of cases. Finally, we explore the effect of an imprecise surrounding environment, in which side chains, but not the backbone, are initially in perturbed geometries. In these cases, loops perturbed to 3Å RMSD from the native environment were restored to their native conformation with sub-Ångström RMSD.
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Affiliation(s)
- Edward B Miller
- Department of Chemistry, Columbia University, New York, New York
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18
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Kim MI, Shin I, Cho S, Lee J, Rhee S. Structural and functional insights into (S)-ureidoglycolate dehydrogenase, a metabolic branch point enzyme in nitrogen utilization. PLoS One 2012; 7:e52066. [PMID: 23284870 PMCID: PMC3527362 DOI: 10.1371/journal.pone.0052066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 11/09/2012] [Indexed: 12/17/2022] Open
Abstract
Nitrogen metabolism is one of essential processes in living organisms. The catabolic pathways of nitrogenous compounds play a pivotal role in the storage and recovery of nitrogen. In Escherichia coli, two different, interconnecting metabolic routes drive nitrogen utilization through purine degradation metabolites. The enzyme (S)-ureidoglycolate dehydrogenase (AllD), which is a member of l-sulfolactate dehydrogenase-like family, converts (S)-ureidoglycolate, a key intermediate in the purine degradation pathway, to oxalurate in an NAD(P)-dependent manner. Therefore, AllD is a metabolic branch-point enzyme for nitrogen metabolism in E. coli. Here, we report crystal structures of AllD in its apo form, in a binary complex with NADH cofactor, and in a ternary complex with NADH and glyoxylate, a possible spontaneous degradation product of oxalurate. Structural analyses revealed that NADH in an extended conformation is bound to an NADH-binding fold with three distinct domains that differ from those of the canonical NADH-binding fold. We also characterized ligand-induced structural changes, as well as the binding mode of glyoxylate, in the active site near the NADH nicotinamide ring. Based on structural and kinetic analyses, we concluded that AllD selectively utilizes NAD+ as a cofactor, and further propose that His116 acts as a general catalytic base and that a hydride transfer is possible on the B-face of the nicotinamide ring of the cofactor. Other residues conserved in the active sites of this novel l-sulfolactate dehydrogenase-like family also play essential roles in catalysis.
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Affiliation(s)
- Myung-Il Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Inchul Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Suhee Cho
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Jeehyun Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Sangkee Rhee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
- Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
- * E-mail:
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19
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Shin I, Percudani R, Rhee S. Structural and functional insights into (S)-ureidoglycine aminohydrolase, key enzyme of purine catabolism in Arabidopsis thaliana. J Biol Chem 2012; 287:18796-805. [PMID: 22493446 DOI: 10.1074/jbc.m111.331819] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ureide pathway has recently been identified as the metabolic route of purine catabolism in plants and some bacteria. In this pathway, uric acid, which is a major product of the early stage of purine catabolism, is degraded into glyoxylate and ammonia via stepwise reactions of seven different enzymes. Therefore, the pathway has a possible physiological role in mobilization of purine ring nitrogen for further assimilation. (S)-Ureidoglycine aminohydrolase enzyme converts (S)-ureidoglycine into (S)-ureidoglycolate and ammonia, providing the final substrate to the pathway. Here, we report a structural and functional analysis of this enzyme from Arabidopsis thaliana (AtUGlyAH). The crystal structure of AtUGlyAH in the ligand-free form shows a monomer structure in the bicupin fold of the β-barrel and an octameric functional unit as well as a Mn(2+) ion binding site. The structure of AtUGlyAH in complex with (S)-ureidoglycine revealed that the Mn(2+) ion acts as a molecular anchor to bind (S)-ureidoglycine, and its binding mode dictates the enantioselectivity of the reaction. Further kinetic analysis characterized the functional roles of the active site residues, including the Mn(2+) ion binding site and residues in the vicinity of (S)-ureidoglycine. These analyses provide molecular insights into the structure of the enzyme and its possible catalytic mechanism.
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Affiliation(s)
- Inchul Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
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20
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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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21
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Completing the purine utilisation pathway of Aspergillus nidulans. Fungal Genet Biol 2011; 48:840-8. [DOI: 10.1016/j.fgb.2011.03.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 03/07/2011] [Accepted: 03/07/2011] [Indexed: 11/22/2022]
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22
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Lu XJ, Chen J, Huang ZA, Zhuang L, Peng LZ, Shi YH. Influence of acute cadmium exposure on the liver proteome of a teleost fish, ayu (Plecoglossus altivelis). Mol Biol Rep 2011; 39:2851-9. [PMID: 21667247 DOI: 10.1007/s11033-011-1044-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Accepted: 06/04/2011] [Indexed: 11/29/2022]
Abstract
Cadmium (Cd) is a toxic heavy metal that causes the disruption of a variety of physiological processes. In this study, the effect of Cd on liver proteome of ayu, Plecoglossus altivelis, was investigated by two-dimensional gel electrophoresis (2-DE) and matrix assisted laser desorption ionization time-of-flight tandem mass spectrometry (MALDI-TOF-MS/MS). Twenty-three altered protein spots were successfully identified. They were involved in oxidative stress response, metal metabolism, methylation, and so on. The mRNA expression of 60S acidic ribosomal protein P0, heat shock protein 70, apolipoprotein A-I, betaine-homocysteine S-methyltransferase, parahox cluster neighbor, and transferrin was subsequently determined by real-time PCR. The mRNA expression of these genes was consistent with proteomic results. These findings enrich our knowledge on the influence of Cd toxicity to teleost fish, and may be worthy of further investigation to develop biomarkers.
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Affiliation(s)
- Xin-Jiang Lu
- Faculty of Life Science and Biotechnology, Ningbo University, Ningbo 315211, People's Republic of China
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23
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Pipolo S, Percudani R, Cammi R. Absolute stereochemistry and preferred conformations of urate degradation intermediates from computed and experimental circular dichroism spectra. Org Biomol Chem 2011; 9:5149-55. [PMID: 21647520 DOI: 10.1039/c1ob05433c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The enzymatic oxidation of urate leads to the sequential formation of optically active intermediates with unknown stereochemistry: (-)-5-hydroxyisourate (HIU) and (-)-2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU). In accordance with the observation that a defect in HIU hydrolase causes hepatocarcinoma in mouse, a detoxification role has been proposed for the enzymes accelerating the conversion of HIU and OHCU into optically active (+)-allantoin. The enzymatic products of urate oxidation are normally not present in humans, but are formed in patients treated with urate oxidase. We used time-dependent density functional theory (TDDFT) to compute the electronic circular dichroism (ECD) spectra of the chiral compounds of urate degradation (HIU, OHCU, allantoin) and we compared the results with experimentally measured ECD spectra. The calculated ECD spectra for (S)-HIU and (S)-OHCU reproduced well the experimental spectra obtained through the enzymatic degradation of urate. Less conclusive results were obtained with allantoin, although the computed optical rotations in the transparent region supported the original assignment of the (+)-S configuration. These absolute configuration assignments can facilitate the study of the enzymes involved in urate metabolism and help us to understand the mechanism leading to the toxicity of urate oxidation products.
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Affiliation(s)
- Silvio Pipolo
- Dipartimento di Chimica G.I.A.F, Universitá di Parma, 43100, Parma, Italy
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24
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Lee KJ, Jeong CS, An YJ, Lee HJ, Park SJ, Seok YJ, Kim P, Lee JH, Lee KH, Cha SS. FrsA functions as a cofactor-independent decarboxylase to control metabolic flux. Nat Chem Biol 2011; 7:434-6. [PMID: 21623357 DOI: 10.1038/nchembio.589] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 04/07/2011] [Indexed: 01/09/2023]
Abstract
The interaction between fermentation-respiration switch (FrsA) protein and glucose-specific enzyme IIA(Glc) increases glucose fermentation under oxygen-limited conditions. We show that FrsA converts pyruvate to acetaldehyde and carbon dioxide in a cofactor-independent manner and that its pyruvate decarboxylation activity is enhanced by the dephosphorylated form of IIA(Glc) (d-IIA(Glc)). Crystal structures of FrsA and its complex with d-IIA(Glc) revealed residues required for catalysis as well as the structural basis for the activation by d-IIA(Glc).
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Affiliation(s)
- Kyung-Jo Lee
- Department of Environmental Science, Hankuk University of Foreign Studies, Yongin, Republic of Korea
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25
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Gu W, Yang J, Lou Z, Liang L, Sun Y, Huang J, Li X, Cao Y, Meng Z, Zhang KQ. Structural basis of enzymatic activity for the ferulic acid decarboxylase (FADase) from Enterobacter sp. Px6-4. PLoS One 2011; 6:e16262. [PMID: 21283705 PMCID: PMC3025021 DOI: 10.1371/journal.pone.0016262] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 12/07/2010] [Indexed: 11/22/2022] Open
Abstract
Microbial ferulic acid decarboxylase (FADase) catalyzes the transformation of ferulic acid to 4-hydroxy-3-methoxystyrene (4-vinylguaiacol) via non-oxidative decarboxylation. Here we report the crystal structures of the Enterobacter sp. Px6-4 FADase and the enzyme in complex with substrate analogues. Our analyses revealed that FADase possessed a half-opened bottom β-barrel with the catalytic pocket located between the middle of the core β-barrel and the helical bottom. Its structure shared a high degree of similarity with members of the phenolic acid decarboxylase (PAD) superfamily. Structural analysis revealed that FADase catalyzed reactions by an "open-closed" mechanism involving a pocket of 8 × 8 × 15 Å dimension on the surface of the enzyme. The active pocket could directly contact the solvent and allow the substrate to enter when induced by substrate analogues. Site-directed mutagenesis showed that the E134A mutation decreased the enzyme activity by more than 60%, and Y21A and Y27A mutations abolished the enzyme activity completely. The combined structural and mutagenesis results suggest that during decarboxylation of ferulic acid by FADase, Trp25 and Tyr27 are required for the entering and proper orientation of the substrate while Glu134 and Asn23 participate in proton transfer.
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Affiliation(s)
- Wen Gu
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Jinkui Yang
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Zhiyong Lou
- Structural Biology Laboratory, Tsinghua University, Beijing, China
| | - Lianming Liang
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Yuna Sun
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Jingwen Huang
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Xuemei Li
- Yunnan Academy of Tobacco Science, Kunming, China
| | - Yi Cao
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
- Guizhou Tobacco Research Institute, Guiyang, China
| | - Zhaohui Meng
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
- Laboratory of Molecular Cardiology, Department of Cardiology, The First Affiliated Hospital of Kunming Medical College, Kunming, China
| | - Ke-Qin Zhang
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
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26
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French JB, Ealick SE. Structural and mechanistic studies on Klebsiella pneumoniae 2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase. J Biol Chem 2010; 285:35446-54. [PMID: 20826786 PMCID: PMC2975168 DOI: 10.1074/jbc.m110.156034] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 08/31/2010] [Indexed: 11/06/2022] Open
Abstract
The stereospecific oxidative degradation of uric acid to (S)-allantoin was recently shown to proceed via three enzymatic steps. The final conversion is a decarboxylation of the unstable intermediate 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) and is catalyzed by OHCU decarboxylase. Here we present the structures of Klebsiella pneumoniae OHCU decarboxylase in unliganded form and with bound allantoin. These structures provide evidence that ligand binding organizes the active site residues for catalysis. Modeling of the substrate and intermediates provides additional support for this hypothesis. In addition we characterize the steady state kinetics of this enzyme and report the first OHCU decarboxylase inhibitor, allopurinol, a structural isomer of hypoxanthine. This molecule is a competitive inhibitor of K. pneumoniae OHCU decarboxylase with a K(i) of 30 ± 2 μM. Circular dichroism measurements confirm structural observations that this inhibitor disrupts the necessary organization of the active site. Our structural and biochemical studies also provide further insights into the mechanism of catalysis of OHCU decarboxylation.
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Affiliation(s)
- Jarrod B. French
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Steven E. Ealick
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
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27
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Lamberto I, Percudani R, Gatti R, Folli C, Petrucco S. Conserved alternative splicing of Arabidopsis transthyretin-like determines protein localization and S-allantoin synthesis in peroxisomes. THE PLANT CELL 2010; 22:1564-74. [PMID: 20511299 PMCID: PMC2899872 DOI: 10.1105/tpc.109.070102] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 04/14/2010] [Accepted: 05/10/2010] [Indexed: 05/19/2023]
Abstract
S-allantoin, a major ureide compound, is produced in plant peroxisomes from oxidized purines. Sequence evidence suggested that the Transthyretin-like (TTL) protein, which interacts with brassinosteroid receptors, may act as a bifunctional enzyme in the synthesis of S-allantoin. Here, we show that recombinant TTL from Arabidopsis thaliana catalyzes two enzymatic reactions leading to the stereoselective formation of S-allantoin, hydrolysis of hydroxyisourate through a C-terminal Urah domain, and decarboxylation of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline through an N-terminal Urad domain. We found that two different mRNAs are produced from the TTL gene through alternative use of two splice acceptor sites. The corresponding proteins differ in the presence (TTL(1-)) and the absence (TTL(2-)) of a rare internal peroxisomal targeting signal (PTS2). The two proteins have similar catalytic activity in vitro but different in vivo localization: TTL(1-) localizes in peroxisomes, whereas TTL(2-) localizes in the cytosol. Similar splice variants are present in monocots and dicots. TTL originated in green algae through a Urad-Urah fusion, which entrapped an N-terminal PTS2 between the two domains. The presence of this gene in all Viridiplantae indicates that S-allantoin biosynthesis has general significance in plant nitrogen metabolism, while conservation of alternative splicing suggests that this mechanism has general implications in the regulation of the ureide pathway in flowering plants.
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Affiliation(s)
- Ilaria Lamberto
- Dipartimento di Biochimica e Biologia Molecolare, Università di Parma, 43124 Parma, Italy
| | - Riccardo Percudani
- Dipartimento di Biochimica e Biologia Molecolare, Università di Parma, 43124 Parma, Italy
- Address correspondence to
| | - Rita Gatti
- Dipartimento di Medicina Sperimentale, Sezione di Istologia, Università di Parma, 43125 Parma, Italy
| | - Claudia Folli
- Dipartimento di Biochimica e Biologia Molecolare, Università di Parma, 43124 Parma, Italy
| | - Stefania Petrucco
- Dipartimento di Biochimica e Biologia Molecolare, Università di Parma, 43124 Parma, Italy
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28
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Pessoa J, Sárkány Z, Ferreira-da-Silva F, Martins S, Almeida MR, Li J, Damas AM. Functional characterization of Arabidopsis thaliana transthyretin-like protein. BMC PLANT BIOLOGY 2010; 10:30. [PMID: 20167108 PMCID: PMC2834698 DOI: 10.1186/1471-2229-10-30] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Accepted: 02/18/2010] [Indexed: 05/20/2023]
Abstract
BACKGROUND Arabidopsis thaliana transthyretin-like (TTL) protein is a potential substrate in the brassinosteroid signalling cascade, having a role that moderates plant growth. Moreover, sequence homology revealed two sequence domains similar to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) decarboxylase (N-terminal domain) and 5-hydroxyisourate (5-HIU) hydrolase (C-terminal domain). TTL is a member of the transthyretin-related protein family (TRP), which comprises a number of proteins with sequence homology to transthyretin (TTR) and the characteristic C-terminal sequence motif Tyr-Arg-Gly-Ser. TRPs are single domain proteins that form tetrameric structures with 5-HIU hydrolase activity. Experimental evidence is fundamental for knowing if TTL is a tetrameric protein, formed by the association of the 5-HIU hydrolase domains and, in this case, if the structural arrangement allows for OHCU decarboxylase activity. This work reports about the biochemical and functional characterization of TTL. RESULTS The TTL gene was cloned and the protein expressed and purified for biochemical and functional characterization. The results show that TTL is composed of four subunits, with a moderately elongated shape. We also found evidence for 5-HIU hydrolase and OHCU decarboxylase activities in vitro, in the full-length protein. CONCLUSIONS The Arabidopsis thaliana transthyretin-like (TTL) protein is a tetrameric bifunctional enzyme, since it has 5-HIU hydrolase and OHCU decarboxylase activities, which were simultaneously observed in vitro.
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Affiliation(s)
- João Pessoa
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Zsuzsa Sárkány
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Frederico Ferreira-da-Silva
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Sónia Martins
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Maria R Almeida
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
- ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Largo Prof. Abel Salazar 2, 4099-003 Porto, Portugal
| | - Jianming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1048, USA
| | - Ana M Damas
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
- ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Largo Prof. Abel Salazar 2, 4099-003 Porto, Portugal
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29
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O'Leary SE, Hicks KA, Ealick SE, Begley TP. Biochemical characterization of the HpxO enzyme from Klebsiella pneumoniae, a novel FAD-dependent urate oxidase. Biochemistry 2009; 48:3033-5. [PMID: 19260710 DOI: 10.1021/bi900160b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The HpxO enzyme from Klebsiella pneumoniae was recently proposed, on the basis of genetic studies, to catalyze the hydroxylation of uric acid to 5-hydroxyisourate as part of the purine catabolic pathway. Its primary sequence suggests that the HpxO catalytic activity depends on a flavin cofactor (FAD), contrasting with all previously studied urate oxidase enzymes, which have no cofactor requirement. Here we demonstrate biochemically that HpxO is an FAD-dependent urate oxidase. Our data are consistent with the proposal that HpxO-bound flavin hydroperoxide is the hydroxylating species. These results confirm the existence of a novel mechanistic paradigm in purine catabolism.
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Affiliation(s)
- Seán E O'Leary
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA
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30
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Kim K, Kim MI, Chung J, Ahn JH, Rhee S. Crystal structure of metal-dependent allantoinase from Escherichia coli. J Mol Biol 2009; 387:1067-74. [PMID: 19248789 DOI: 10.1016/j.jmb.2009.02.041] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2008] [Revised: 02/13/2009] [Accepted: 02/16/2009] [Indexed: 10/21/2022]
Abstract
Allantoinase acts as a key enzyme for the biogenesis and degradation of ureides by catalyzing the conversion of (S)-allantoin into allantoate, the final step in the ureide pathway. Despite limited sequence similarity, biochemical studies of the enzyme suggested that allantoinase belongs to the amidohydrolase family. In this study, the crystal structure of allantoinase from Escherichia coli was determined at 2.1 A resolution. The enzyme consists of a homotetramer in which each monomer contains two domains: a pseudo-triosephosphate-isomerase barrel and a beta-sheet. Analogous to other enzymes in the amidohydrolase family, allantoinase retains a binuclear metal center in the active site, embedded within the barrel fold. Structural analyses demonstrated that the metal ions in the active site ligate one hydroxide and six residues that are conserved among allantoinases from other organisms. Functional analyses showed that the presence of zinc in the metal center is essential for catalysis and enantioselectivity of substrate. Both the metal center and active site residues Asn94 and Ser317 play crucial roles in dictating enzyme activity. These structural and functional features are distinctively different from those of the metal-independent allantoinase, which was very recently identified.
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Affiliation(s)
- Kwangsoo Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
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31
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Pope SD, Chen LL, Stewart V. Purine utilization by Klebsiella oxytoca M5al: genes for ring-oxidizing and -opening enzymes. J Bacteriol 2009; 191:1006-17. [PMID: 19060149 PMCID: PMC2632102 DOI: 10.1128/jb.01281-08] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 11/25/2008] [Indexed: 11/20/2022] Open
Abstract
The enterobacterium Klebsiella oxytoca uses a variety of inorganic and organic nitrogen sources, including purines, nitrogen-rich compounds that are widespread in the biosphere. We have identified a 23-gene cluster that encodes the enzymes for utilizing purines as the sole nitrogen source. Growth and complementation tests with insertion mutants, combined with sequence comparisons, reveal functions for the products of these genes. Here, we report our characterization of 12 genes, one encoding guanine deaminase and the others encoding enzymes for converting (hypo)xanthine to allantoate. Conventionally, xanthine dehydrogenase, a broadly distributed molybdoflavoenzyme, catalyzes sequential hydroxylation reactions to convert hypoxanthine via xanthine to urate. Our results show that these reactions in K. oxytoca are catalyzed by a two-component oxygenase (HpxE-HpxD enzyme) homologous to Rieske nonheme iron aromatic-ring-hydroxylating systems, such as phthalate dioxygenase. Our results also reveal previously undescribed enzymes involved in urate oxidation to allantoin, catalyzed by a flavoprotein monooxygenase (HpxO enzyme), and in allantoin conversion to allantoate, which involves allantoin racemase (HpxA enzyme). The pathway also includes the recently described PuuE allantoinase (HpxB enzyme). The HpxE-HpxD and HpxO enzymes were discovered independently by de la Riva et al. (L. de la Riva, J. Badia, J. Aguilar, R. A. Bender, and L. Baldoma, J. Bacteriol. 190:7892-7903, 2008). Thus, several enzymes in this K. oxytoca purine utilization pathway differ from those in other microorganisms. Isofunctional homologs of these enzymes apparently are encoded by other species, including Acinetobacter, Burkholderia, Pseudomonas, Saccharomyces, and Xanthomonas.
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Affiliation(s)
- Scott D Pope
- Department of Microbiology, University of California, One Shields Ave., Davis, CA 95616-8665, USA
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The hpx genetic system for hypoxanthine assimilation as a nitrogen source in Klebsiella pneumoniae: gene organization and transcriptional regulation. J Bacteriol 2008; 190:7892-903. [PMID: 18849434 DOI: 10.1128/jb.01022-08] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Growth experiments showed that adenine and hypoxanthine can be used as nitrogen sources by several strains of K. pneumoniae under aerobic conditions. The assimilation of all nitrogens from these purines indicates that the catabolic pathway is complete and proceeds past allantoin. Here we identify the genetic system responsible for the oxidation of hypoxanthine to allantoin in K. pneumoniae. The hpx cluster consists of seven genes, for which an organization in four transcriptional units, hpxDE, hpxR, hpxO, and hpxPQT, is proposed. The proteins involved in the oxidation of hypoxanthine (HpxDE) or uric acid (HpxO) did not display any similarity to other reported enzymes known to catalyze these reactions but instead are similar to oxygenases acting on aromatic compounds. Expression of the hpx system is activated by nitrogen limitation and by the presence of specific substrates, with hpxDE and hpxPQT controlled by both signals. Nitrogen control of hpxPQT transcription, which depends on sigma(54), is mediated by the Ntr system. In contrast, neither NtrC nor the nitrogen assimilation control protein is involved in the nitrogen control of hpxDE, which is dependent on sigma(70) for transcription. Activation of these operons by the specific substrates is also mediated by different effectors and regulatory proteins. Induction of hpxPQT requires uric acid formation, whereas expression of hpxDE is induced by the presence of hypoxanthine through the regulatory protein HpxR. This LysR-type regulator binds to a TCTGC-N(4)-GCAAA site in the intergenic hpxD-hpxR region. When bound to this site for hpxDE activation, HpxR negatively controls its own transcription.
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Gabison L, Prangé T, Colloc'h N, El Hajji M, Castro B, Chiadmi M. Structural analysis of urate oxidase in complex with its natural substrate inhibited by cyanide: mechanistic implications. BMC STRUCTURAL BIOLOGY 2008; 8:32. [PMID: 18638417 PMCID: PMC2490695 DOI: 10.1186/1472-6807-8-32] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Accepted: 07/20/2008] [Indexed: 11/10/2022]
Abstract
Background Urate oxidase (EC 1.7.3.3 or UOX) catalyzes the conversion of uric acid and gaseous molecular oxygen to 5-hydroxyisourate and hydrogen peroxide, in the absence of cofactor or particular metal cation. The functional enzyme is a homo-tetramer with four active sites located at dimeric interfaces. Results The catalytic mechanism was investigated through a ternary complex formed between the enzyme, uric acid, and cyanide that stabilizes an intermediate state of the reaction. When uric acid is replaced by a competitive inhibitor, no complex with cyanide is formed. Conclusion The X-ray structure of this compulsory ternary complex led to a number of mechanistic evidences that support a sequential mechanism in which the two reagents, dioxygen and a water molecule, process through a common site located 3.3 Å above the mean plane of the ligand. This site is built by the side chains of Asn 254, and Thr 57, two conserved residues belonging to two different subunits of the homo-tetramer. The absence of a ternary complex between the enzyme, a competitive inhibitor, and cyanide suggests that cyanide inhibits the hydroxylation step of the reaction, after the initial formation of a hydroperoxyde type intermediate.
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Affiliation(s)
- Laure Gabison
- LCRB, UMR CNRS 8015, Université Paris Descartes, 4 avenue de l'Observatoire, 75270 Paris cedex 06, France.
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Ramazzina I, Cendron L, Folli C, Berni R, Monteverdi D, Zanotti G, Percudani R. Logical identification of an allantoinase analog (puuE) recruited from polysaccharide deacetylases. J Biol Chem 2008; 283:23295-304. [PMID: 18550550 DOI: 10.1074/jbc.m801195200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hydrolytic cleavage of the hydantoin ring of allantoin, catalyzed by allantoinase, is required for the utilization of the nitrogen present in purine-derived compounds. The allantoinase gene (DAL1), however, is missing in many completely sequenced organisms able to use allantoin as a nitrogen source. Here we show that an alternative allantoinase gene (puuE) can be precisely identified by analyzing its logic relationship with three other genes of the pathway. The novel allantoinase is annotated in structure and sequence data bases as polysaccharide deacetylase for its homology with enzymes that catalyze hydrolytic reactions on chitin or peptidoglycan substrates. The recombinant PuuE protein from Pseudomonas fluorescens exhibits metal-independent allantoinase activity and stereospecificity for the S enantiomer of allantoin. The crystal structures of the protein and of protein-inhibitor complexes reveal an overall similarity with the polysaccharide deacetylase beta/alpha barrel and remarkable differences in oligomeric assembly and active site geometry. The conserved Asp-His-His metal-binding triad is replaced by Glu-His-Trp, a configuration that is distinctive of PuuE proteins within the protein family. An extra domain at the top of the barrel offers a scaffold for protein tetramerization and forms a small substrate-binding cleft by hiding the large binding groove of polysaccharide deacetylases. Substrate positioning at the active site suggests an acid/base mechanism of catalysis in which only one member of the catalytic pair of polysaccharide deacetylases has been conserved. These data provide a structural rationale for the shifting of substrate specificity that occurred during evolution.
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Affiliation(s)
- Ileana Ramazzina
- Department of Biochemistry and Molecular Biology and Mathematics, University of Parma, 43100, Parma, Italy
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Kim K, Park J, Rhee S. Structural and Functional Basis for (S)-Allantoin Formation in the Ureide Pathway. J Biol Chem 2007; 282:23457-64. [PMID: 17567580 DOI: 10.1074/jbc.m703211200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ureide pathway, which mediates the oxidative degradation of uric acid to (S)-allantoin, represents the late stage of purine catabolism in most organisms. The details of uric acid metabolism remained elusive until the complete pathway involving three enzymes was recently identified and characterized. However, the molecular details of the exclusive production of one enantiomer of allantoin in this pathway are still undefined. Here we report the crystal structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) decarboxylase, which catalyzes the last reaction of the pathway, in a complex with the product, (S)-allantoin, at 2.5-A resolution. The homodimeric helical protein represents a novel structural motif and reveals that the active site in each monomer contains no cofactors, distinguishing this enzyme mechanistically from other cofactor-dependent decarboxylases. On the basis of structural analysis, along with site-directed mutagenesis, a mechanism for the enzyme is proposed in which a decarboxylation reaction occurs directly, and the invariant histidine residue in the OHCU decarboxylase family plays an essential role in producing (S)-allantoin through a proton transfer from the hydroxyl group at C4 to C5 at the re-face of OHCU. These results provide molecular details that address a longstanding question of how living organisms selectively produce (S)-allantoin.
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Affiliation(s)
- Kwangsoo Kim
- Department of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Room 7117, Building 200, Seoul 151-921, Korea
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