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Scott BM, Koh K, Rix GD. Structural and functional profile of phytases across the domains of life. Curr Res Struct Biol 2024; 7:100139. [PMID: 38562944 PMCID: PMC10982552 DOI: 10.1016/j.crstbi.2024.100139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/03/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
Phytase enzymes are a crucial component of the natural phosphorus cycle, as they help make phosphate bioavailable by releasing it from phytate, the primary reservoir of organic phosphorus in grain and soil. Phytases also comprise a significant segment of the agricultural enzyme market, used primarily as an animal feed additive. At least four structurally and mechanistically distinct classes of phytases have evolved in bacteria and eukaryotes, and the natural diversity of each class is explored here using advances in protein structure prediction and functional annotation. This graphical review aims to provide a succinct description of the major classes of phytase enzymes across phyla, including their structures, conserved motifs, and mechanisms of action.
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Affiliation(s)
- Benjamin M. Scott
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Road, S7N 4L8, Saskatoon, Saskatchewan, Canada
| | - Kevin Koh
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Road, S7N 4L8, Saskatoon, Saskatchewan, Canada
| | - Gregory D. Rix
- Inspiralis Ltd., Innovation Centre, Norwich Research Park, Colney Lane, NR4 7UH, Norwich, UK
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2
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Priyodip P, Balaji S. Characterization of a putative metal-dependent PTP-like phosphatase from Lactobacillus helveticus 2126. Int Microbiol 2024; 27:37-47. [PMID: 37365352 PMCID: PMC10830716 DOI: 10.1007/s10123-023-00390-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 04/01/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023]
Abstract
To date, there are very limited reports on sequence analysis and structure-based molecular modeling of phosphatases produced by probiotic bacteria. Therefore, a novel protein tyrosine-like phosphatase was characterized from L. helveticus 2126 in this study. The purified bacterial phosphatase was subjected to mass spectrometric analysis, and the identity of constructed sequence was analyzed using peptide mass fingerprint. The 3-D structure of protein was elucidated using homology modeling, while its stability was assessed using Ramachandran plot, VERIFY 3D, and PROCHECK. The bacterium produced an extracellular phosphatase of zone diameter 15 ± 0.8 mm on screening medium within 24 h of incubation. This bacterial phosphatase was highly specific towards sodium phytate as it yielded the lowest Km value of 299.50 ± 4.95 μM compared to other phosphorylated substrates. The activity was effectively stimulated in the presence of zinc, magnesium, and manganese ions thereby showing its PTP-like behavior. The phosphatase showed a molecular mass of 43 kDa, and the corresponding M/Z ratio data yielded 46% query coverage to Bacillus subtilis (3QY7). This showed a 61.1% sequence similarity to Ligilactobacillus ruminis (WP_046923835.1). The final sequence construct based on these bacteria showed a conserved motif "HCHILPGIDD" in their active site. In addition, homology modeling showed a distorted Tim barrel structure with a trinuclear metal center. The final model after energy minimization showed 90.9% of the residues in the favorable region of Ramachandran's plot. This structural information can be used in genetic engineering for improving the overall stability and catalytic efficiency of probiotic bacterial phosphatases.
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Affiliation(s)
- Paul Priyodip
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, -576104, Manipal, Karnataka, India
| | - Seetharaman Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, -576104, Manipal, Karnataka, India.
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3
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Nezhad NG, Rahman RNZRA, Normi YM, Oslan SN, Shariff FM, Leow TC. Isolation, screening and molecular characterization of phytase-producing microorganisms to discover the novel phytase. Biologia (Bratisl) 2023; 78:2527-2537. [DOI: 10.1007/s11756-023-01391-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/10/2023] [Indexed: 09/02/2023]
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4
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Burroughs A, Aravind L. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. NAR Genom Bioinform 2023; 5:lqad029. [PMID: 36968430 PMCID: PMC10034599 DOI: 10.1093/nargab/lqad029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 03/25/2023] Open
Abstract
The protein-tyrosine/dual-specificity phosphatases and rhodanese domains constitute a sprawling superfamily of Rossmannoid domains that use a conserved active site with a cysteine to catalyze a range of phosphate-transfer, thiotransfer, selenotransfer and redox activities. While these enzymes have been extensively studied in the context of protein/lipid head group dephosphorylation and various thiotransfer reactions, their overall diversity and catalytic potential remain poorly understood. Using comparative genomics and sequence/structure analysis, we comprehensively investigate and develop a natural classification for this superfamily. As a result, we identified several novel clades, both those which retain the catalytic cysteine and those where a distinct active site has emerged in the same location (e.g. diphthine synthase-like methylases and RNA 2' OH ribosyl phosphate transferases). We also present evidence that the superfamily has a wider range of catalytic capabilities than previously known, including a set of parallel activities operating on various sugar/sugar alcohol groups in the context of NAD+-derivatives and RNA termini, and potential phosphate transfer activities involving sugars and nucleotides. We show that such activities are particularly expanded in the RapZ-C-DUF488-DUF4326 clade, defined here for the first time. Some enzymes from this clade are predicted to catalyze novel DNA-end processing activities as part of nucleic-acid-modifying systems that are likely to function in biological conflicts between viruses and their hosts.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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5
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Kuang M, Zhang Y, Lam TW, Ting HF. MLProbs: A Data-Centric Pipeline for Better Multiple Sequence Alignment. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:524-533. [PMID: 35120007 DOI: 10.1109/tcbb.2022.3148382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In this paper, we explore using the data-centric approach to tackle the Multiple Sequence Alignment (MSA) construction problem. Unlike the algorithm-centric approach, which reduces the construction problem to a combinatorial optimization problem based on an abstract mathematical model, the data-centric approach explores using classification models trained from existing benchmark data to guide the construction. We identified two simple classifications to help us choose a better alignment tool and determine whether and how much to carry out realignment. We show that shallow machine-learning algorithms suffice to train sensitive models for these classifications. Based on these models, we implemented a new multiple sequence alignment pipeline, called MLProbs. Compared with 10 other popular alignment tools over four benchmark databases (namely, BAliBASE, OXBench, OXBench-X and SABMark), MLProbs consistently gives the highest TC score. More importantly, MLProbs shows non-trivial improvement for protein families with low similarity; in particular, when evaluated against the 1,356 protein families with similarity ≤ 50%, MLProbs achieves a TC score of 56.93, while the next best three tools are in the range of [55.41, 55.91] (increased by more than 1.8%). We also compared the performance of MLProbs and other MSA tools in two real-life applications - Phylogenetic Tree Construction Analysis and Protein Secondary Structure Prediction - and MLProbs also had the best performance. In our study, we used only shallow machine-learning algorithms to train our models. It would be interesting to study whether deep-learning methods can help make further improvements, so we suggest some possible research directions in the conclusion section.
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Characterisation of a soil MINPP phytase with remarkable long-term stability and activity from Acinetobacter sp. PLoS One 2022; 17:e0272015. [DOI: 10.1371/journal.pone.0272015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/12/2022] [Indexed: 11/19/2022] Open
Abstract
Phylogenetic analysis, homology modelling and biochemical methods have been employed to characterize a phytase from a Gram-negative soil bacterium. Acinetobacter sp. AC1-2 phytase belongs to clade 2 of the histidine (acid) phytases, to the Multiple Inositol Polyphosphate Phosphatase (MINPP) subclass. The enzyme was extraordinarily stable in solution both at room temperature and 4°C, retaining near 100% activity over 755 days. It showed a broad pH activity profile from 2–8.5 with maxima at 3, 4.5–5 and 6. The enzyme showed Michaelis-Menten kinetics and substrate inhibition (Vmax, Km, and Ki, 228 U/mg, 0.65 mM and 2.23 mM, respectively). Homology modelling using the crystal structure of a homologous MINPP from a human gut commensal bacterium indicated the presence of a potentially stabilising polypeptide loop (a U-loop) straddling the active site. By employ of the enantiospecificity of Arabidopsis inositol tris/tetrakisphosphate kinase 1 for inositol pentakisphosphates, we show AC1-2 MINPP to possess D6-phytase activity, which allowed modelling of active site specificity pockets for InsP6 substrate. While phytase gene transcription was unaltered in rich media, it was repressed in minimal media with phytic acid and orthophosphate as phosphate sources. The results of this study reveal AC1-2 MINPP to possess desirable attributes relevant to biotechnological use.
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Insights to the Structural Basis for the Stereospecificity of the Escherichia coli Phytase, AppA. Int J Mol Sci 2022; 23:ijms23116346. [PMID: 35683026 PMCID: PMC9181005 DOI: 10.3390/ijms23116346] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/30/2022] [Accepted: 06/02/2022] [Indexed: 02/01/2023] Open
Abstract
AppA, the Escherichia coli periplasmic phytase of clade 2 of the histidine phosphatase (HP2) family, has been well-characterized and successfully engineered for use as an animal feed supplement. AppA is a 1D-6-phytase and highly stereospecific but transiently accumulates 1D-myo-Ins(2,3,4,5)P4 and other lower phosphorylated intermediates. If this bottleneck in liberation of orthophosphate is to be obviated through protein engineering, an explanation of its rather rigid preference for the initial site and subsequent cleavage of phytic acid is required. To help explain this behaviour, the role of the catalytic proton donor residue in determining AppA stereospecificity was investigated. Four variants were generated by site-directed mutagenesis of the active site HDT amino acid sequence motif containing the catalytic proton donor, D304. The identity and position of the prospective proton donor residue was found to strongly influence stereospecificity. While the wild-type enzyme has a strong preference for 1D-6-phytase activity, a marked reduction in stereospecificity was observed for a D304E variant, while a proton donor-less mutant (D304A) displayed exclusive 1D-1/3-phytase activity. High-resolution X-ray crystal structures of complexes of the mutants with a non-hydrolysable substrate analogue inhibitor point to a crucial role played by D304 in stereospecificity by influencing the size and polarity of specificity pockets A and B. Taken together, these results provide the first evidence for the involvement of the proton donor residue in determining the stereospecificity of HP2 phytases and prepares the ground for structure-informed engineering studies targeting the production of animal feed enzymes capable of the efficient and complete dephosphorylation of dietary phytic acid.
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Faba-Rodriguez R, Gu Y, Salmon M, Dionisio G, Brinch-Pedersen H, Brearley CA, Hemmings AM. Structure of a cereal purple acid phytase provides new insights to phytate degradation in plants. PLANT COMMUNICATIONS 2022; 3:100305. [PMID: 35529950 PMCID: PMC9073318 DOI: 10.1016/j.xplc.2022.100305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/02/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Grain phytate, a mixed metal ion salt of inositol hexakisphosphate, accounts for 60%-80% of stored phosphorus in plants and is a potent antinutrient of non-ruminant animals including humans. Through neofunctionalization of purple acid phytases (PAPhy), some cereals such as wheat and rye have acquired particularly high mature grain phytase activity. As PAPhy activity supplies phosphate, liberates metal ions necessary for seedling emergence, and obviates antinutrient effects of phytate, its manipulation and control are targeted crop traits. Here we show the X-ray crystal structure of the b2 isoform of wheat PAPhy induced during germination. This high-resolution crystal structure suggests a model for phytate recognition that, validated by molecular dynamics simulations, implicates elements of two sequence inserts (termed PAPhy motifs) relative to a canonical metallophosphoesterase (MPE) domain in forming phytate-specific substrate specificity pockets. These motifs are well conserved in PAPhys from monocot cereals, enzymes which are characterized by high specificity for phytate. Tested by mutagenesis, residues His229 in PAPhy motif 4 and Lys410 in the MPE domain, both conserved in PAPhys, are found to strongly influence phytase activity. These results explain the observed phytase activity of cereal PAPhys and open the way to the rational engineering of phytase activity in planta.
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Affiliation(s)
- Raquel Faba-Rodriguez
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Yinghong Gu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Melissa Salmon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Giuseppe Dionisio
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark
| | - Henrik Brinch-Pedersen
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark
| | - Charles A. Brearley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Andrew M. Hemmings
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
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Oskoueian E, Oskoueian A, Shakeri M, Jahromi MF. Benefits and Challenges of Jatropha Meal as Novel Biofeed for Animal Production. Vet Sci 2021; 8:179. [PMID: 34564573 PMCID: PMC8472097 DOI: 10.3390/vetsci8090179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 11/30/2022] Open
Abstract
Jatropha curcas L. has gained importance as a source of seed oil for biodiesel production. The meal contained about 60% protein with a good balance of essential amino acids, containing various bioactive compounds, including saponins, phytic acids, trypsin inhibitors, lectins, phenolics, and flavonoids, which render it as a potential biofeed for animal production. The Jatropha meal demonstrated various biological activities, including antioxidant, antibacterial, and anti-inflammatory effects which enhance its property as a bio-feed. The levels of these bioactive compounds in the seeds are dependent on the genotypes. The J. curcas possessed different varieties which are either toxic or non-toxic according to the presence of phorbol esters. The presence of phorbol esters in the meal confirmed the toxic variety of Jatropha resulting in the limited application of meal as a biofeed. The Jatropha meal devoid of phorbol esters could be applied as a biofeed in the animal production industry, and for the toxic varieties, various techniques such as physicochemical and biological treatments have been introduced to the industry to remove the phorbol esters from Jatropha meal. Several studies employing various cells and animals confirmed the toxicity of the phorbol esters. The molecular mechanism of action of phorbol esters is through up-regulation of PKC-β II gene, overexpression of down-stream proto-oncogenes resulted in inflammation and oxidative stress ending by apoptotic cell death. Despite the presence of valuable bioactive compounds in the Jatropha meal, its nutritional application is not recommended unless the phorbol esters are completely removed.
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Affiliation(s)
- Ehsan Oskoueian
- Department of Research and Development, Arka Biotechnology Corporation, Mashhad 1696700, Iran; (A.O.); (M.F.J.)
| | - Arshin Oskoueian
- Department of Research and Development, Arka Biotechnology Corporation, Mashhad 1696700, Iran; (A.O.); (M.F.J.)
| | - Majid Shakeri
- Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Mohammad Faseleh Jahromi
- Department of Research and Development, Arka Biotechnology Corporation, Mashhad 1696700, Iran; (A.O.); (M.F.J.)
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10
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Zhao T, Yong X, Zhao Z, Dolce V, Li Y, Curcio R. Research status of Bacillus phytase. 3 Biotech 2021; 11:415. [PMID: 34485008 DOI: 10.1007/s13205-021-02964-9] [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: 05/28/2021] [Accepted: 07/27/2021] [Indexed: 10/20/2022] Open
Abstract
Phytic acid is abundant in seeds, roots and stems of plants, it acts as an anti-nutrient in food and feed industry, since it affects the absorption of nutrients by humans and monogastric animals. Furthermore, phosphorus produced through its decomposition by microorganisms can cause environmental pollution. Phytase degrades phytic acid generating precursors of inositol that can be used in clinical practice; in addition, phytase treatment can minimize the anti-nutritional effect of phytic acid. The use of phytase synthesized from Bacillus is more advantageous due to its high activity. Additionally, its good heat resistance under neutral conditions greatly fills the gap of commercial utilization of acid phytase. In this review, we summarize the latest research results on Bacillus phytase, including its physiological and biochemical characteristics, molecular structure information, calcium effects on its catalytic activity and stability, its catalytic mechanism and molecular modification.
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Affiliation(s)
- Ting Zhao
- College of Life Science and Technology, Xinjiang University, Urumqi, China
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China
| | - Xihao Yong
- College of Life Science and Technology, Xinjiang University, Urumqi, China
- Faculty of Bioengineering, Sichuan University of Science and Engineering, Zigong, People's Republic of China
| | - Ziming Zhao
- Faculty of Bioengineering, Sichuan University of Science and Engineering, Zigong, People's Republic of China
| | - Vincenza Dolce
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Yuan Li
- College of Life Science and Technology, Xinjiang University, Urumqi, China
- Department of Bioscience, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy
| | - Rosita Curcio
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
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11
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Fungal Phytases: Current Research and Applications in Food Industry. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Lin HC, Li WH, Chen CC, Cheng TH, Lan YH, Huang MD, Chen WM, Chang JS, Chang HY. Diverse Enzymes With Industrial Applications in Four Thraustochytrid Genera. Front Microbiol 2020; 11:573907. [PMID: 33193181 PMCID: PMC7641610 DOI: 10.3389/fmicb.2020.573907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/24/2020] [Indexed: 11/19/2022] Open
Abstract
Thraustochytrids are heterotrophic fungus-like protists that can dissolve organic matters with enzymes. Four strains, AP45, ASP1, ASP2, and ASP4, were isolated from the coastal water of Taiwan, and respectively identified as Aurantiochytrium sp., Schizochytrium sp., Parietichytrium sp., and Botryochytrium sp. based on 18S rRNA sequences. Transcriptome datasets of these four strains at days 3-5 were generated using Next Generation Sequencing technology, and screened for enzymes with potential industrial applications. Functional annotations based on KEGG database suggest that many unigenes of all four strains were related to the pathways of industrial enzymes. Most of all four strains contained homologous genes for 15 out of the 17 targeted enzymes, and had extra- and/or intra-cellular enzymatic activities, including urease, asparaginase, lipase, glucosidase, alkaline phosphatase and protease. Complete amino sequences of the first-time identified L-asparaginase and phytase in thraustochytrids were retrieved, and respectively categorized to the Type I and BPPhy families based on phylogenetic relationships, protein structural modeling and active sites. Milligram quantities of highly purified, soluble protein of urease and L-asparaginase were successfully harvested and analyzed for recombinant enzymatic activities. These analytical results highlight the diverse enzymes for wide-range applications in thraustochytrids.
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Affiliation(s)
- Hsiu-Chin Lin
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan.,Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wei-Hao Li
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Chi-Chih Chen
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Tien-Hsing Cheng
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yu-Hsuan Lan
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Ming-Der Huang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wen-Ming Chen
- Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan
| | - Jo-Shu Chang
- Department of Chemical and Materials Engineering, College of Engineering, Tunghai University, Taichung, Taiwan.,Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung, Taiwan.,Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Hsin-Yang Chang
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan.,Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
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Corrêa TLR, de Araújo EF. Fungal phytases: from genes to applications. Braz J Microbiol 2020; 51:1009-1020. [PMID: 32410091 PMCID: PMC7455620 DOI: 10.1007/s42770-020-00289-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/30/2020] [Indexed: 12/18/2022] Open
Abstract
Phytic acid stores 60-90% of the inorganic phosphorus in legumes, oil seeds, and cereals, making it inaccessible for metabolic processes in living systems. In addition, given its negative charge, phytic acid complexes with divalent cations, starch, and proteins. Inorganic phosphorous can be released from phytic acid upon the action of phytases. Phytases are phosphatases produced by animals, plants, and microorganisms, notably Aspergillus niger, and are employed as animal feed additive, in chemical industry and for ethanol production. Given the industrial relevance of phytases produced by filamentous fungi, this work discusses the functional characterization of fungal phytase-coding genes/proteins, highlighting the physicochemical parameters that govern the enzymatic activity, the development of phytase super-producing strains, and key features for industrial applications.
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Affiliation(s)
- Thamy Lívia Ribeiro Corrêa
- Department of Microbiology/BIOAGRO, Federal University of Viçosa, Av. Peter Henry Rolfs s/n, Vicosa, MG, 36570-000, Brazil.
| | - Elza Fernandes de Araújo
- Department of Microbiology/BIOAGRO, Federal University of Viçosa, Av. Peter Henry Rolfs s/n, Vicosa, MG, 36570-000, Brazil
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Zhang H, Xiang Y, He N, Liu X, Liu H, Fang L, Zhang F, Sun X, Zhang D, Li X, Terzaghi W, Yan J, Dai M. Enhanced Vitamin C Production Mediated by an ABA-Induced PTP-like Nucleotidase Improves Plant Drought Tolerance in Arabidopsis and Maize. MOLECULAR PLANT 2020; 13:760-776. [PMID: 32068157 DOI: 10.1016/j.molp.2020.02.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 02/09/2020] [Accepted: 02/10/2020] [Indexed: 05/26/2023]
Abstract
Abscisic acid (ABA) is a key phytohormone that mediates environmental stress responses. Vitamin C, or L-ascorbic acid (AsA), is the most abundant antioxidant protecting against stress damage in plants. How the ABA and AsA signaling pathways interact in stress responses remains elusive. In this study, we characterized the role of a previously unidentified gene, PTPN (PTP-like Nucleotidase) in plant drought tolerance. In Arabidopsis, (AtPTPN was expressed in multiple tissues and upregulated by ABA and drought treatments. Loss-of-function mutants of AtPTPN were hyposensitive to ABA but hypersensitive to drought stresses, whereas plants with enhanced expression of AtPTPN showed opposite phenotypes to . Overexpression of maize PTPN (ZmPTPN) promoted, while knockdown of ZmPTPN inhibited plant drought tolerance, indicating conserved and positive roles of PTPN in plant drought tolerance. We found that both AtPTPN and ZmPTPN release Pi by hydrolyzing GDP/GMP/dGMP/IMP/dIMP, and that AtPTPN positively regulated AsA production via endogenous Pi content control. Consistently, overexpression of VTC2, the rate-limiting synthetic enzyme in AsA biosynthesis, promoted AsA production and plant drought tolerance, and these effects were largely dependent on AtPTPN activity. Furthermore, we demonstrated that the heat shock transcription factor HSFA6a directly binds the AtPTPN promoter and activates AtPTPN expression. Genetic analyses showed that AtPTPN is required for HSFA6a to regulate ABA and drought responses. Taken together, our data indicate that PTPN-mediated crosstalk between the ABA signaling and AsA biosynthesis pathways positively controls plant drought tolerance.
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Affiliation(s)
- Hui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanli Xiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Neng He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangguo Liu
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Agro-Biotechnology Institute, Jilin Academy of Agricultural Sciences, Changchun 130124, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Liping Fang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaopeng Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - William Terzaghi
- Department of Biology, Wilkes University, Wilkes-Barre, PA 18766, USA
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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Handa V, Sharma D, Kaur A, Arya SK. Biotechnological applications of microbial phytase and phytic acid in food and feed industries. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101600] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Sonne C, Ok YS, Dietz R, Alstrup AKO. Pig slurry needs modifications to be a sustainable fertilizer in crop production. ENVIRONMENTAL RESEARCH 2019; 178:108718. [PMID: 31520831 DOI: 10.1016/j.envres.2019.108718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/02/2019] [Accepted: 09/02/2019] [Indexed: 06/10/2023]
Abstract
Pig slurry from modern high-technological farms contain copper and zinc, which is under suspicion of being co-factors in the development of antibiotic resistance. In addition, these two elements contaminate the surrounding environment when spread in large quantities. Therefore, biogas plants and biomembranes should be used to remove hazardous substances such as copper, zink, antibiotics and antibiotic resistant bacteria before pig slurry is used as a fertilizer in crop production. That would allow recycling of phosphorous in a way that only to a limited extent affect the health of the environment.
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Affiliation(s)
- Christian Sonne
- Aarhus University, Department of Bioscience, Arctic Research Centre (ARC), Frederiksborgvej 399, PO Box 358, DK-4000, Roskilde, Denmark.
| | - Yong Sik Ok
- Korea Biochar Research Center & Division of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Rune Dietz
- Aarhus University, Department of Bioscience, Arctic Research Centre (ARC), Frederiksborgvej 399, PO Box 358, DK-4000, Roskilde, Denmark
| | - Aage K O Alstrup
- Aarhus University, Department of Nuclear Medicine and PET Center, Palle Juul-Jensens Boulevard 99, DK-8200, Aarhus N, Denmark
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Wang X, Du J, Zhang ZY, Fu YJ, Wang WM, Liang AH. A rational design to enhance the resistance of Escherichia coli phytase appA to trypsin. Appl Microbiol Biotechnol 2018; 102:9647-9656. [DOI: 10.1007/s00253-018-9327-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 10/28/2022]
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18
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Angelovičová M, Mellen M, Zajác P, Čapla J, Angelovič M. Tibia mineralization of chickens determined to meat production using a microbial phytase. POTRAVINARSTVO 2018. [DOI: 10.5219/805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The target of the research was 6-phytase of microbial origin. It was used in feed mixtures for chickens determined to meat production. Its effect has been studied in relation to the tibia mineralization by calcium, phosphorus and magnesium. 6-phytase is a product of Aspergillus oryzae. That was obtained by means of biotechnological processes of production of commercially available enzymes. It was incorporated in the feed mixtures 0.1%. In a 38-day feeding trial, 300 one-day-old, as hatched, Cobb 500 chickens determined to meat production (100 birds per group) were fed on one concentrations of dietary non-phytate phosphorus (2.32, 2.31 g.kg-1, respectively and supplemental microbial phytase (0 and 500 FTU.kg-1 feed mixtures). Control group was used to compare the results and control feed mixtures contained 4.5 g.kg-1 without microbial phytase. At days 40 it was selected 6 birds in every group, which were slaughter in accordance with the principles of welfare. Left tibias of every bird were used to determination of calcium, phosphorus and magnesium contents. According to in vivo, it was found that the addition of microbial phytase to reduced dietary non-phytate phosphorus increased concentrations of calcium (Ca), phosphorus (P) and magnesium (Mg) in tibia. The differences among groups were statistically significant (p <0.05). It was concluded that reducing of dietary non-phytate phosphorus on the 2.32, 2.31 g.kg-1, respectively, by monocalcium phosphate and microbial phytase supplementation in feed mixtures facilitated tibia mineralization at chicken determined to meat production.
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Abstract
In higher eukaryotes, the Tyr phosphorylation status of cellular proteins results from the coordinated action of Protein Tyrosine Kinases (PTKs) and Protein Tyrosine Phosphatases (PTPs). PTPs have emerged as highly regulated enzymes with diverse substrate specificity, and proteins with Tyr-dephosphorylation or Tyr-dephosphorylation-like properties can be clustered as the PTPome. This includes proteins from the PTP superfamily, which display a Cys-based catalytic mechanism, as well as enzymes from other gene families (Asp-based phosphatases, His-based phosphatases) that have converged in protein Tyr-dephosphorylation-related functions by using non-Cys-based catalytic mechanisms. Within the Cys-based members of the PTPome, classical PTPs dephosphorylate specific phosphoTyr (pTyr) residues from protein substrates, whereas VH1-like dual-specificity PTPs dephosphorylate pTyr, pSer, and pThr residues, as well as nonproteinaceous substrates, including phosphoinositides and phosphorylated carbohydrates. In addition, several PTPs have impaired catalytic activity as a result of amino acid substitutions at their active sites, but retain regulatory functions related with pTyr signaling. As a result of their relevant biological activity, many PTPs are linked to human disease, including cancer, neurodevelopmental, and metabolic diseases, making these proteins important drug targets and molecular markers in the clinic. Here, a brief overview on the biochemistry and physiology of the different groups of proteins that belong to the mammalian PTPome is presented.
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Blüher D, Laha D, Thieme S, Hofer A, Eschen-Lippold L, Masch A, Balcke G, Pavlovic I, Nagel O, Schonsky A, Hinkelmann R, Wörner J, Parvin N, Greiner R, Weber S, Tissier A, Schutkowski M, Lee J, Jessen H, Schaaf G, Bonas U. A 1-phytase type III effector interferes with plant hormone signaling. Nat Commun 2017; 8:2159. [PMID: 29255246 PMCID: PMC5735085 DOI: 10.1038/s41467-017-02195-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 11/13/2017] [Indexed: 11/16/2022] Open
Abstract
Most Gram-negative phytopathogenic bacteria inject type III effector (T3E) proteins into plant cells to manipulate signaling pathways to the pathogen's benefit. In resistant plants, specialized immune receptors recognize single T3Es or their biochemical activities, thus halting pathogen ingress. However, molecular function and mode of recognition for most T3Es remains elusive. Here, we show that the Xanthomonas T3E XopH possesses phytase activity, i.e., dephosphorylates phytate (myo-inositol-hexakisphosphate, InsP6), the major phosphate storage compound in plants, which is also involved in pathogen defense. A combination of biochemical approaches, including a new NMR-based method to discriminate inositol polyphosphate enantiomers, identifies XopH as a naturally occurring 1-phytase that dephosphorylates InsP6 at C1. Infection of Nicotiana benthamiana and pepper by Xanthomonas results in a XopH-dependent conversion of InsP6 to InsP5. 1-phytase activity is required for XopH-mediated immunity of plants carrying the Bs7 resistance gene, and for induction of jasmonate- and ethylene-responsive genes in N. benthamiana.
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Affiliation(s)
- Doreen Blüher
- Institute for Biology, Department of Genetics, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Debabrata Laha
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115, Bonn, Germany
- Center for Plant Molecular Biology, Department of Plant Physiology, Eberhard Karls University Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Sabine Thieme
- Institute for Biology, Department of Genetics, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Alexandre Hofer
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Lennart Eschen-Lippold
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Antonia Masch
- Institute for Biochemistry and Biotechnology, Department of Enzymology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle (Saale), Germany
| | - Gerd Balcke
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Igor Pavlovic
- Institute of Organic Chemistry, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Oliver Nagel
- Institute for Biology, Department of Genetics, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Antje Schonsky
- Institute for Biology, Department of Genetics, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Rahel Hinkelmann
- Institute of Organic Chemistry, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Jakob Wörner
- Institute of Physical Chemistry, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Nargis Parvin
- Center for Plant Molecular Biology, Department of Plant Physiology, Eberhard Karls University Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Ralf Greiner
- Department of Food Technology and Bioprocess Engineering, Max-Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131, Karlsruhe, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Mike Schutkowski
- Institute for Biochemistry and Biotechnology, Department of Enzymology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle (Saale), Germany
| | - Justin Lee
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Henning Jessen
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
- Institute of Organic Chemistry, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104, Freiburg, Germany.
| | - Gabriel Schaaf
- Institute of Crop Science and Resource Conservation, Department of Plant Nutrition, University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115, Bonn, Germany.
- Center for Plant Molecular Biology, Department of Plant Physiology, Eberhard Karls University Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany.
| | - Ulla Bonas
- Institute for Biology, Department of Genetics, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany.
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Greiner R. Activity of Escherichia coli, Aspergillus niger, and Rye Phytase toward Partially Phosphorylated myo-Inositol Phosphates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:9603-9607. [PMID: 29052415 DOI: 10.1021/acs.jafc.7b03897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Kinetic parameters for the dephosphorylation of sodium phytate and a series of partially phosphorylated myo-inositol phosphates were determined at pH 3.0 and pH 5.0 for three phytase preparations (Aspergillus niger, Escherichia coli, rye). The enzymes showed lower affinity and turnover numbers at pH 3 compared to pH 5 toward all myo-inositol phosphates included in the study. The number and distribution of phosphate groups on the myo-inositol ring affected the kinetic parameters. Representatives of the individual phytate dephosphorylation pathways were identified as the best substrates of the phytases. Within the individual phytate dephosphorylation pathways, the pentakisphosphates were better substrates compared to the tetrakisphosphates or phytate itself. E. coli and rye phytase showed comparable activities at both pH values toward the tetrakis- and trisphosphate, whereas A. niger phytase exhibited a higher activity toward the tetrakisphosphate. A myo-inositol phosphate with alternate phosphate groups was shown to be not significantly dephosphorylated by the phytases.
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Affiliation(s)
- Ralf Greiner
- Federal Research Institute of Nutrition and Food, Department of Food Technology and Bioprocess Engineering, Max Rubner-Institut , Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
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22
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Bruder LM, Gruninger RJ, Cleland CP, Mosimann SC. Bacterial PhyA protein-tyrosine phosphatase-like myo-inositol phosphatases in complex with the Ins(1,3,4,5)P 4 and Ins(1,4,5)P 3 second messengers. J Biol Chem 2017; 292:17302-17311. [PMID: 28848052 DOI: 10.1074/jbc.m117.787853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 08/24/2017] [Indexed: 11/06/2022] Open
Abstract
myo-Inositol phosphates (IPs) are important bioactive molecules that have multiple activities within eukaryotic cells, including well-known roles as second messengers and cofactors that help regulate diverse biochemical processes such as transcription and hormone receptor activity. Despite the typical absence of IPs in prokaryotes, many of these organisms express IPases (or phytases) that dephosphorylate IPs. Functionally, these enzymes participate in phosphate-scavenging pathways and in plant pathogenesis. Here, we determined the X-ray crystallographic structures of two catalytically inactive mutants of protein-tyrosine phosphatase-like myo-inositol phosphatases (PTPLPs) from the non-pathogenic bacteria Selenomonas ruminantium (PhyAsr) and Mitsuokella multacida (PhyAmm) in complex with the known eukaryotic second messengers Ins(1,3,4,5)P4 and Ins(1,4,5)P3 Both enzymes bound these less-phosphorylated IPs in a catalytically competent manner, suggesting that IP hydrolysis has a role in plant pathogenesis. The less-phosphorylated IP binding differed in both the myo-inositol ring position and orientation when compared with a previously determined complex structure in the presence of myo-inositol-1,2,3,4,5,6-hexakisphosphate (InsP6 or phytate). Further, we have demonstrated that PhyAsr and PhyAmm have different specificities for Ins(1,2,4,5,6)P5, have identified structural features that account for this difference, and have shown that the absence of these features results in a broad specificity toward Ins(1,2,4,5,6)P5 These features are main-chain conformational differences in loops adjacent to the active site that include the extended loop prior to the penultimate helix, the extended Ω-loop, and a β-hairpin turn of the Phy-specific domain.
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Affiliation(s)
- Lisza M Bruder
- From the Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge AB T1K 3M4, Canada and
| | - Robert J Gruninger
- the Lethbridge Research Centre, Agriculture and Agri-Foods Canada, Lethbridge AB T1J 4B1, Canada
| | - Colyn P Cleland
- From the Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge AB T1K 3M4, Canada and
| | - Steven C Mosimann
- From the Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge AB T1K 3M4, Canada and
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Balwani I, Chakravarty K, Gaur S. Role of phytase producing microorganisms towards agricultural sustainability. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Irshad M, Asgher M, Bhatti KH, Zafar M, Anwar Z. Anticancer and Nutraceutical Potentialities of Phytase/Phytate. INT J PHARMACOL 2017. [DOI: 10.3923/ijp.2017.808.817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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25
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Molecular advancements in the development of thermostable phytases. Appl Microbiol Biotechnol 2017; 101:2677-2689. [PMID: 28233043 DOI: 10.1007/s00253-017-8195-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 02/12/2017] [Accepted: 02/13/2017] [Indexed: 12/20/2022]
Abstract
Since the discovery of phytic acid in 1903 and phytase in 1907, extensive research has been carried out in the field of phytases, the phytic acid degradatory enzymes. Apart from forming backbone enzyme in the multimillion dollar-based feed industry, phytases extend a multifaceted role in animal nutrition, industries, human physiology, and agriculture. The utilization of phytases in industries is not effectively achieved most often due to the loss of its activity at high temperatures. The growing demand of thermostable phytases with high residual activity could be addressed by the combinatorial use of efficient phytase sources, protein engineering techniques, heterologous expression hosts, or thermoprotective coatings. The progress in phytase research can contribute to its economized production with a simultaneous reduction of various environmental problems such as eutrophication, greenhouse gas emission, and global warming. In the current review, we address the recent advances in the field of various natural as well as recombinant thermotolerant phytases, their significance, and the factors contributing to their thermotolerance.
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26
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Balaban NP, Suleimanova AD, Valeeva LR, Shakirov EV, Sharipova MR. Structural Characteristics and Catalytic Mechanism of Bacillus β-Propeller Phytases. BIOCHEMISTRY (MOSCOW) 2017; 81:785-93. [PMID: 27677548 DOI: 10.1134/s0006297916080010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
β-Propeller phytases of Bacillus are unique highly conservative and highly specific enzymes capable of cleaving insoluble phytate compounds. In this review, we analyzed data on the properties of these enzymes, their differences from other phytases, and their unique spatial structures and substrate specificities. We considered influences of different factors on the catalytic activity and thermostability of these enzymes. There are few data on the hydrolysis mechanism of these enzymes, which makes it difficult to analyze their mechanism of action and their final products. We analyzed the available data on hydrolysis by β-propeller phytases of calcium complexes with myo-inositol hexakisphosphate.
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Affiliation(s)
- N P Balaban
- Kazan (Volga Region) Federal University, Kazan, 420008, Russia.
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27
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Regulation of Soluble Phosphate on the Ability of Phytate Mineralization and β-Propeller Phytase Gene Expression of Pseudomonas fluorescens JZ-DZ1, a Phytate-Mineralizing Rhizobacterium. Curr Microbiol 2016; 73:915-923. [DOI: 10.1007/s00284-016-1139-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 09/13/2016] [Indexed: 10/21/2022]
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Alonso A, Pulido R. The extended human PTPome: a growing tyrosine phosphatase family. FEBS J 2015; 283:1404-29. [PMID: 26573778 DOI: 10.1111/febs.13600] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 10/02/2015] [Accepted: 11/13/2015] [Indexed: 12/13/2022]
Abstract
Tyr phosphatases are, by definition, enzymes that dephosphorylate phospho-Tyr (pTyr) from proteins. This activity is found in several structurally diverse protein families, including the protein Tyr phosphatase (PTP), arsenate reductase, rhodanese, haloacid dehalogenase (HAD) and His phosphatase (HP) families. Most of these families include members with substrate specificity for non-pTyr substrates, such as phospho-Ser/phospho-Thr, phosphoinositides, phosphorylated carbohydrates, mRNAs, or inorganic moieties. A Cys is essential for catalysis in PTPs, rhodanese and arsenate reductase enzymes, whereas this work is performed by an Asp in HAD phosphatases and by a His in HPs, via a catalytic mechanism shared by all of the different families. The category that contains most Tyr phosphatases is the PTP family, which, although it received its name from this activity, includes Ser, Thr, inositide, carbohydrate and RNA phosphatases, as well as some inactive pseudophosphatase proteins. Here, we propose an extended collection of human Tyr phosphatases, which we call the extended human PTPome. The addition of new members (SACs, paladin, INPP4s, TMEM55s, SSU72, and acid phosphatases) to the currently categorized PTP group of enzymes means that the extended human PTPome contains up to 125 proteins, of which ~ 40 are selective for pTyr. We set criteria to ascribe proteins to the extended PTPome, and summarize the more important features of the new PTPome members in the context of their phosphatase activity and their relationship with human disease.
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Affiliation(s)
- Andrés Alonso
- Instituto de Biología y Genética Molecular (IBGM), CSIC-Universidad de Valladolid, Valladolid, Spain
| | - Rafael Pulido
- Biocruces Health Research Institute, Barakaldo, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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Cong J, Liu X, Lu H, Xu H, Li Y, Deng Y, Li D, Zhang Y. Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest. BMC Microbiol 2015; 15:167. [PMID: 26289044 PMCID: PMC4546036 DOI: 10.1186/s12866-015-0491-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 07/21/2015] [Indexed: 02/02/2023] Open
Abstract
Background Tropical rainforests cover over 50 % of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, largely mediated by metabolic activities of soil microbial communities. A deep analysis of soil microbial communities and their roles in ecological processes would improve our understanding on biogeochemical elemental cycles. However, soil microbial functional gene diversity in tropical rainforests and causative factors remain unclear. GeoChip, contained almost all of the key functional genes related to biogeochemical cycles, could be used as a specific and sensitive tool for studying microbial gene diversity and metabolic potential. In this study, soil microbial functional gene diversity in tropical rainforest was analyzed by using GeoChip technology. Results Gene categories detected in the tropical rainforest soils were related to different biogeochemical processes, such as carbon (C), nitrogen (N) and phosphorus (P) cycling. The relative abundance of genes related to C and P cycling detected mostly derived from the cultured bacteria. C degradation gene categories for substrates ranging from labile C to recalcitrant C were all detected, and gene abundances involved in many recalcitrant C degradation gene categories were significantly (P < 0.05) different among three sampling sites. The relative abundance of genes related to N cycling detected was significantly (P < 0.05) different, mostly derived from the uncultured bacteria. The gene categories related to ammonification had a high relative abundance. Both canonical correspondence analysis and multivariate regression tree analysis showed that soil available N was the most correlated with soil microbial functional gene structure. Conclusions Overall high microbial functional gene diversity and different soil microbial metabolic potential for different biogeochemical processes were considered to exist in tropical rainforest. Soil available N could be the key factor in shaping the soil microbial functional gene structure and metabolic potential. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0491-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jing Cong
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China. .,Institute of Forestry Ecology, Environment and Protection, and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China.
| | - Hui Lu
- Institute of Forestry Ecology, Environment and Protection, and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Han Xu
- Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China.
| | - Yide Li
- Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China.
| | - Ye Deng
- Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Diqiang Li
- Institute of Forestry Ecology, Environment and Protection, and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Yuguang Zhang
- Institute of Forestry Ecology, Environment and Protection, and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Chinese Academy of Forestry, Beijing, 100091, China.
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Novel Glucose-1-Phosphatase with High Phytase Activity and Unusual Metal Ion Activation from Soil Bacterium Pantoea sp. Strain 3.5.1. Appl Environ Microbiol 2015. [PMID: 26209662 DOI: 10.1128/aem.01384-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phosphorus is an important macronutrient, but its availability in soil is limited. Many soil microorganisms improve the bioavailability of phosphate by releasing it from various organic compounds, including phytate. To investigate the diversity of phytate-hydrolyzing bacteria in soil, we sampled soils of various ecological habitats, including forest, private homesteads, large agricultural complexes, and urban landscapes. Bacterial isolate Pantoea sp. strain 3.5.1 with the highest level of phytase activity was isolated from forest soil and investigated further. The Pantoea sp. 3.5.1 agpP gene encoding a novel glucose-1-phosphatase with high phytase activity was identified, and the corresponding protein was purified to apparent homogeneity, sequenced by mass spectroscopy, and biochemically characterized. The AgpP enzyme exhibits maximum activity and stability at pH 4.5 and at 37°C. The enzyme belongs to a group of histidine acid phosphatases and has the lowest Km values toward phytate, glucose-6-phosphate, and glucose-1-phosphate. Unexpectedly, stimulation of enzymatic activity by several divalent metal ions was observed for the AgpP enzyme. High-performance liquid chromatography (HPLC) and high-performance ion chromatography (HPIC) analyses of phytate hydrolysis products identify dl-myo-inositol 1,2,4,5,6-pentakisphosphate as the final product of the reaction, indicating that the Pantoea sp. AgpP glucose-1-phosphatase can be classified as a 3-phytase. The identification of the Pantoea sp. AgpP phytase and its unusual regulation by metal ions highlight the remarkable diversity of phosphorus metabolism regulation in soil bacteria. Furthermore, our data indicate that natural forest soils harbor rich reservoirs of novel phytate-hydrolyzing enzymes with unique biochemical features.
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Chen CC, Cheng KJ, Ko TP, Guo RT. Current Progresses in Phytase Research: Three-Dimensional Structure and Protein Engineering. CHEMBIOENG REVIEWS 2015. [DOI: 10.1002/cben.201400026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Weber S, Stirnimann CU, Wieser M, Frey D, Meier R, Engelhardt S, Li X, Capitani G, Kammerer RA, Hilbi H. A type IV translocated Legionella cysteine phytase counteracts intracellular growth restriction by phytate. J Biol Chem 2014; 289:34175-88. [PMID: 25339170 DOI: 10.1074/jbc.m114.592568] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The causative agent of Legionnaires' pneumonia, Legionella pneumophila, colonizes diverse environmental niches, including biofilms, plant material, and protozoa. In these habitats, myo-inositol hexakisphosphate (phytate) is prevalent and used as a phosphate storage compound or as a siderophore. L. pneumophila replicates in protozoa and mammalian phagocytes within a unique "Legionella-containing vacuole." The bacteria govern host cell interactions through the Icm/Dot type IV secretion system (T4SS) and ∼300 different "effector" proteins. Here we characterize a hitherto unrecognized Icm/Dot substrate, LppA, as a phytate phosphatase (phytase). Phytase activity of recombinant LppA required catalytically essential cysteine (Cys(231)) and arginine (Arg(237)) residues. The structure of LppA at 1.4 Å resolution revealed a mainly α-helical globular protein stabilized by four antiparallel β-sheets that binds two phosphate moieties. The phosphates localize to a P-loop active site characteristic of dual specificity phosphatases or to a non-catalytic site, respectively. Phytate reversibly abolished growth of L. pneumophila in broth, and growth inhibition was relieved by overproduction of LppA or by metal ion titration. L. pneumophila lacking lppA replicated less efficiently in phytate-loaded Acanthamoeba castellanii or Dictyostelium discoideum, and the intracellular growth defect was complemented by the phytase gene. These findings identify the chelator phytate as an intracellular bacteriostatic component of cell-autonomous host immunity and reveal a T4SS-translocated L. pneumophila phytase that counteracts intracellular bacterial growth restriction by phytate. Thus, bacterial phytases might represent therapeutic targets to combat intracellular pathogens.
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Affiliation(s)
- Stephen Weber
- From the Max von Pettenkofer Institute, Department of Medicine, Ludwig-Maximilians University Munich, 80336 Munich, Germany
| | - Christian U Stirnimann
- the Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Mara Wieser
- the Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Daniel Frey
- the Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Roger Meier
- the Scientific Center for Optical and Electron Microscopy, ETH Zurich, 8093 Zurich, Switzerland
| | - Sabrina Engelhardt
- the Institute of Veterinary Physiology and Zurich Center for Integrative Human Physiology (ZIHP), Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland, and
| | - Xiaodan Li
- the Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Guido Capitani
- the Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Richard A Kammerer
- the Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Hubert Hilbi
- From the Max von Pettenkofer Institute, Department of Medicine, Ludwig-Maximilians University Munich, 80336 Munich, Germany, the Institute of Medical Microbiology, Department of Medicine, University of Zurich, 8006 Zurich, Switzerland
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Singh B, Satyanarayana T. Fungal phytases: characteristics and amelioration of nutritional quality and growth of non-ruminants. J Anim Physiol Anim Nutr (Berl) 2014; 99:646-60. [DOI: 10.1111/jpn.12236] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 07/08/2014] [Indexed: 11/27/2022]
Affiliation(s)
- B. Singh
- Laboratory of Bioprocess Technology; Department of Microbiology; Maharshi Dayanand University; Haryana India
| | - T. Satyanarayana
- Department of Microbiology; University of Delhi South Campus; New Delhi India
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Wu TH, Chen CC, Cheng YS, Ko TP, Lin CY, Lai HL, Huang TY, Liu JR, Guo RT. Improving specific activity and thermostability of Escherichia coli phytase by structure-based rational design. J Biotechnol 2014; 175:1-6. [DOI: 10.1016/j.jbiotec.2014.01.034] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 01/27/2014] [Accepted: 01/31/2014] [Indexed: 11/16/2022]
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Ariza A, Moroz OV, Blagova EV, Turkenburg JP, Waterman J, Roberts SM, Vind J, Sjøholm C, Lassen SF, De Maria L, Glitsoe V, Skov LK, Wilson KS. Degradation of phytate by the 6-phytase from Hafnia alvei: a combined structural and solution study. PLoS One 2013; 8:e65062. [PMID: 23741456 PMCID: PMC3669009 DOI: 10.1371/journal.pone.0065062] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 04/20/2013] [Indexed: 11/19/2022] Open
Abstract
Phytases hydrolyse phytate (myo-inositol hexakisphosphate), the principal form of phosphate stored in plant seeds to produce phosphate and lower phosphorylated myo-inositols. They are used extensively in the feed industry, and have been characterised biochemically and structurally with a number of structures in the PDB. They are divided into four distinct families: histidine acid phosphatases (HAP), β-propeller phytases, cysteine phosphatases and purple acid phosphatases and also split into three enzyme classes, the 3-, 5- and 6-phytases, depending on the position of the first phosphate in the inositol ring to be removed. We report identification, cloning, purification and 3D structures of 6-phytases from two bacteria, Hafnia alvei and Yersinia kristensenii, together with their pH optima, thermal stability, and degradation profiles for phytate. An important result is the structure of the H. alvei enzyme in complex with the substrate analogue myo-inositol hexakissulphate. In contrast to the only previous structure of a ligand-bound 6-phytase, where the 3-phosphate was unexpectedly in the catalytic site, in the H. alvei complex the expected scissile 6-phosphate (sulphate in the inhibitor) is placed in the catalytic site.
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Affiliation(s)
- Antonio Ariza
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Olga V. Moroz
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Elena V. Blagova
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Johan P. Turkenburg
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Jitka Waterman
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Shirley M. Roberts
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | | | | | | | | | | | | | - Keith S. Wilson
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
- * E-mail:
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Koveal D, Clarkson MW, Wood TK, Page R, Peti W. Ligand binding reduces conformational flexibility in the active site of tyrosine phosphatase related to biofilm formation A (TpbA) from Pseudomonasaeruginosa. J Mol Biol 2013; 425:2219-31. [PMID: 23524133 DOI: 10.1016/j.jmb.2013.03.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 03/06/2013] [Accepted: 03/13/2013] [Indexed: 10/27/2022]
Abstract
Tyrosine phosphatase related to biofilm formation A (TpbA) is a periplasmic dual-specificity phosphatase (DUSP) that controls biofilm formation in the pathogenic bacterium Pseudomonas aeruginosa. While DUSPs are known to regulate important cellular functions in both prokaryotes and eukaryotes, very few structures of bacterial DUSPs are available. Here, we present the solution structure of TpbA in the ligand-free open conformation, along with an analysis of the structural and dynamic changes that accompany ligand/phosphate binding. While TpbA adopts a typical DUSP fold, it also possesses distinct structural features that distinguish it from eukaryotic DUSPs. These include additional secondary structural elements, β0 and α6, and unique conformations of the variable insert, the α4-α5 loop and helix α5 that impart TpbA with a flat active-site surface. In the absence of ligand, the protein tyrosine phosphatase loop is disordered and the general acid loop adopts an open conformation, placing the catalytic aspartate, Asp105, more than 11Å away from the active site. Furthermore, the loops surrounding the active site experience motions on multiple timescales, consistent with a combination of conformational heterogeneity and fast (picosecond to nanosecond) timescale dynamics, which are significantly reduced upon ligand binding. Taken together, these data structurally distinguish TpbA and possibly other bacterial DUSPs from eukaryotic DUSPs and provide a rich picture of active-site dynamics in the ligand-free state that are lost upon ligand binding.
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Affiliation(s)
- Dorothy Koveal
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903, USA
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Thoetkiattikul H, Mhuantong W, Laothanachareon T, Tangphatsornruang S, Pattarajinda V, Eurwilaichitr L, Champreda V. Comparative analysis of microbial profiles in cow rumen fed with different dietary fiber by tagged 16S rRNA gene pyrosequencing. Curr Microbiol 2013; 67:130-7. [PMID: 23471692 DOI: 10.1007/s00284-013-0336-3] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 02/04/2013] [Indexed: 01/28/2023]
Abstract
The ruminal microbiome of cattle plays an important role not only in animal health and productivity but also in food safety and environment. Microbial profiles of rumen fluid obtained from dairy cows fed on three different fiber/starch diet compositions were characterized. Tagged 16S rRNA gene pyrosequencing and statistical analysis revealed that the dominant ruminal bacteria shared by all three sample groups belonged to phyla Bacteroidetes, Firmicutes, and Proteobacteria. However, the relative abundance of these bacterial groups was markedly affected by diet composition. In animals fed with a high fiber diet, the fibrolytic and cellulolytic bacteria Lachnospiraceae, Ruminococcaceae, and Fibrobacteraceae were found in highest abundance compared with animals fed other diets with lower fiber content. The polysaccharide-degrading Prevotellaceae and Flavobacteriaceae bacteria were most abundant in the rumen of cows fed on diet with the highest starch content. These data highlight the ruminal microbiome's ability to adapt to feed composition and also provide a basis for the development of feed formulation systems designed to improve livestock productivity.
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Affiliation(s)
- Honglada Thoetkiattikul
- Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Paholyothin Road, Khlong Luang, Pathumthani, 12120, Thailand.
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Böhmer F, Szedlacsek S, Tabernero L, Ostman A, den Hertog J. Protein tyrosine phosphatase structure-function relationships in regulation and pathogenesis. FEBS J 2013; 280:413-31. [PMID: 22682070 DOI: 10.1111/j.1742-4658.2012.08655.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein phosphorylation on tyrosine residues is tightly controlled by protein tyrosine phosphatases (PTPs) at multiple levels: spatio-temporal expression, subcellular localization and post-translational modification. Structural and functional analysis of the PTP domains has provided insight into catalysis and regulatory mechanisms that control the enzymatic activity. Understanding the molecular basis of PTP regulation is of fundamental importance to dissect the pleiotropic effect of these enzymes in both health and disease. Here, we review recent insights into the regulation of receptor-like PTPs by extracellular ligands and into regulation by reversible oxidation that impairs catalysis directly. The physiological roles of PTPs are essential in homeostasis in eukaryotic cells and pertubation of their functional attributes causes different disease states. As an example, we discuss recent findings indicating how inappropriate oxidation of PTPs in cancer cells may contribute to cell transformation. On the other hand, PTPs from many pathogens are key virulence factors and manipulate signalling pathways in the host cells to promote invasion and survival of the microorganisms. This research area has received relatively little attention but has advanced remarkably. We review the structural features of pathogenic PTPs, their similarities and differences with eukaryotic PTPs, and the possible exploitation of this knowledge for therapeutic intervention.
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Affiliation(s)
- Frank Böhmer
- Center for Molecular Biomedicine, Jena University Hospital, Jena, Germany
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40
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Abstract
Phytases are phosphohydrolytic enzymes that initiate stepwise removal of phosphate from phytate. Simple-stomached species such as swine, poultry, and fish require extrinsic phytase to digest phytate, the major form of phosphorus in plant-based feeds. Consequently, this enzyme is supplemented in these species’ diets to decrease their phosphorus excretion, and it has emerged as one of the most effective and lucrative feed additives. This chapter provides a comprehensive review of the evolving course of phytase science and technology. It gives realistic estimates of the versatile roles of phytase in animal feeding, environmental protection, rock phosphorus preservation, human nutrition and health, and industrial applications. It elaborates on new biotechnology and existing issues related to developing novel microbial phytases as well as phytase-transgenic plants and animals. And it targets critical and integrated analyses on the global impact, novel application, and future demand of phytase in promoting animal agriculture, human health, and societal sustainability.
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Affiliation(s)
- Xin Gen Lei
- Department of Animal Science, Cornell University, Ithaca, New York 14853
| | | | | | | | - Michael J. Azain
- Department of Animal Science, University of Georgia, Athens, Georgia 30602
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41
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Unno Y, Shinano T. Metagenomic analysis of the rhizosphere soil microbiome with respect to phytic acid utilization. Microbes Environ 2012; 28:120-7. [PMID: 23257911 PMCID: PMC4070688 DOI: 10.1264/jsme2.me12181] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
While phytic acid is a major form of organic phosphate in many soils, plant utilization of phytic acid is normally limited; however, culture trials of Lotus japonicus using experimental field soil that had been managed without phosphate fertilizer for over 90 years showed significant usage of phytic acid applied to soil for growth and flowering and differences in the degree of growth, even in the same culture pot. To understand the key metabolic processes involved in soil phytic acid utilization, we analyzed rhizosphere soil microbial communities using molecular ecological approaches. Although molecular fingerprint analysis revealed changes in the rhizosphere soil microbial communities from bulk soil microbial community, no clear relationship between the microbiome composition and flowering status that might be related to phytic acid utilization of L. japonicus could be determined. However, metagenomic analysis revealed changes in the relative abundance of the classes Bacteroidetes, Betaproteobacteria, Chlorobi, Dehalococcoidetes and Methanobacteria, which include strains that potentially promote plant growth and phytic acid utilization, and some gene clusters relating to phytic acid utilization, such as alkaline phosphatase and citrate synthase, with the phytic acid utilization status of the plant. This study highlights phylogenetic and metabolic features of the microbial community of the L. japonicus rhizosphere and provides a basic understanding of how rhizosphere microbial communities affect the phytic acid status in soil.
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Affiliation(s)
- Yusuke Unno
- NARO Hokkaido Agricultural Research Center, Hokkaido, Japan.
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42
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Kumar V, Singh G, Verma AK, Agrawal S. In silico characterization of histidine Acid phytase sequences. Enzyme Res 2012; 2012:845465. [PMID: 23304454 PMCID: PMC3523131 DOI: 10.1155/2012/845465] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 11/19/2012] [Indexed: 11/18/2022] Open
Abstract
Histidine acid phytases (HAPhy) are widely distributed enzymes among bacteria, fungi, plants, and some animal tissues. They have a significant role as an animal feed enzyme and in the solubilization of insoluble phosphates and minerals present in the form of phytic acid complex. A set of 50 reference protein sequences representing HAPhy were retrieved from NCBI protein database and characterized for various biochemical properties, multiple sequence alignment (MSA), homology search, phylogenetic analysis, motifs, and superfamily search. MSA using MEGA5 revealed the presence of conserved sequences at N-terminal "RHGXRXP" and C-terminal "HD." Phylogenetic tree analysis indicates the presence of three clusters representing different HAPhy, that is, PhyA, PhyB, and AppA. Analysis of 10 commonly distributed motifs in the sequences indicates the presence of signature sequence for each class. Motif 1 "SPFCDLFTHEEWIQYDYLQSLGKYYGYGAGNPLGPAQGIGF" was present in 38 protein sequences representing clusters 1 (PhyA) and 2 (PhyB). Cluster 3 (AppA) contains motif 9 "KKGCPQSGQVAIIADVDERTRKTGEAFAAGLAPDCAITVHTQADTSSPDP" as a signature sequence. All sequences belong to histidine acid phosphatase family as resulted from superfamily search. No conserved sequence representing 3- or 6-phytase could be identified using multiple sequence alignment. This in silico analysis might contribute in the classification and future genetic engineering of this most diverse class of phytase.
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Affiliation(s)
- Vinod Kumar
- Department of Biochemistry, G. B. Pant University of Agriculture & Technology, Pantnagar 263145, India
- Akal School of Biotechnology, Eternal University, Baru Sahib, Sirmour 173101, India
| | - Gopal Singh
- Department of Biochemistry, G. B. Pant University of Agriculture & Technology, Pantnagar 263145, India
| | - A. K. Verma
- Department of Biochemistry, G. B. Pant University of Agriculture & Technology, Pantnagar 263145, India
| | - Sanjeev Agrawal
- Department of Biochemistry, G. B. Pant University of Agriculture & Technology, Pantnagar 263145, India
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43
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Bai S, Li J, He Z, Van Nostrand JD, Tian Y, Lin G, Zhou J, Zheng T. GeoChip-based analysis of the functional gene diversity and metabolic potential of soil microbial communities of mangroves. Appl Microbiol Biotechnol 2012; 97:7035-48. [PMID: 23135227 DOI: 10.1007/s00253-012-4496-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 10/02/2012] [Accepted: 10/03/2012] [Indexed: 11/25/2022]
Abstract
Mangroves are unique and highly productive ecosystems and harbor very special microbial communities. Although the phylogenetic diversity of sediment microbial communities of mangrove habitats has been examined extensively, little is known regarding their functional gene diversity and metabolic potential. In this study, a high-throughput functional gene array (GeoChip 4.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of microbial communities in mangrove habitats from mangrove national nature reserves in China. GeoChip data indicated that these microbial communities were functionally diverse as measured by the number of genes detected, unique genes, and various diversity indices. Almost all key functional gene categories targeted by GeoChip 4.0 were detected in the mangrove microbial communities, including carbon (C) fixation, C degradation, methane generation, nitrogen (N) fixation, nitrification, denitrification, ammonification, N reduction, sulfur (S) metabolism, metal resistance, antibiotic resistance, and organic contaminant degradation. Detrended correspondence analysis (DCA) of all detected genes showed that Spartina alterniflora (HH), an invasive species, did not harbor significantly different microbial communities from Aegiceras corniculatum (THY), a native species, but did differ from other species, Kenaelia candel (QQ), Aricennia marina (BGR), and mangrove-free mud flat (GT). Canonical correspondence analysis (CCA) results indicated the microbial community structure was largely shaped by surrounding environmental variables, such as total nitrogen (TN), total carbon (TC), pH, C/N ratio, and especially salinity. This study presents a comprehensive survey of functional gene diversity of soil microbial communities from different mangrove habitats/species and provides new insights into our understanding of the functional potential of microbial communities in mangrove ecosystems.
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Affiliation(s)
- Shijie Bai
- State Key Lab. of Marine Environmental Sciences and Key Lab. of MOE for Coast and Wetland Ecosystem, School of Life Sciences, Xiamen University, Xiamen, 361005, China
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Gruninger RJ, Dobing S, Smith AD, Bruder LM, Selinger LB, Wieden HJ, Mosimann SC. Substrate binding in protein-tyrosine phosphatase-like inositol polyphosphatases. J Biol Chem 2011; 287:9722-9730. [PMID: 22139834 DOI: 10.1074/jbc.m111.309872] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Protein-tyrosine phosphatase-like inositol polyphosphatases are microbial enzymes that catalyze the stepwise removal of one or more phosphates from highly phosphorylated myo-inositols via a relatively ordered pathway. To understand the substrate specificity and kinetic mechanism of these enzymes we have determined high resolution, single crystal, x-ray crystallographic structures of inactive Selenomonas ruminantium PhyA in complex with myo-inositol hexa- and pentakisphosphate. These structures provide the first glimpse of a myo-inositol polyphosphatase-ligand complex consistent with its known specificity and reveal novel features of the kinetic mechanism. To complement the structural studies, fluorescent binding assays have been developed and demonstrate that the K(d) for this enzyme is several orders of magnitude lower than the K(m). Together with rapid kinetics data, these results suggest that the protein tyrosine phosphatase-like inositol polyphosphatases have a two-step, substrate-binding mechanism that facilitates catalysis.
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Affiliation(s)
- Robert J Gruninger
- Departments of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Selina Dobing
- Departments of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Adam D Smith
- Departments of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Lisza M Bruder
- Departments of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - L Brent Selinger
- Departments of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Hans-Joachim Wieden
- Departments of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Steven C Mosimann
- Departments of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4.
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45
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Yao MZ, Zhang YH, Lu WL, Hu MQ, Wang W, Liang AH. Phytases: crystal structures, protein engineering and potential biotechnological applications. J Appl Microbiol 2011; 112:1-14. [DOI: 10.1111/j.1365-2672.2011.05181.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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46
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Zeng YF, Ko TP, Lai HL, Cheng YS, Wu TH, Ma Y, Chen CC, Yang CS, Cheng KJ, Huang CH, Guo RT, Liu JR. Crystal Structures of Bacillus Alkaline Phytase in Complex with Divalent Metal ions and Inositol Hexasulfate. J Mol Biol 2011; 409:214-24. [DOI: 10.1016/j.jmb.2011.03.063] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 03/20/2011] [Accepted: 03/28/2011] [Indexed: 11/26/2022]
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47
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Huang H, Zhang R, Fu D, Luo J, Li Z, Luo H, Shi P, Yang P, Diao Q, Yao B. Diversity, abundance and characterization of ruminal cysteine phytases suggest their important role in phytate degradation. Environ Microbiol 2010; 13:747-57. [PMID: 21105982 DOI: 10.1111/j.1462-2920.2010.02379.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A novel class of cysteine phytase showing ability to degrade phytate has recently been isolated from rumen bacteria. To expand our knowledge of this enzyme class, a total of 101 distinct cysteine phytase gene fragments were identified from the ruminal genomic DNA of Bore goats and Holstein cows, and most of them shared low identities (< 50%) with known sequences. By phylogenetic analysis, these sequences were separated into three clusters that showed substantial diversity. The two most abundant cysteine phytase genes of goat rumens were cloned and their protein products were characterized. Four findings were revealed based on our results. (i) Compared with soil and water environment, where β-propeller phytase is the most important phytate-degrading enzyme, cysteine phytase is the major phytate-degrading enzyme in the anaerobic ruminal environment. (ii) Cysteine phytase fragments in the rumen contents of goat and cow have the same diversity profile, although most of the sequences and their abundance differ in the two species. (iii) Each species has their respective high-abundance genes, which may play major roles for phytate degradation. (iv) Compared with previously reported cysteine phytases that have pH optimum at 4.5, the pH optima of the two most abundant secreted goat cysteine phytases are 6.5 and 6.0, which are within the pH range found in the rumens. This study provides valuable information about the diversity, abundance and enzymatic properties of the ruminal cysteine phytases and emphasizes the important role(s) of these cysteine phytases probably in the terrestrial cycle of phosphorus.
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Affiliation(s)
- Huoqing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Oakley AJ. The structure of Aspergillus niger phytase PhyA in complex with a phytate mimetic. Biochem Biophys Res Commun 2010; 397:745-9. [DOI: 10.1016/j.bbrc.2010.06.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 06/06/2010] [Indexed: 10/19/2022]
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49
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Li R, Zhao J, Sun C, Lu W, Guo C, Xiao K. Biochemical properties, molecular characterizations, functions, and application perspectives of phytases. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/s11703-010-0103-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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50
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Structural Analysis of a Multifunctional, Tandemly Repeated Inositol Polyphosphatase. J Mol Biol 2009; 392:75-86. [DOI: 10.1016/j.jmb.2009.05.079] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 05/26/2009] [Accepted: 05/28/2009] [Indexed: 11/21/2022]
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