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Castillo Villamizar GA, Nacke H, Daniel R. Functional Metagenomics Approach for the Discovery of Novel Genes Encoding Phosphatase Activity. Methods Mol Biol 2023; 2555:103-114. [PMID: 36306081 DOI: 10.1007/978-1-0716-2795-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Phosphate release from inorganic and organic phosphorus compounds can be enzymatically mediated. Phosphate-releasing enzymes, comprising acid and alkaline phosphatases, are recognized as useful biocatalysts in applications such as plant and animal nutrition, bioremediation, and diagnostic analysis. Here, we describe a functional metagenomics approach enabling rapid identification of genes encoding these enzymes. The target genes are detected based on small- and large-insert metagenomic libraries derived from diverse environments. This approach has the potential to unveil entirely new phosphatase families or subfamilies and members of known enzyme classes that hydrolyze phosphomonoester bonds such as phytases. Additionally, we provide a strategy for efficient heterologous expression of phosphatase genes.
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Affiliation(s)
- Genis A Castillo Villamizar
- Corporación para la investigación de la corrosión (CIC), Santander, Piedecuesta, Colombia
- Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany
| | - Heiko Nacke
- Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Institute of Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany.
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Nuge T, Hayyan A, A. M. Elgharbawy A, Mohd. Salleh H, Jun Yong Y, Kamarudin AF, Hizaddin HF, Zuhanis Has-Yun Hashim Y, Liu X, Saleh J, Ibrahim Daoud J, S.M. Aljohani A, Alhumaydhi FA, Zulkifli M, Roslan Mohd Nor M, Al Abdulmonem W. Enhanced large-scale production of recombinant phytase in E. coli DH5 α: Medium components optimization and thermodynamic studies. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Zhu L, Zhang Y, Cui X, Zhu Y, Dai Q, Chen H, Liu G, Yao R, Yang Z. Host Bias in Diet-Source Microbiome Transmission in Wild Cohabitating Herbivores: New Knowledge for the Evolution of Herbivory and Plant Defense. Microbiol Spectr 2021; 9:e0075621. [PMID: 34406815 PMCID: PMC8552726 DOI: 10.1128/spectrum.00756-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 07/28/2021] [Indexed: 12/27/2022] Open
Abstract
It is commonly understood that dietary nutrition will influence the composition and function of the animal gut microbiome. However, the transmission of organisms from the diet-source microbiome to the animal gut microbiome in the natural environment remains poorly understood, and elucidating this process may help in understanding the evolution of herbivores and plant defenses. Here, we investigated diet-source microbiome transmission across a range of herbivores (insects and mammals) living in both captive and wild environments. We discovered a host bias among cohabitating herbivores (leaf-eating insects and deer), where a significant portion of the herbivorous insect gut microbiome may originate from the diet, while in deer, only a tiny fraction of the gut microbiome is of dietary origin. We speculated that the putative difference in the oxygenation level in the host digestion systems would lead to these host biases in plant-source (diet) microbiome transmission due to the oxygenation living condition of the dietary plant's symbiotic microbiome. IMPORTANCE We discovered a host bias among cohabitating herbivores (leaf-eating insects and deer), where a significant portion of the herbivorous insect gut microbiome may originate from the diet, while in deer, only a tiny fraction of the gut microbiome is of dietary origin. We speculated that the putative difference in the oxygenation level in the host digestion systems would lead to these host biases in plant-source (diet) microbiome transmission due to the oxygenation living condition of the dietary plant's symbiotic microbiome. This study shed new light on the coevolution of herbivory and plant defense.
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Affiliation(s)
- Lifeng Zhu
- College of Life Sciences, Nanjing Norma University, Nanjing, China
| | - Yongyong Zhang
- College of Life Sciences, Nanjing Norma University, Nanjing, China
| | - Xinyuan Cui
- College of Life Sciences, Nanjing Norma University, Nanjing, China
| | - Yudong Zhu
- Sichuan Liziping National Nature Reserve, Shimian, China
- Shimian Research Center of Giant Panda Small Population Conservation and Rejuvenation, Shimian, China
| | - Qinlong Dai
- Sichuan Liziping National Nature Reserve, Shimian, China
- Shimian Research Center of Giant Panda Small Population Conservation and Rejuvenation, Shimian, China
| | - Hua Chen
- Mingke Biotechnology Co., Ltd., Hangzhou, China
| | - Guoqi Liu
- Mingke Biotechnology Co., Ltd., Hangzhou, China
| | - Ran Yao
- College of Life Sciences, Nanjing Norma University, Nanjing, China
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Greiner R. Limitations of an in vitro model of the poultry digestive tract on the evaluation of the catalytic performance of phytases. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:2519-2524. [PMID: 33058193 DOI: 10.1002/jsfa.10878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 10/08/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The study aims to investigate the limitation of a poultry digestive tract model developed by Menezes-Blackburn et al. [J Agric Food Chem 63: 6142-6149 (2015)] on the evaluation of the bioefficacy of phytases. RESULTS It was confirmed that the in vitro model does not mimic the in vivo situation in the birds sufficiently well to identify the best phytase product under real conditions, or to draw conclusion on the effect of phytate concentration, phytate source or feed composition on the bioefficacy of phytase. Addition of calcium ion (Ca2+ ) up to a concentration of 10 g kg-1 to the feed substrate, for example, did not affect enzymatic phytate dephosphorylation in the in vitro model in contrast to the observation in poultry. CONCLUSION The in vitro approach was shown to be applicable as a complementary tool in the pre-selection of promising phytase candidates, resulting in a reduction in the number of feeding trials in the initial screening phase. © 2020 The Author. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Ralf Greiner
- Department of Food Technology and Bioprocess Engineering, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany
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Rasul M, Yasmin S, Yahya M, Breitkreuz C, Tarkka M, Reitz T. The wheat growth-promoting traits of Ochrobactrum and Pantoea species, responsible for solubilization of different P sources, are ensured by genes encoding enzymes of multiple P-releasing pathways. Microbiol Res 2021; 246:126703. [PMID: 33482437 DOI: 10.1016/j.micres.2021.126703] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/22/2020] [Accepted: 01/06/2021] [Indexed: 02/01/2023]
Abstract
Production and release of organic acids and phosphatase enzymes by microbes are important for inorganic and organic phosphorus cycling in soil. The presence of microorganisms with corresponding traits in the plant rhizosphere lead to improved plant P uptake and ultimately growth promotion. We studied the potential of two rhizosphere-competent strains, Pantoea sp. MR1 and Ochrobactrum sp. SSR, for solubilization of different organic and inorganic P sources in vitro. In a pot experiment we further revealed the impact of the two strains on wheat seedling performance in soil amended with either phytate, rock phosphate or K2HPO4 as solely P source. To directly link P-solubilizing activity to the strain-specific genetic potential, we designed novel primers for glucose dehydrogenase (gcd), phosphatase (pho) and phytase (phy) genes, which are related to the organic and inorganic P solubilization potential. Quantitative tracing of these functional genes in the inoculated soils of the conducted pot experiment further allowed to compare strain abundances in the soil in dependency on the present P source. We observed strain- and P source-dependent patterns of the P solubilization in vitro as well as in the pot experiment, whereby P release, particularly from phytate, was linked to the strain abundance. We further revealed that the activity of microbial phosphatases is determined by the interplay between functional gene abundance, available soil P, and substrate availability. Moreover, positive impacts of microbial seed inoculation on wheat root architecture and aboveground growth parameters were observed. Our results suggest that screening for rhizosphere-competent strains with gcd, pho and phy genes may help to identify new microbial taxa that are able to solubilize and mineralize inorganic as well as organic bound P. Subsequently, the targeted use of corresponding strains may improve P availability in agricultural soils and consequently reduce fertilizer application.
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Affiliation(s)
- Maria Rasul
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Sumera Yasmin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
| | - Mahreen Yahya
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Claudia Breitkreuz
- UFZ - Helmholtz-Centre for Environmental Research, Soil Ecology Department, Theodor-Lieser-Straße 4, 06120, Halle, Germany
| | - Mika Tarkka
- UFZ - Helmholtz-Centre for Environmental Research, Soil Ecology Department, Theodor-Lieser-Straße 4, 06120, Halle, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
| | - Thomas Reitz
- UFZ - Helmholtz-Centre for Environmental Research, Soil Ecology Department, Theodor-Lieser-Straße 4, 06120, Halle, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
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Sarikhani MR, Malboobi MA, Aliasgharzad N, Greiner R. Identification of two novel bacterial phosphatase-encoding genes in Pseudomonas putida strain P13. J Appl Microbiol 2019; 127:1113-1124. [PMID: 31287935 DOI: 10.1111/jam.14376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 06/23/2019] [Accepted: 07/03/2019] [Indexed: 12/18/2022]
Abstract
AIMS Isolation and identification of genes encoding putative phosphatases from Pseudomonas putida strain P13 DSM 23335. METHODS AND RESULTS By functional screening of a P. putida P13 genomic library, a number of Pho+ clones were identified. Two genes were identified that encoded proteins exhibiting both phytase and sugar phosphatase activities. The proteins were 249 and 462 amino acids, with molecular masses of 26 and 50 kDa respectively. Sequence alignments revealed no significant similarities to representatives of known phosphatase or phytase gene families. However, the genes were found to have a high similarity to members of the major facilitator superfamily (MFS). Both genes were overexpressed in Escherichia coli and the corresponding partially purified recombinant enzymes were found to have significant phytate-dephosphorylating activity. The protein designated P. putida phytase 1 (Ppp1) displayed the highest activity among potential substrates studied on Na phytate, whereas Ppp2 more likely represents a sugar phosphatase than a phytase. The optimal conditions for phytate dephosphorylation were determined as 60°C and pH 4·5 (Ppp1) or pH 5·0 (Ppp2). CONCLUSIONS Two novel bacterial phosphatase-encoding genes, named ppp1 and ppp2, were isolated from P. putida P13 DSM 23335 by a functional screening procedure. SIGNIFICANCE AND IMPACT OF THE STUDY Phosphatase-encoding genes are of great importance for industrial applications, particularly in agriculture. The identified phosphatase genes represent a new class of acid phosphatases.
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Affiliation(s)
- M R Sarikhani
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - M A Malboobi
- Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - N Aliasgharzad
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - R Greiner
- Max Rubner-Institute, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany
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Castillo Villamizar GA, Funkner K, Nacke H, Foerster K, Daniel R. Functional Metagenomics Reveals a New Catalytic Domain, the Metallo-β-Lactamase Superfamily Domain, Associated with Phytase Activity. mSphere 2019; 4:e00167-19. [PMID: 31217298 PMCID: PMC6584368 DOI: 10.1128/msphere.00167-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/29/2019] [Indexed: 11/20/2022] Open
Abstract
Inositol-6-phosphate, also known as phytic acid, is a phosphorus source that plays several important roles in the phosphorus cycle and in cell metabolism. The known characterized enzymes responsible for its degradation, the phytases, are mostly derived from cultured individual microorganisms. The catalytic signatures of phytases are restricted to the molecular domains of four protein superfamilies: histidine phosphatases, protein tyrosine phosphatases, the purple acid phosphatases and the β-propeller phosphatases. During function-based screening of previously generated forest soil metagenomic libraries for Escherichia coli clones conferring phytase activity, two positive clones harboring the plasmids pLP05 and pLP12 were detected. Analysis of the insert sequences revealed the absence of classic phosphatase/phytase signatures of the proteins deduced from the putative genes, but the genes mblp01 (pLP05) and mblp02 (pLP12) encoded putative metallo-β-lactamases (MBLs). Several MBL representatives are promiscuous proteins with phosphoesterase activity, but phytase activity was previously not reported. Both mblp01 and mblp02 were subcloned, expressed, and analyzed. Mblp01 and Mblp02 are members of the lactamase B2 family. Protein modeling showed that the closest structural homologue of both proteins was ZipD of E. coli Mblp01 and Mblp02 showed activity toward the majority of the tested phosphorylated substrates, including phytate. The maximal enzyme activities were recorded for Mblp01 at 50°C under acidic conditions and for Mblp02 at 35°C and a neutral pH. In the presence of Cu2+ or SDS, the activities of Mblp01 and Mblp02 were strongly inhibited. Analyses of the minimal inhibitory concentrations of several β-lactam antibiotics revealed that recombinant E. coli cells carrying mblp01 or mblp02 showed reduced sensitivity toward β-lactam antibiotics.IMPORTANCE Phytic acid is a phosphorus storage molecule in many plant tissues, a source of phosphorus alternative to phosphate rocks, but it can also be a problematic antinutrient. In comparison to other phosphorus sources, phytic acid exhibits reduced bioavailability. Additionally, it influences functions of secondary messengers and acts as antioxidant in tumor growth prevention. The enzymatic capability to process phytate has been reported for a limited number of protein families. This might be due to the almost exclusive use of proteins derived from individual microorganisms to analyze phytase activity. With such a restriction, the study of the complexity and diversity of the phytases remains incomplete. By using metagenome-derived samples, this study demonstrates the existence of phytase activity in one of the most promiscuous superfamilies, the metallo-β-lactamases. Our results increase the general knowledge on phytase diversity in environmental samples and could provide new avenues for the study and engineering of new biocatalysts.
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Affiliation(s)
- Genis Andrés Castillo Villamizar
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
- Línea Tecnológica Biocorrosión, Corporación para la Investigación de la Corrosión C.I.C., Piedecuesta, Santander, Colombia
| | - Katrina Funkner
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Heiko Nacke
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Karolin Foerster
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
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Characteristics of the First Protein Tyrosine Phosphatase with Phytase Activity from a Soil Metagenome. Genes (Basel) 2019; 10:genes10020101. [PMID: 30700057 PMCID: PMC6409689 DOI: 10.3390/genes10020101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/19/2019] [Accepted: 01/24/2019] [Indexed: 11/30/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) fulfil multiple key regulatory functions. Within the group of PTPs, the atypical lipid phosphatases (ALPs) are known for their role as virulence factors associated with human pathogens. Another group of PTPs, which is capable of using inositol-hexakisphosphate (InsP6) as substrate, are known as phytases. Phytases play major roles in the environmental phosphorus cycle, biotechnology, and pathogenesis. So far, all functionally characterized PTPs, including ALPs and PTP-phytases, have been derived exclusively from isolated microorganisms. In this study, screening of a soil-derived metagenomic library resulted in identification of a gene (pho16B), encoding a PTP, which shares structural characteristics with the ALPs. In addition, the characterization of the gene product (Pho16B) revealed the capability of the protein to use InsP6 as substrate, and the potential of soil as a source of phytases with so far unknown characteristics. Thus, Pho16B represents the first functional environmentally derived PTP-phytase. The enzyme has a molecular mass of 38 kDa. The enzyme is promiscuous, showing highest activity and affinity toward naphthyl phosphate (Km 0.966 mM). Pho16B contains the HCXXGKDR[TA]G submotif of PTP-ALPs, and it is structurally related to PtpB of Mycobacterium tuberculosis. This study demonstrates the presence and functionality of an environmental gene codifying a PTP-phytase homologous to enzymes closely associated to bacterial pathogenicity.
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Functional Metagenomics Reveals an Overlooked Diversity and Novel Features of Soil-Derived Bacterial Phosphatases and Phytases. mBio 2019; 10:mBio.01966-18. [PMID: 30696742 PMCID: PMC6355987 DOI: 10.1128/mbio.01966-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phosphatases, including phytases, play a major role in cell metabolism, phosphorus cycle, biotechnology, and pathogenic processes. Nevertheless, their discovery by functional metagenomics is challenging. Here, soil metagenomic libraries were successfully screened for genes encoding phosphatase activity. In this context, we report the largest number and diversity of phosphatase genes derived from functional metagenome analysis. Two of the detected gene products carry domains which have never been associated with phosphatase activity before. One of these domains, the SNARE-associated domain DedA, harbors a so-far-overlooked motif present in numerous bacterial SNARE-associated proteins. Our analysis revealed a previously unreported phytase activity of the alkaline phosphatase and sulfatase superfamily (cl23718) and of purple acid phosphatases from nonvegetal origin. This suggests that the classical concept comprising four classes of phytases should be modified and indicates high performance of our screening method for retrieving novel types of phosphatases/phytases hidden in metagenomes of complex environments.IMPORTANCE Phosphorus (P) is a key element involved in numerous cellular processes and essential to meet global food demand. Phosphatases play a major role in cell metabolism and contribute to control the release of P from phosphorylated organic compounds, including phytate. Apart from the relationship with pathogenesis and the enormous economic relevance, phosphatases/phytases are also important for reduction of phosphorus pollution. Almost all known functional phosphatases/phytases are derived from cultured individual microorganisms. We demonstrate here for the first time the potential of functional metagenomics to exploit the phosphatase/phytase pools hidden in environmental soil samples. The recovered diversity of phosphatases/phytases comprises new types and proteins exhibiting largely unknown characteristics, demonstrating the potential of the screening method for retrieving novel target enzymes. The insights gained into the unknown diversity of genes involved in the P cycle highlight the power of function-based metagenomic screening strategies to study Earth's phosphatase pools.
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Ghorbani Nasrabadi R, Greiner R, Yamchi A, Nourzadeh Roshan E. A novel purple acid phytase from an earthworm cast bacterium. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:3667-3674. [PMID: 29266239 DOI: 10.1002/jsfa.8845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Phytases are a diverse group of enzymes initiating the dephosphorylation of phytate. Phytate is considered as an anti-nutritional compound because of its capability to chelate nutrients such as Fe2+ , Zn2+ , Mg2+ , and Ca2+ . In this study, several bacterial isolates obtained from earthworm casts were evaluated for their phytate degrading capability. Enzymatic properties and the sequence of the corresponding phytase-encoding gene of the selected isolate were determined. RESULTS The phytase exhibited its highest activity at pH 4.0 and was stable from pH 3 up to pH 9. The temperature optimum was determined to be 65 °C. The strongest inhibitors of enzymatic activity were identified as vanadate, Cu2+ , and Zn2+ . High-performance ion chromatography analysis of enzymatic phytate dephosphorylation revealed that the first dephosphorylation product was d/l-myo-inositol(1,2,3,4,5)pentakisphosphate. CONCLUSION Owing to its enzymatic properties, such as tolerance to tartrate and the presence of the consensus motifs PDTVY, GNHE, DLG, VLFH, and GHDH, this phytase could be classified as a purple acid phytase. To the best of our knowledge, this is the first report describing a bacterial purple acid phytase. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Reza Ghorbani Nasrabadi
- Department of Soil Science, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Ralf Greiner
- Department of Food Technology and Bioprocess Engineering, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany
| | - Ahad Yamchi
- Department of Plant Breeding and Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Elham Nourzadeh Roshan
- Department of Soil Science, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
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Valeeva LR, Nyamsuren C, Sharipova MR, Shakirov EV. Heterologous Expression of Secreted Bacterial BPP and HAP Phytases in Plants Stimulates Arabidopsis thaliana Growth on Phytate. FRONTIERS IN PLANT SCIENCE 2018; 9:186. [PMID: 29515604 PMCID: PMC5826191 DOI: 10.3389/fpls.2018.00186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 01/31/2018] [Indexed: 05/21/2023]
Abstract
Phytases are specialized phosphatases capable of releasing inorganic phosphate from myo-inositol hexakisphosphate (phytate), which is highly abundant in many soils. As inorganic phosphorus reserves decrease over time in many agricultural soils, genetic manipulation of plants to enable secretion of potent phytases into the rhizosphere has been proposed as a promising approach to improve plant phosphorus nutrition. Several families of biotechnologically important phytases have been discovered and characterized, but little data are available on which phytase families can offer the most benefits toward improving plant phosphorus intake. We have developed transgenic Arabidopsis thaliana plants expressing bacterial phytases PaPhyC (HAP family of phytases) and 168phyA (BPP family) under the control of root-specific inducible promoter Pht1;2. The effects of each phytase expression on growth, morphology and inorganic phosphorus accumulation in plants grown on phytate hydroponically or in perlite as the only source of phosphorus were investigated. The most enzymatic activity for both phytases was detected in cell wall-bound fractions of roots, indicating that these enzymes were efficiently secreted. Expression of both bacterial phytases in roots improved plant growth on phytate and resulted in larger rosette leaf area and diameter, higher phosphorus content and increased shoot dry weight, implying that these plants were indeed capable of utilizing phytate as the source of phosphorus for growth and development. When grown on phytate the HAP-type phytase outperformed its BPP-type counterpart for plant biomass production, though this effect was only observed in hydroponic conditions and not in perlite. Furthermore, we found no evidence of adverse side effects of microbial phytase expression in A. thaliana on plant physiology and seed germination. Our data highlight important functional differences between these members of bacterial phytase families and indicate that future crop biotechnologies involving such enzymes will require a very careful evaluation of phytase source and activity. Overall, our data suggest feasibility of using bacterial phytases to improve plant growth in conditions of phosphorus deficiency and demonstrate that inducible expression of recombinant enzymes should be investigated further as a viable approach to plant biotechnology.
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Affiliation(s)
- Lia R. Valeeva
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Chuluuntsetseg Nyamsuren
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Margarita R. Sharipova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Eugene V. Shakirov
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
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Abstract
The release of phosphate from inorganic and organic phosphorus compounds can be mediated enzymatically. Phosphate-releasing enzymes, comprising acid and alkaline phosphatases, are recognized as useful biocatalysts in applications such as plant and animal nutrition, bioremediation and diagnostic analysis. Metagenomic approaches provide access to novel phosphatase-encoding genes. Here, we describe a function-based screening approach for rapid identification of genes conferring phosphatase activity from small-insert and large-insert metagenomic libraries derived from various environments. This approach bears the potential for discovery of entirely novel phosphatase families or subfamilies and members of known enzyme classes hydrolyzing phosphomonoester bonds such as phytases. In addition, we provide a strategy for efficient heterologous phosphatase gene expression.
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Spier MR, Behsnilian D, Zielinski A, Konietzny U, Greiner R. Studies Towards the Stabilisation of a Mushroom Phytase Produced by Submerged Cultivation. Protein J 2015; 34:367-79. [DOI: 10.1007/s10930-015-9631-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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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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15
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Graminho ER, Takaya N, Nakamura A, Hoshino T. Purification, biochemical characterization, and genetic cloning of the phytase produced by Burkholderia sp. strain a13. J GEN APPL MICROBIOL 2015; 61:15-23. [DOI: 10.2323/jgam.61.15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | - Akira Nakamura
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | - Takayuki Hoshino
- Faculty of Life and Environmental Sciences, University of Tsukuba
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16
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Sharma A, Trivedi S. Evaluation ofin vitroprobiotic potential of phytase-producing bacterial strain as a new probiotic candidate. Int J Food Sci Technol 2014. [DOI: 10.1111/ijfs.12697] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anjana Sharma
- Bacteriology Laboratory; Department of P. G. Studies and Research in Biological Science; Rani Durgavati University; Pachpedi Jabalpur Madhya Pradesh 482001 India
| | - Shraddha Trivedi
- Bacteriology Laboratory; Department of P. G. Studies and Research in Biological Science; Rani Durgavati University; Pachpedi Jabalpur Madhya Pradesh 482001 India
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17
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Akhmetova AI, Nyamsuren C, Balaban NP, Sharipova MR. [Isolation and characterisation of a new bacillar phytase]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2014; 39:430-6. [PMID: 24707724 DOI: 10.1134/s1068162013040031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bacillus ginsengihumi phytase has been firstly isolated and studied from the recombinant Escherichia coli strain cellular lysates. The enzyme was obtained from the cellular lysate, purified till homogeneous condition, primary structure was determined. It's concluded that phytase relates to beta-propeller class of phosphatases. The molecular weight of the protein was 41 kDa, pI was 4.8. Some physical and chemical properties of the enzyme were studied.
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18
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Suleĭmanova AD, Danilova IV, Greiner R, Sharipova MR. [The novel intracellular phytase of enterobacteriaceae: isolation and properties]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2014; 39:424-9. [PMID: 24707723 DOI: 10.1134/s1068162013040146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
For the first time phytase enzyme was isolated from Pantoea vagans 3.2 strain and was subjected to investigation. The enzyme was purified about 474-fold to apparent homogeneity from the crude extract of the strain, its primary structure was determined and it was concluded that phytase of Pantoea vagans 3.2 belongs to the family of histidine acid phosphatases. It has a molecular mass of about 46 kDa and Km for the hydrolysis of sodium phytate was 0.28 mM. Some physicochemical properties ofphytase were investigated.
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19
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Nuge T, Hashim YZHY, Farouk AEA, Salleh HM. Cloning and Expression of a Novel Phytase Gene (phyMS) from <em>Mycobacterium smegmatis</em>. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/aer.2014.21003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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A bioprocess for the production of phytase from Schizophyllum commune: studies of its optimization, profile of fermentation parameters, characterization and stability. Bioprocess Biosyst Eng 2012; 35:1067-79. [PMID: 22349925 DOI: 10.1007/s00449-012-0692-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 01/16/2012] [Indexed: 10/14/2022]
Abstract
Schizophyllum commune produces phytase through solid-state fermentation using different agroindustrial residues. After optimization of phytase production, a maximal level of phytase (113.7 Units/gram of dry substrate) was obtained in wheat bran based medium containing 5% sucrose, 50% humidity, 7.5% of biomass at 33 °C pH 7.0 during 72 h and a 285% improvement in enzyme titre was achieved. Analysis of fermentation parameters profile for phytase production showed the highest productivity (1.466 Units/gram of dry substrate/hour) in 66 h of fermentation. Phytase has an optimal pH of 5.0, an optimal temperature of 50 °C and K (m) and V (max) values of 0.16 mM and 1.85 μmol mL(-1) min(-1), respectively. Phytase activity was stimulated essentially in the presence of K(+), Ca(2+), Mg(2+), Mn(2+), Zn(2+), Cu(2+), Fe(2+), Fe(3+), Co(2+), Ni(2+), acetate and citrate at concentrations of 1 mM. Phytase had the best shelf life when stored at a cooling temperature, maintaining 38% of its initial activity after 112 days of storage, and still presenting enzymatic activity after 125 days of storage. Stability studies of phytase performed in aqueous enzyme extracts showed satisfactory results using polyethyleneglycol 3350, carboxymethylcellulose, methylparaben, mannitol and benzoic acid in concentrations of 0.25, 0.025, 0.025, 0.25, and 0.0025%, respectively. PEG 3350 was shown to be the best stabilizing agent, resulting in 109% of phytase activity from the initial crude extract remaining activity in after 90 days.
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21
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Jorquera MA, Crowley DE, Marschner P, Greiner R, Fernández MT, Romero D, Menezes-Blackburn D, De La Luz Mora M. Identification of β-propeller phytase-encoding genes in culturable Paenibacillus and Bacillus spp. from the rhizosphere of pasture plants on volcanic soils. FEMS Microbiol Ecol 2010; 75:163-72. [DOI: 10.1111/j.1574-6941.2010.00995.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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22
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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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23
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Greiner R, da Silva LG, Couri S. Purification and characterisation of an extracellular phytase from Aspergillus niger 11T53A9. Braz J Microbiol 2009; 40:795-807. [PMID: 24031427 PMCID: PMC3768570 DOI: 10.1590/s1517-838220090004000010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 02/10/2009] [Accepted: 06/28/2009] [Indexed: 12/02/2022] Open
Abstract
An extracellular phytase from Aspergillus niger 11T53A9 was purified about 51-fold to apparent homogeneity with a recovery of 20.3% referred to the phytase activity in the crude extract. Purification was achieved by ammonium sulphate precipitation, ion chromataography and gel filtration. The purified enzyme behaved as a monomeric protein with a molecular mass of about 85 kDa and exhibited maximal phytate-degrading activity at pH 5.0. Optimum temperature for the degradation of phytate was 55°C. The kinetic parameters for the hydrolysis of sodium phytate were determined to be KM = 54 µmol l-1 and kcat = 190 sec-1 at pH 5.0 and 37°C. The purified enzyme was rather specific for phytate dephosphorylation. It was shown that the phytase preferably dephosphorylates myo-inositol hexakisphosphate in a stereospecific way by sequential removal of phosphate groups via D-Ins(1,2,4,5,6)P5, D-Ins(1,2,5,6)P4, D-Ins(1,2,6)P3, D-Ins(1,2)P2 to finally Ins(2)P.
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Affiliation(s)
- Ralf Greiner
- Department of Food and Bio Process Engineering, Max Rubner-Institute, Federal Research Institute of Nutrition and Food, Haidund-Neu-Straβe 9 , D-76131 Karlsruhe , Germany
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24
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Rao D, Rao K, Reddy T, Reddy V. Molecular characterization, physicochemical properties, known and potential applications of phytases: An overview. Crit Rev Biotechnol 2009; 29:182-98. [DOI: 10.1080/07388550902919571] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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25
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Jorquera M, Martínez O, Maruyama F, Marschner P, de la Luz Mora M. Current and Future Biotechnological Applications of Bacterial Phytases and Phytase-Producing Bacteria. Microbes Environ 2008; 23:182-91. [DOI: 10.1264/jsme2.23.182] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Milko Jorquera
- Centro de Ciencias y Biotecnología de Recursos Naturales, Universidad de La Frontera
| | - Oscar Martínez
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera
| | - Fumito Maruyama
- Institute of Medical Science, Internacional Research Center for Infectious Diseases, University of Tokyo
| | - Petra Marschner
- Soil and Land Systems, School of Earth and Environmental Sciences, University of Adelaide
| | - Maria de la Luz Mora
- Centro de Ciencias y Biotecnología de Recursos Naturales, Universidad de La Frontera
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26
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Hill JE, Kysela D, Elimelech M. Isolation and assessment of phytate-hydrolysing bacteria from the DelMarVa Peninsula. Environ Microbiol 2007; 9:3100-7. [DOI: 10.1111/j.1462-2920.2007.01420.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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