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Udaondo Z, Duque E, Daddaoua A, Caselles C, Roca A, Pizarro-Tobias P, Ramos JL. Developing robust protein analysis profiles to identify bacterial acid phosphatases in genomes and metagenomic libraries. Environ Microbiol 2020; 22:3561-3571. [PMID: 32564477 DOI: 10.1111/1462-2920.15138] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 12/16/2022]
Abstract
Phylogenetic analysis of more than 4000 annotated bacterial acid phosphatases was carried out. Our analysis enabled us to sort these enzymes into the following three types: (1) class B acid phosphatases, which were distantly related to the other types, (2) class C acid phosphatases and (3) generic acid phosphatases (GAP). Although class B phosphatases are found in a limited number of bacterial families, which include known pathogens, class C acid phosphatases and GAP proteins are found in a variety of microbes that inhabit soil, fresh water and marine environments. As part of our analysis, we developed three profiles, named Pfr-B-Phos, Pfr-C-Phos and Pfr-GAP, to describe the three groups of acid phosphatases. These sequence-based profiles were then used to scan genomes and metagenomes to identify a large number of formerly unknown acid phosphatases. A number of proteins in databases annotated as hypothetical proteins were also identified by these profiles as putative acid phosphatases. To validate these in silico results, we cloned genes encoding candidate acid phosphatases from genomic DNA or recovered from metagenomic libraries or genes synthesized in vitro based on protein sequences recovered from metagenomic data. Expression of a number of these genes, followed by enzymatic analysis of the proteins, further confirmed that sequence similarity searches using our profiles could successfully identify previously unknown acid phosphatases.
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Affiliation(s)
- Zulema Udaondo
- Estación Experimental del Zaidín, CSIC, Granada, E-18008, Spain.,Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA
| | - Estrella Duque
- Estación Experimental del Zaidín, CSIC, Granada, E-18008, Spain
| | - Abdelali Daddaoua
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Carlos Caselles
- Estación Experimental del Zaidín, CSIC, Granada, E-18008, Spain
| | | | | | - Juan L Ramos
- Estación Experimental del Zaidín, CSIC, Granada, E-18008, Spain
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Jatuwong K, Suwannarach N, Kumla J, Penkhrue W, Kakumyan P, Lumyong S. Bioprocess for Production, Characteristics, and Biotechnological Applications of Fungal Phytases. Front Microbiol 2020; 11:188. [PMID: 32117182 PMCID: PMC7034034 DOI: 10.3389/fmicb.2020.00188] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/27/2020] [Indexed: 12/30/2022] Open
Abstract
Phytases are a group of enzymes that hydrolyze the phospho-monoester bonds of phytates. Phytates are one of the major forms of phosphorus found in plant tissues. Fungi are mainly used for phytase production. The production of fungal phytases has been achieved under three different fermentation methods including solid-state, semi-solid-state, and submerged fermentation. Agricultural residues and other waste materials have been used as substrates for the evaluation of enzyme production in the fermentation process. Nutrients, physical conditions such as pH and temperature, and protease resistance are important factors for increasing phytase production. Fungal phytases are considered monomeric proteins and generally possess a molecular weight of between 14 and 353 kDa. Fungal phytases display a broad substrate specificity with optimal pH and temperature ranges between 1.3 and 8.0 and 37-67°C, respectively. The crystal structure of phytase has been studied in Aspergillus. Notably, thermostability engineering has been used to improve relevant enzyme properties. Furthermore, fungal phytases are widely used in food and animal feed additives to improve the efficiency of phosphorus intake and reduce the amount of phosphorus in the environment.
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Affiliation(s)
- Kritsana Jatuwong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Ph.D. Degree Program in Applied Microbiology, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Nakarin Suwannarach
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Jaturong Kumla
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Watsana Penkhrue
- School of Preclinic, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Pattana Kakumyan
- School of Science, Mae Fah Luang University, Chiang Rai, Thailand
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
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Zore OV, Pande P, Okifo O, Basu AK, Kasi RM, Kumar CV. Nanoarmoring: strategies for preparation of multi-catalytic enzyme polymer conjugates and enhancement of high temperature biocatalysis. RSC Adv 2017; 7:29563-29574. [PMID: 29403641 PMCID: PMC5796544 DOI: 10.1039/c7ra05666d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We report a general and modular approach for the synthesis of multi enzyme-polymer conjugates (MECs) consisting of five different enzymes of diverse isoelectric points and distinct catalytic properties conjugated within a single universal polymer scaffold. The five model enzymes chosen include glucose oxidase (GOx), acid phosphatase (AP), lactate dehydrogenase (LDH), horseradish peroxidase (HRP) and lipase (Lip). Poly(acrylic acid) (PAA) is used as the model synthetic polymer scaffold that will covalently conjugate and stabilize multiple enzymes concurrently. Parallel and sequential synthetic protocols are used to synthesise MECs, 5-P and 5-S, respectively. Also, five different single enzyme-PAA conjugates (SECs) including GOx-PAA, AP-PAA, LDH-PAA, HRP-PAA and Lip-PAA are synthesized. The composition, structure and morphology of MECs and SECs are confirmed by agarose gel electrophoresis, dynamic light scattering, circular dichroism spectroscopy and transmission electron microscopy. The bioreactor comprising MEC functions as a single biocatalyst can carry out at least five different or orthogonal catalytic reactions by virtue of the five stabilized enzymes, which has never been achieved to-date. Using activity assays relevant for each of the enzymes, for example AP, the specific activity of AP at room temperature and 7.4 pH in PB is determined and set at 100%. Interestingly, MECs 5-P and 5-S show specific activities of 1800% and 600%, respectively, compared to 100% specific activity of AP at room temperature (RT). The catalytic efficiencies of 5-P and 5-S are 1.55 × 10-3 and 1.68 × 10-3, respectively, compared to 9.11 × 10-5 for AP under similar RT conditions. Similarly, AP relevant catalytic activities of 5-P and 5-S at 65 °C show 100 and 300%, respectively, relative to native AP activity at RT as the native AP is catalytically inactive at 65 °C The catalytic activity trends suggest: (1) MECs show enhanced catalytic activities compared to native enzymes under similar assay conditions and (2) 5-S is better suited for high temperature biocatalysis, while both 5-S and 5-P are suitable for room temperature biocatalysis. Initial cytotoxicity results show that these MECs are non-lethal to human cells including human embryonic kidney [HEK] cells when treated with doses of 0.01 mg mL-1 for 72 h. This cytotoxicity data is relevant for future biological applications.
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Affiliation(s)
- Omkar V. Zore
- Department of Chemistry, University of Connecticut Storrs, CT 06269-3060, USA
- Institute of Materials Science, U-3136, University of Connecticut Storrs, CT 06269-3069, USA
| | - Paritosh Pande
- Department of Chemistry, University of Connecticut Storrs, CT 06269-3060, USA
| | | | - Ashis K. Basu
- Department of Chemistry, University of Connecticut Storrs, CT 06269-3060, USA
| | - Rajeswari M. Kasi
- Department of Chemistry, University of Connecticut Storrs, CT 06269-3060, USA
- Institute of Materials Science, U-3136, University of Connecticut Storrs, CT 06269-3069, USA
| | - Challa V. Kumar
- Department of Chemistry, University of Connecticut Storrs, CT 06269-3060, USA
- Institute of Materials Science, U-3136, University of Connecticut Storrs, CT 06269-3069, USA
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT 06269-3125, USA
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Souza AA, Leitão VO, Ramada MH, Mehdad A, Georg RDC, Ulhôa CJ, de Freitas SM. Trichoderma harzianum Produces a New Thermally Stable Acid Phosphatase, with Potential for Biotechnological Application. PLoS One 2016; 11:e0150455. [PMID: 26938873 PMCID: PMC4777480 DOI: 10.1371/journal.pone.0150455] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/12/2016] [Indexed: 11/18/2022] Open
Abstract
Acid phosphatases (ACPases) are produced by a variety of fungi and have gained attention due their biotechnological potential in industrial, diagnosis and bioremediation processes. These enzymes play a specific role in scavenging, mobilization and acquisition of phosphate, enhancing soil fertility and plant growth. In this study, a new ACPase from Trichoderma harzianum, named ACPase II, was purified and characterized as a glycoprotein belonging to the acid phosphatase family. ACPase II presents an optimum pH and temperature of 3.8 and 65 °C, respectively, and is stable at 55 °C for 120 min, retaining 60% of its activity. The enzyme did not require metal divalent ions, but was inhibited by inorganic phosphate and tungstate. Affinity for several phosphate substrates was observed, including phytate, which is the major component of phosphorus in plant foods. The inhibition of ACPase II by tungstate and phosphate at different pH values is consistent with the inability of the substrate to occupy its active site due to electrostatic contacts that promote conformational changes, as indicated by fluorescence spectroscopy. A higher affinity for tungstate rather than phosphate at pH 4.0 was observed, in accordance with its highest inhibitory effect. Results indicate considerable biotechnological potential of the ACPase II in soil environments.
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Affiliation(s)
- Amanda Araújo Souza
- Laboratory of Biophysics, Department of Cellular Biology, University of Brasília, 70910-900, Brasília, Brazil
| | - Vanessa Oliveira Leitão
- Laboratory of Enzymology, Department of Cellular Biology, University of Brasília, 70910-900, Brasília, Brazil
| | - Marcelo Henrique Ramada
- Laboratory of Mass Espectrometry, Embrapa Recursos Genéticos e Biotecnologia – 70770-917, Brasília, Brazil
| | - Azadeh Mehdad
- Laboratory of Biophysics, Department of Cellular Biology, University of Brasília, 70910-900, Brasília, Brazil
| | - Raphaela de Castro Georg
- Laboratory of Enzymology, Institute of Biology, University Federal of Goiás, 74001-970, Goiania, Brazil
| | - Cirano José Ulhôa
- Laboratory of Enzymology, Institute of Biology, University Federal of Goiás, 74001-970, Goiania, Brazil
| | - Sonia Maria de Freitas
- Laboratory of Biophysics, Department of Cellular Biology, University of Brasília, 70910-900, Brasília, Brazil
- * E-mail:
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