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Jadhav R, Mach RL, Mach-Aigner AR. Protein secretion and associated stress in industrially employed filamentous fungi. Appl Microbiol Biotechnol 2024; 108:92. [PMID: 38204136 PMCID: PMC10781871 DOI: 10.1007/s00253-023-12985-4] [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: 12/21/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Application of filamentous fungi for the production of commercial enzymes such as amylase, cellulase, or xylanase is on the rise due to the increasing demand to degrade several complex carbohydrates as raw material for biotechnological processes. Also, protein production by fungi for food and feed gains importance. In any case, the protein production involves both cellular synthesis and secretion outside of the cell. Unfortunately, the secretion of proteins or enzymes can be hampered due to accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) as a result of too high synthesis of enzymes or (heterologous) protein expression. To cope with this ER stress, the cell generates a response known as unfolded protein response (UPR). Even though this mechanism should re-establish the protein homeostasis equivalent to a cell under non-stress conditions, the enzyme expression might still suffer from repression under secretory stress (RESS). Among eukaryotes, Saccharomyces cerevisiae is the only fungus, which is studied quite extensively to unravel the UPR pathway. Several homologs of the proteins involved in this signal transduction cascade are also found in filamentous fungi. Since RESS seems to be absent in S. cerevisiae and was only reported in Trichoderma reesei in the presence of folding and glycosylation inhibitors such as dithiothreitol and tunicamycin, more in-depth study about this mechanism, specifically in filamentous fungi, is the need of the hour. Hence, this review article gives an overview on both, protein secretion and associated stress responses in fungi. KEY POINTS: • Enzymes produced by filamentous fungi are crucial in industrial processes • UPR mechanism is conserved among many fungi, but mediated by different proteins • RESS is not fully understood or studied in industrially relevant filamentous fungi.
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Affiliation(s)
- Reshma Jadhav
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
| | - Robert L Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
| | - Astrid R Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria.
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria.
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2
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Tian Z, Liu L, Wu L, Yang Z, Zhang Y, Du L, Zhang D. Enhancement of vitamin B 6 production driven by omics analysis combined with fermentation optimization. Microb Cell Fact 2024; 23:137. [PMID: 38750497 PMCID: PMC11095007 DOI: 10.1186/s12934-024-02405-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/24/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Microbial engineering aims to enhance the ability of bacteria to produce valuable products, including vitamin B6 for various applications. Numerous microorganisms naturally produce vitamin B6, yet the metabolic pathways involved are rigorously controlled. This regulation by the accumulation of vitamin B6 poses a challenge in constructing an efficient cell factory. RESULTS In this study, we conducted transcriptome and metabolome analyses to investigate the effects of the accumulation of pyridoxine, which is the major commercial form of vitamin B6, on cellular processes in Escherichia coli. Our omics analysis revealed associations between pyridoxine and amino acids, as well as the tricarboxylic acid (TCA) cycle. Based on these findings, we identified potential targets for fermentation optimization, including succinate, amino acids, and the carbon-to-nitrogen (C/N) ratio. Through targeted modifications, we achieved pyridoxine titers of approximately 514 mg/L in shake flasks and 1.95 g/L in fed-batch fermentation. CONCLUSION Our results provide insights into pyridoxine biosynthesis within the cellular metabolic network for the first time. Our comprehensive analysis revealed that the fermentation process resulted in a remarkable final yield of 1.95 g/L pyridoxine, the highest reported yield to date. This work lays a foundation for the green industrial production of vitamin B6 in the future.
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Affiliation(s)
- Zhizhong Tian
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Linxia Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Lijuan Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Zixuan Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yahui Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Liping Du
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Abdelrazek NA, Saleh SE, Raafat MM, Ali AE, Aboulwafa MM. Production of highly cytotoxic and low immunogenic L-asparaginase from Stenotrophomonas maltophilia EMCC2297. AMB Express 2024; 14:51. [PMID: 38704453 PMCID: PMC11069494 DOI: 10.1186/s13568-024-01700-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/09/2024] [Indexed: 05/06/2024] Open
Abstract
L-asparaginase is an important therapeutic enzyme that is frequently utilized in the chemotherapy regimens of adults as well as pediatric patients with acute lymphoblastic leukemia. However, a high rate of hypersensitivity with prolonged use has limited its utilization. Stenotrophomonas maltophilia (S. maltophilia) EMCC2297 isolate was reported as a novel and promising source for L- asparaginase. The present study aimed at the production, purification, and characterization of L- asparaginase from S. maltophilia EMCC2297 isolate. The microbial production of L-asparaginase by the test isolate could be increased by pre-exposure to chloramphenicol at 200 µg/ml concentration. S. maltophilia EMCC2297 L-asparaginase could be purified to homogeneity by ammonium sulphate precipitation and the purified form obtained by gel exclusion chromatography showed total activity of 96.4375 IU/ml and specific activity of 36.251 IU/mg protein. SDS-PAGE analysis revealed that the purified form of the enzyme is separated at an apparent molecular weight of 17 KDa. Michaelis-Menten constant analysis showed a Km value of 4.16 × 10- 2 M with L-asparagine as substrate and Vmax of 10.67 IU/ml. The antitumor activity of the purified enzyme was evaluated on different cell lines and revealed low IC50 of 2.2 IU/ml and 2.83 IU/ml for Hepatocellular cancer cell line (HepG-2), human leukemia cancer cell line (K-562), respectively whereas no cytotoxic effect could be detected on normal human lung fibroblast cells (MRC-5). However, mice treated with native L-asparaginase showed lower IgG titre compared to commercial L-asparaginase. This study highlights the promising characteristics of this enzyme making it a valuable candidate for further research and development to be an adduct in cancer chemotherapy.
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Affiliation(s)
- Nada A Abdelrazek
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Al Khalifa Al Maamoun St., Abbassia, Cairo, 11517, Egypt
| | - Sarra E Saleh
- Department of Microbiology and immunology, Faculty of Pharmacy, Future University in Egypt, Cairo, Egypt
| | - Marwa M Raafat
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Al Khalifa Al Maamoun St., Abbassia, Cairo, 11517, Egypt
| | - Amal E Ali
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Al Khalifa Al Maamoun St., Abbassia, Cairo, 11517, Egypt
| | - Mohammad M Aboulwafa
- Department of Microbiology and immunology, Faculty of Pharmacy, Future University in Egypt, Cairo, Egypt.
- Department of Microbiology and Immunology, Faculty of Pharmacy, King Salman International University, South Sinai, Ras-Sudr, Egypt.
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Itakorode BO, Itakorode DI, Torimiro N, Okonji RE. Kinetic and thermodynamic investigation of Rhodanese synthesized by enhanced Klebsiella oxytoca JCM 1665 strain: a comparative between the free and immobilized enzyme entrapped in alginate beads. Prep Biochem Biotechnol 2024:1-10. [PMID: 38696619 DOI: 10.1080/10826068.2024.2347407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
Klebsiella oxytoca JCM 1665 was subjected to extracellular rhodanese production using a submerged fermentation technique. The organism was further engineered for higher cyanide tolerance and rhodanese yield using ethylmethanesulfonate as a mutagen. Mutagenesis resulted in an improved mutant with high cyanide tolerance (100 mM) and rhodanese yield (26.7 ± 0.67 U/mL). This yield was 4.34-fold higher than the wild strain (6.15 ± 0.65 U/mL). At temperatures ranging from 30 to 80 °C, the first-order thermal denaturation constant (Kd) for free enzyme increases from 0.00818 to 0.0333 min-1 while the immobilized enzyme increases from 0.003 to 0.0204 min-1. The equivalent half-life reduces from 99 to 21 minutes and 231 to 35 minutes, respectively. Residual activity tests were used to assess the thermodynamic parameters for both enzyme preparations. For the free enzyme, the parameters obtained were enthalpy (29.40 to 29.06 kJ.mol-1), entropy (-194.24 to -197.50 J.mol-1K-1) and Gibbs free energy (90.20 to 98.80 kJ.mol-1). In addition, for immobilized rhodanese, we obtained enthalpy (40.40 to 40.07 kJ.mol-1), entropy (-164.21 to - 165.20 J.mol-1K-1) and Gibbs free energy (91.80 to 98.40 kJ.mol-1. Regarding its operational stability, the enzyme was able to maintain 63% of its activity after being used for five cycles. Immobilized K. oxytoca rhodanese showed a marked resistance to heat inactivation compared to free enzyme forms; making it of utmost significance in many biotechnological applications.
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Affiliation(s)
- Babamotemi Oluwasola Itakorode
- Department of Biotechnology, Osun State University, Osogbo, Nigeria
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University Ile-Ife, Osun State, Nigeria
| | | | - Nkem Torimiro
- Department of Microbiology, Obafemi Awolowo University Ile-Ife, Osun state, Nigeria
| | - Raphael Emuebie Okonji
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University Ile-Ife, Osun State, Nigeria
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Hosseini Hooshiar M, Badkoobeh A, Kolahdouz S, Tadayonfard A, Mozaffari A, Nasiri K, Salari S, Safaralizadeh R, Yasamineh S. The potential use of nanozymes as an antibacterial agents in oral infection, periodontitis, and peri-implantitis. J Nanobiotechnology 2024; 22:207. [PMID: 38664778 PMCID: PMC11044492 DOI: 10.1186/s12951-024-02472-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/07/2024] [Indexed: 04/29/2024] Open
Abstract
Several studies suggest that oral pathogenic biofilms cause persistent oral infections. Among these is periodontitis, a prevalent condition brought on by plaque biofilm. It can even result in tooth loss. Furthermore, the accumulation of germs around a dental implant may lead to peri-implantitis, which damages the surrounding bone and gum tissue. Furthermore, bacterial biofilm contamination on the implant causes soft tissue irritation and adjacent bone resorption, severely compromising dental health. On decontaminated implant surfaces, however, re-osseointegration cannot be induced by standard biofilm removal techniques such as mechanical cleaning and antiseptic treatment. A family of nanoparticles known as nanozymes (NZs) comprise highly catalytically active multivalent metal components. The most often employed NZs with antibacterial activity are those that have peroxidase (POD) activity, among other types of NZs. Since NZs are less expensive, more easily produced, and more stable than natural enzymes, they hold great promise for use in various applications, including treating microbial infections. NZs have significantly contributed to studying implant success rates and periodontal health maintenance in periodontics and implantology. An extensive analysis of the research on various NZs and their applications in managing oral health conditions, including dental caries, dental pulp disorders, oral ulcers, peri-implantitis, and bacterial infections of the mouth. To combat bacteria, this review concentrates on NZs that imitate the activity of enzymes in implantology and periodontology. With a view to the future, there are several ways that NZs might be used to treat dental disorders antibacterially.
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Affiliation(s)
| | - Ashkan Badkoobeh
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Qom University of Medical Sciences, Qom, Iran
| | - Shirin Kolahdouz
- School of Dentistry, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Azadeh Tadayonfard
- Postgraduate Department of Prosthodontics, Dental Faculty, Tehran University of Medical Sciences, Tehran, Iran
| | - Asieh Mozaffari
- Department of Periodontics, Faculty of Dentistry, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Kamyar Nasiri
- Department of Dentistry, Islamic Azad University of Medical Sciences, Tehran, Iran
| | - Sara Salari
- Islamic Azad University of Medical Sciences, Esfahan, Iran
| | - Reza Safaralizadeh
- Restarative Dentistry, Department of Dental, Faculty Tabriz Medical University, Tabriz, Iran.
| | - Saman Yasamineh
- Young Researchers and Elite Club, Tabriz Branch, Islamic Azad University, Tabriz, Iran.
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Ainousah BE, Ibrahim SRM, Alzain AA, Mohamed SGA, Hussein HGA, Ashour A, Abdallah HM, Mohamed GA. Exploring the potential of Aspergillus wentii: secondary metabolites and biological properties. Arch Microbiol 2024; 206:216. [PMID: 38619638 DOI: 10.1007/s00203-024-03934-4] [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] [Received: 02/07/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
Fungi are of considerable importance due to their capacity to biosynthesize various secondary metabolites with bioactive properties that draw high attention in new drug discovery with beneficial uses for improving human well-being and life quality. Aspergillus genus members are widespread and cosmopolitan species with varying economic significance in the fields of industry, medicine, and agriculture. Its species are renowned for their biosynthesis of secondary metabolites, characterized by both potent biological activity and structural novelty, making them a substantial reservoir for the development of new pharmaceuticals. The current work aimed at focusing on one species of this genus, Aspergillus wentii Wehmer, including its reported secondary metabolites in the period from 1951 to November 2023. A total of 97 compounds, including nitro-compounds, terpenoids, anthraquinones, xanthones, benzamides, and glucans. A summary of their bioactivities, as well as their biosynthesis was highlighted. Additionally, the reported applications of this fungus and its enzymes have been discussed. This review offers a useful reference that can direct future research into this fungus and its active metabolites, as well as their possible pharmacological and biotechnological applications.
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Affiliation(s)
- Bayan E Ainousah
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Umm Al-Qura University, 21955, Makkah, Saudi Arabia
| | - Sabrin R M Ibrahim
- Preparatory Year Program, Department of Chemistry, Batterjee Medical College, 21442, Jeddah, Saudi Arabia.
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut, 71526, Egypt.
| | - Abdulrahim A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Medani, Gezira, Sudan
| | - Shaimaa G A Mohamed
- Faculty of Dentistry, British University, El Sherouk City, Suez Desert Road, Cairo, 11837, Egypt
| | - Hazem G A Hussein
- Preparatory Year Program, Batterjee Medical College, 21442, Jeddah, Saudi Arabia
| | - Ahmed Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Prince Sattam Bin Abdulaziz University, 11942, Al-Kharj, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Hossam M Abdallah
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Gamal A Mohamed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
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7
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Abdul Kareem ZG, Yasser Al-Zamily OM, Al-Khafaji NSK. Purification and characterization of α-galactosidase isolated from Klebsiella pneumoniae in the human oral cavity. Int J Biol Macromol 2024; 261:129550. [PMID: 38244734 DOI: 10.1016/j.ijbiomac.2024.129550] [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] [Received: 11/22/2023] [Revised: 01/06/2024] [Accepted: 01/15/2024] [Indexed: 01/22/2024]
Abstract
The enzyme α-Galactosidase (α-D-galactoside galactohydrolase [EC 3.2.1.22]) is an exoglycosidase that hydrolyzes the terminal α-galactosyl moieties of glycolipids and glycoproteins. It is ubiquitous in nature and possesses extensive applications in the food, pharma, and biotechnology industries. The present study aimed to purify α-galactosidase from Klebsiella pneumoniae, a bacterium isolated from the human oral cavity. The purification steps involved ammonium sulfate precipitation (70 %), dialysis, ion exchange chromatography using a DEAE-cellulose column, and affinity monolith chromatography. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis was used to determine the molecular weight of the purified enzyme. The kinetic constants, Michaelis constant (Km) and maximal velocity (Vmax), for this enzyme were determined by using p-nitrophenyl-α-D-galactopyranoside as substrate. The results showed that the purification fold, specific activity, and yield were 126.52, 138.58 units/mg, and 21.5 %, respectively. The SDS-PAGE showed that the molecular weight of the purified enzyme was 75 kDa. The optimum pH and temperature of the purified α-galactosidase were detected at pH 6.0 and 50 °C, respectively. The kinetic constants, Michaelis constant (Km) and maximal velocity (Vmax), for this enzyme were 4.6 mM and 769.23 U/ml, respectively. α-galactosidase from Klebsiella pneumoniae was purified and characterized. (SDS-PAGE) analysis showed that the purified enzyme appeared as single band with a molecular weight of 75 kDa.
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Affiliation(s)
- Zainab G Abdul Kareem
- Department of Chemistry, College of Science, University of Babylon, Iraq; Department of Basic Science, College of Dentistry, University of Babylon, Iraq.
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8
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Scheibel DM, Gitsov IPI, Gitsov I. Enzymes in "Green" Synthetic Chemistry: Laccase and Lipase. Molecules 2024; 29:989. [PMID: 38474502 DOI: 10.3390/molecules29050989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/14/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Enzymes play an important role in numerous natural processes and are increasingly being utilized as environmentally friendly substitutes and alternatives to many common catalysts. Their essential advantages are high catalytic efficiency, substrate specificity, minimal formation of byproducts, and low energy demand. All of these benefits make enzymes highly desirable targets of academic research and industrial development. This review has the modest aim of briefly overviewing the classification, mechanism of action, basic kinetics and reaction condition effects that are common across all six enzyme classes. Special attention is devoted to immobilization strategies as the main tools to improve the resistance to environmental stress factors (temperature, pH and solvents) and prolong the catalytic lifecycle of these biocatalysts. The advantages and drawbacks of methods such as macromolecular crosslinking, solid scaffold carriers, entrapment, and surface modification (covalent and physical) are discussed and illustrated using numerous examples. Among the hundreds and possibly thousands of known and recently discovered enzymes, hydrolases and oxidoreductases are distinguished by their relative availability, stability, and wide use in synthetic applications, which include pharmaceutics, food and beverage treatments, environmental clean-up, and polymerizations. Two representatives of those groups-laccase (an oxidoreductase) and lipase (a hydrolase)-are discussed at length, including their structure, catalytic mechanism, and diverse usage. Objective representation of the current status and emerging trends are provided in the main conclusions.
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Affiliation(s)
- Dieter M Scheibel
- Department of Chemistry, State University of New York-ESF, Syracuse, NY 13210, USA
| | - Ioan Pavel Ivanov Gitsov
- Science and Technology, Medtronic Incorporated, 710 Medtronic Parkway, Minneapolis, MN 55432, USA
| | - Ivan Gitsov
- Department of Chemistry, State University of New York-ESF, Syracuse, NY 13210, USA
- The Michael M. Szwarc Polymer Research Institute, Syracuse, NY 13210, USA
- Biomedical and Chemical Engineering Department, Syracuse University, Syracuse, NY 13210, USA
- BioInspired Institute, Syracuse, NY 13210, USA
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Simau FA, Ahmed U, Khan KM, Khan NA, Siddiqui R, Alharbi AM, Alfahemi H, Anwar A. Lactase can target cellular differentiation of Acanthamoeba castellanii belonging to the T4 genotype. Parasitol Res 2024; 123:117. [PMID: 38294565 DOI: 10.1007/s00436-024-08131-2] [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: 10/10/2023] [Accepted: 01/17/2024] [Indexed: 02/01/2024]
Abstract
The free living Acanthamoeba spp. are ubiquitous amoebae associated with potentially blinding disease known as Acanthamoeba keratitis (AK) and a fatal central nervous system infection granulomatous amoebic encephalitis (GAE). With the inherent ability of cellular differentiation, it can phenotypically transform to a dormant cyst form from an active trophozoite form. Acanthamoeba cysts are highly resistant to therapeutic agents as well as contact lens cleaning solutions. One way to tackle drug resistance against Acanthamoeba is by inhibiting the formation of cysts from trophozoites. The biochemical analysis showed that the major component of Acanthamoeba cyst wall is composed of carbohydrate moieties such as galactose and glucose. The disaccharide of galactose and glucose is lactose. In this study, we analyzed the potential of lactase enzyme to target carbohydrate moieties of cyst walls. Amoebicidal assessment showed that lactase was ineffective against trophozoite of A. castellanii but enhanced amoebicidal effects of chlorhexidine. The lactase enzyme did not show any toxicity against normal human keratinocyte cells (HaCaT) at the tested range. Hence, lactase can be used for further assessment for development of potential therapeutic agents in the management of Acanthamoeba infection as well as formulation of effective contact lens disinfectants.
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Affiliation(s)
- Fathimath Afaaf Simau
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Subang Jaya, 47500, Selangor, Malaysia
| | - Usman Ahmed
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Subang Jaya, 47500, Selangor, Malaysia
| | - Khalid Mohammed Khan
- International Center for Chemical and Biological Sciences, H. E. J. Research Institute of Chemistry, University of Karachi, Karachi, Pakistan
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Naveed Ahmed Khan
- Microbiota Research Center, Istinye University, Istanbul, 34010, Turkey.
| | - Ruqaiyyah Siddiqui
- Microbiota Research Center, Istinye University, Istanbul, 34010, Turkey
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Ahmad M Alharbi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, 21944, Taif, Saudi Arabia
| | - Hasan Alfahemi
- Department of Medical Microbiology, Faculty of Medicine, Al-Baha University, 65799, Al-Baha, Saudi Arabia
| | - Ayaz Anwar
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Subang Jaya, 47500, Selangor, Malaysia.
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Ariaeenejad S, Gharechahi J, Foroozandeh Shahraki M, Fallah Atanaki F, Han JL, Ding XZ, Hildebrand F, Bahram M, Kavousi K, Hosseini Salekdeh G. Precision enzyme discovery through targeted mining of metagenomic data. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:7. [PMID: 38200389 PMCID: PMC10781932 DOI: 10.1007/s13659-023-00426-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024]
Abstract
Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms, which may serve as promising sources of enzymes and natural products for industrial applications. Identifying enzymes with improved catalytic properties from the vast amount of available metagenomic data poses a significant challenge that demands the development of novel computational and functional screening tools. The catalytic properties of all enzymes are primarily dictated by their structures, which are predominantly determined by their amino acid sequences. However, this aspect has not been fully considered in the enzyme bioprospecting processes. With the accumulating number of available enzyme sequences and the increasing demand for discovering novel biocatalysts, structural and functional modeling can be employed to identify potential enzymes with novel catalytic properties. Recent efforts to discover new polysaccharide-degrading enzymes from rumen metagenome data using homology-based searches and machine learning-based models have shown significant promise. Here, we will explore various computational approaches that can be employed to screen and shortlist metagenome-derived enzymes as potential biocatalyst candidates, in conjunction with the wet lab analytical methods traditionally used for enzyme characterization.
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Affiliation(s)
- Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mehdi Foroozandeh Shahraki
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Fereshteh Fallah Atanaki
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Jian-Lin Han
- Livestock Genetics Program, International Livestock Research, Institute (ILRI), Nairobi, 00100, Kenya
- CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, 730050, China
| | - Falk Hildebrand
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, Norfolk, UK
- Digital Biology, Earlham Institute, Norwich, Norfolk, UK
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls Väg 16, 756 51, Uppsala, Sweden
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, Estonia
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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Koilybayeva M, Shynykul Z, Ustenova G, Waleron K, Jońca J, Mustafina K, Amirkhanova A, Koloskova Y, Bayaliyeva R, Akhayeva T, Alimzhanova M, Turgumbayeva A, Kurmangaliyeva G, Kantureyeva A, Batyrbayeva D, Alibayeva Z. Gas Chromatography-Mass Spectrometry Profiling of Volatile Metabolites Produced by Some Bacillus spp. and Evaluation of Their Antibacterial and Antibiotic Activities. Molecules 2023; 28:7556. [PMID: 38005278 PMCID: PMC10673538 DOI: 10.3390/molecules28227556] [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] [Received: 10/09/2023] [Revised: 10/27/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Bacillus species produce different classes of antimicrobial and antioxidant substances: peptides or proteins with different structural compositions and molecular masses and a broad range of volatile organic compounds (VOCs), some of which may serve as biomarkers for microorganism identification. The aim of this study is the identification of biologically active compounds synthesized by five Bacillus species using gas chromatography coupled to mass spectrometry (GC-MS). The current study profoundly enhances the knowledge of antibacterial and antioxidant metabolites ensuring the unambiguous identification of VOCs produced by some Bacillus species, which were isolated from vegetable samples of potato, carrot, and tomato. Phylogenetic and biochemical studies were used to identify the bacterial isolates after culturing. Phylogenetic analysis proved that five bacterial isolates BSS12, BSS13, BSS16, BSS21, and BSS25 showed 99% nucleotide sequence similarities with Bacillus safensis AS-08, Bacillus cereus WAB2133, Bacillus acidiproducens NiuFun, Bacillus toyonesis FORT 102, and Bacillus thuringiensis F3, respectively. The crude extract was prepared from bacterial isolates to assess the antibiotic resistance potency and the antimicrobial potential against various targeted multidrug-resistant strains, including yeast strains such as Candida albicans, Candida krusei, and bacterial strains of Enterococcus hirae, Escherichia coli, Klebsiella aerogenes, Klebsiella pneumoniae, Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus group B, Streptococcus mutans, Shigella sonnei, Salmonella enteritidis, Serratia marcescens, Pseudomonas aeruginosa, and Proteus vulgaris. GC-MS analysis of bacterial strains found that VOCs from Bacillus species come in a variety of chemical forms, such as ketones, alcohols, terpenoids, alkenes, etc. Overall, 69 volatile organic compounds were identified from five Bacillus species, and all five were found to share different chemical classes of volatile organic components, which have a variety of pharmacological applications. However, eight antibacterial compounds with different concentrations were commonly found in all five species: acetoin, acetic acid, butanoic acid, 2-methyl-, oxime-, methoxy-phenyl, phenol, 1,2-benzenedicarboxylic acid, bis(2-methylpropyl) ester, nonanoic acid, and hexadecanoic acid, methyl. The present study has demonstrated that bacterial isolates BSS25, BSS21, and BSS16 display potent inhibitory effects against Candida albicans, while BSS25, BSS21, and BSS13 exhibit the ability to restrain the growth and activity of Candida krusei. Notably, BSS25 and BSS21 are the only isolates that demonstrate substantial inhibitory activity against Klebsiella aerogenes. This disparity in inhibitory effects could be attributed to the higher concentrations of acetoin in BSS25 and BSS21, whereas BSS16 and BSS13 have relatively elevated levels of butanoic acid, 2-methyl-. Certainly, the presence of acetoin and butanoic acid, 2-methyl-, contributes to the enhanced antibacterial potential of these bacterial strains, in conjunction with other organic volatile compounds and peptides, among other factors. The biology and physiology of Bacillus can be better understood using these results, which can also be used to create novel biotechnological procedures and applications. Moreover, because of its exceptional ability to synthesize and produce a variety of different antibacterial compounds, Bacillus species can serve as natural and universal carriers for antibiotic compounds in the form of probiotic cultures and strains to fight different pathogens, including mycobacteria.
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Affiliation(s)
- Moldir Koilybayeva
- School of Pharmacy, S.D. Asfendiyarov Kazakh National Medical University, Tole-bi 94, Almaty 050012, Kazakhstan; (G.U.); (A.A.); (G.K.); (A.K.)
| | - Zhanserik Shynykul
- Higher School of Medicine, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan; (T.A.); (A.T.)
| | - Gulbaram Ustenova
- School of Pharmacy, S.D. Asfendiyarov Kazakh National Medical University, Tole-bi 94, Almaty 050012, Kazakhstan; (G.U.); (A.A.); (G.K.); (A.K.)
| | - Krzysztof Waleron
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdańsk, Gen. Hallera 107, 80-416 Gdańsk, Poland; (K.W.); (J.J.)
| | - Joanna Jońca
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdańsk, Gen. Hallera 107, 80-416 Gdańsk, Poland; (K.W.); (J.J.)
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdańsk, University of Gdansk, 80-307 Gdańsk, Poland
| | - Kamilya Mustafina
- School of Medicine, S.D. Asfendiyarov Kazakh National Medical University, Tole-bi 94, Almaty 050012, Kazakhstan; (K.M.); (Y.K.); (R.B.)
| | - Akerke Amirkhanova
- School of Pharmacy, S.D. Asfendiyarov Kazakh National Medical University, Tole-bi 94, Almaty 050012, Kazakhstan; (G.U.); (A.A.); (G.K.); (A.K.)
| | - Yekaterina Koloskova
- School of Medicine, S.D. Asfendiyarov Kazakh National Medical University, Tole-bi 94, Almaty 050012, Kazakhstan; (K.M.); (Y.K.); (R.B.)
| | - Raushan Bayaliyeva
- School of Medicine, S.D. Asfendiyarov Kazakh National Medical University, Tole-bi 94, Almaty 050012, Kazakhstan; (K.M.); (Y.K.); (R.B.)
| | - Tamila Akhayeva
- Higher School of Medicine, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan; (T.A.); (A.T.)
| | - Mereke Alimzhanova
- Center of Physical Chemical Methods of Research and Analysis, Al-Farabi Kazakh National University, Almaty 050012, Kazakhstan;
| | - Aknur Turgumbayeva
- Higher School of Medicine, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan; (T.A.); (A.T.)
| | - Gulden Kurmangaliyeva
- School of Pharmacy, S.D. Asfendiyarov Kazakh National Medical University, Tole-bi 94, Almaty 050012, Kazakhstan; (G.U.); (A.A.); (G.K.); (A.K.)
| | - Aigerim Kantureyeva
- School of Pharmacy, S.D. Asfendiyarov Kazakh National Medical University, Tole-bi 94, Almaty 050012, Kazakhstan; (G.U.); (A.A.); (G.K.); (A.K.)
| | - Dinara Batyrbayeva
- Scientific Clinical Diagnostic Laboratory, S.D. Asfendiyarov Kazakh National Medical University, Tole-bi 94, Almaty 050012, Kazakhstan; (D.B.); (Z.A.)
| | - Zhazira Alibayeva
- Scientific Clinical Diagnostic Laboratory, S.D. Asfendiyarov Kazakh National Medical University, Tole-bi 94, Almaty 050012, Kazakhstan; (D.B.); (Z.A.)
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12
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Tjørnelund HD, Vind J, Brask J, Woodley JM, Peters GH. Candida antarctica lipase B performance in organic solvent at varying water activities studied by molecular dynamics simulations. Comput Struct Biotechnol J 2023; 21:5451-5462. [PMID: 38022691 PMCID: PMC10665702 DOI: 10.1016/j.csbj.2023.10.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Applications of lipases in low-water environments are found across a broad range of industries, including the pharmaceutical and oleochemical sectors. This includes condensation reactions in organic solvents where the enzyme activity has been found to depend strongly on both the solvent and the water activity (aw). Despite several experimental and computational studies, knowledge is largely empirical, and a general predictive approach is much needed. To close this gap, we chose native Candida antarctica lipase B (CALB) and two mutants thereof and used molecular dynamics (MD) simulations to gain a molecular understanding of the effect of aw on the specific activity of CALB in hexane. Based on the simulations, we propose four criteria to understand the performance of CALB in organic media, which is supported by enzyme kinetics experiments. First, the lipase must be stable in the organic solvent, which was the case for native CALB and the two mutants studied here. Secondly, water clusters that form and grow close to the active site must not block the path of substrate molecules into the active site. Thirdly, the lipase's lid must not cover the active site. Finally, mutations and changes in aw must not disrupt the geometry of the active site. We show that mutating specific residues close to the active site can hinder water cluster formation and growth, making the lipase resistant to changes in aw. Our computational screening criteria could potentially be used to screen in-silico designed variants, so only promising candidates could be pushed forward to characterisation.
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Affiliation(s)
- Helena D. Tjørnelund
- Department of Chemistry, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | | | | | - John M. Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Günther H.J. Peters
- Department of Chemistry, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
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13
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Han M, Huang J, Niu Z, Guo Y, Wei Z, Ding Y, Li C, Wang P, Wen G, Li X. Amorphous hollow manganese silicate nanosphere oxidase mimic for ultrasensitive and high-reliable colorimetric detection of biothiols. Mikrochim Acta 2023; 190:450. [PMID: 37875688 DOI: 10.1007/s00604-023-06034-0] [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] [Received: 08/21/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023]
Abstract
Metal-based nanozymes with exceptional physicochemical property and intrinsic enzymatic properties have been widely used in industrial, medical, and diagnostic fields. However, low substrate affinity results in unsatisfying catalytic kinetic and instability in complicated conditions, which significantly decreases their sensitivity and reliability. Herein, an amorphous hollow manganese silicate nanosphere (defined as AHMS) has been successfully synthesized via a facile one-step hydrothermal method and utilized in the archetype for colorimetric detection of biothiols with high sensitivity and high reliability. The experimental data demonstrates that ultrafast affinity of the substrate contributes to enhanced sensitivity with outstanding catalytic kinetic features (Km = 27.1 μM) and low limit of detection (LODGSH = 20 nM). The designed sensor demonstrates a reliable applicability for analysis of biological liquids (fetal calf serum and Staphylococcus aureus) and design of visual logic gates. Therefore, AHMS provides a promising strategy for ultrasensitive and high-reliable biosensing.
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Affiliation(s)
- Mengxuan Han
- Institute of Engineering Ceramics, School of Materials Science and Engineering, Shandong University of Technology, Zibo, 255000, China
| | - Jianyu Huang
- Institute of Engineering Ceramics, School of Materials Science and Engineering, Shandong University of Technology, Zibo, 255000, China
| | - Zhihui Niu
- School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo, 255000, China.
| | - Yang Guo
- Institute of Engineering Ceramics, School of Materials Science and Engineering, Shandong University of Technology, Zibo, 255000, China
| | - Zicheng Wei
- Institute of Engineering Ceramics, School of Materials Science and Engineering, Shandong University of Technology, Zibo, 255000, China
| | - Yingying Ding
- Institute of Engineering Ceramics, School of Materials Science and Engineering, Shandong University of Technology, Zibo, 255000, China
| | - Chengfeng Li
- Institute of Engineering Ceramics, School of Materials Science and Engineering, Shandong University of Technology, Zibo, 255000, China
| | - Peng Wang
- Institute of Engineering Ceramics, School of Materials Science and Engineering, Shandong University of Technology, Zibo, 255000, China
| | - Guangwu Wen
- Institute of Engineering Ceramics, School of Materials Science and Engineering, Shandong University of Technology, Zibo, 255000, China
| | - Xiaowei Li
- Institute of Engineering Ceramics, School of Materials Science and Engineering, Shandong University of Technology, Zibo, 255000, China.
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14
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Kaur D, Sharma V, Joshi A, Batra N, Ramniwas S, Sharma AK. Pectinases as promising green biocatalysts having broad-spectrum applications: Recent trends, scope, and relevance. Biotechnol Appl Biochem 2023; 70:1663-1678. [PMID: 36977651 DOI: 10.1002/bab.2464] [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] [Received: 10/25/2022] [Revised: 01/07/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
Pectinases are a collection of multiple enzymes that have a common substrate, that is, pectin. They can act on different parts of pectin due to the structural heterogeneity of pectin. Therefore, they have been placed in different groups, such as protopectinases, polygalacturonases, polymethylesterases, pectin lyases, and pectate lyases. They are naturally present both in multicellular organisms such as higher plants and in unicellular organisms such as microbes. In past decade, it has been witnessed that chemical and mechanical methods employed in industrial processes have led to environmental hazards and serious health disorders, thus increasing the search for eco-friendly approaches with minimal health risks. Hence, microbial enzymes have been extensively used as safer alternative for these environmentally unsafe methods. Among these microbial enzymes, pectinases hold great significance and is one of the principal enzymes that have been used commercially. It is predominantly used as a green biocatalyst for fruit, fiber, oil, textile, beverage, pulp, and paper industry. Thus, this review focuses on the structure of pectin, microbial sources of pectin, and principle industrial applications of pectinases.
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Affiliation(s)
- Damanjeet Kaur
- Department of Biotechnology, Sri Guru Gobind Singh College, Chandigarh, India
| | - Varruchi Sharma
- Department of Biotechnology, Sri Guru Gobind Singh College, Chandigarh, India
| | - Amit Joshi
- Department of Biotechnology, Sri Guru Gobind Singh College, Chandigarh, India
| | - Navneet Batra
- Department of Biotechnology, GGDSD College, Chandigarh, India
| | - Seema Ramniwas
- University Centre for Research and Development, University Institute of Biotechnology Chandigarh University, Gharuan, Mohali, India
| | - Anil K Sharma
- Department of Biotechnology, Maharishi Markandeshar Engineering College, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, Haryana, India
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15
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Mendonça APS, Dos Reis KL, Barbosa-Tessmann IP. Aspergillus clavatus UEM 04: An efficient producer of glucoamylase and α-amylase able to hydrolyze gelatinized and raw starch. Int J Biol Macromol 2023; 249:125890. [PMID: 37479205 DOI: 10.1016/j.ijbiomac.2023.125890] [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] [Received: 02/25/2023] [Revised: 06/04/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023]
Abstract
The best amylolytic activity production by Aspergillus clavatus UEM 04 occurred in submersed culture, with starch, for 72 h, at 25 °C, and 100 rpm. Exclusion chromatography partially purified two enzymes, which ran as unique bands in SDS-PAGE with approximately 84 kDa. LC-MS/MS identified a glucoamylase (GH15) and an α-amylase (GH13_1) as the predominant proteins and other co-purified proteins. Zn2+, Cu2+, and Mn2+ activated the glucoamylase, and SDS, Zn2+, Fe3+, and Cu2+ inhibited the α-amylase. The α-amylase optimum pH was 6.5. The optimal temperatures for the glucoamylase and α-amylase were 50 °C and 40 °C, and the Tm was 53.1 °C and 56.3 °C, respectively. Both enzymes remained almost fully active for 28-32 h at 40 °C, but the α-amylase thermal stability was calcium-dependent. Furthermore, the glucoamylase and α-amylase KM for starch were 2.95 and 1.0 mg/mL, respectively. Still, the Vmax was 0.28 μmol/min of released glucose for glucoamylase and 0.1 mg/min of consumed starch for α-amylase. Moreover, the glucoamylase showed greater affinity for amylopectin and α-amylase for maltodextrin. Additionally, both enzymes efficiently degraded raw starch. At last, glucose was the main product of glucoamylase, and α-amylase produced mainly maltose from gelatinized soluble starch hydrolysis.
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Affiliation(s)
- Ana Paula Silva Mendonça
- Biological Sciences Center, Department of Biochemistry, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Karina Lima Dos Reis
- Biological Sciences Center, Department of Biochemistry, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Ione Parra Barbosa-Tessmann
- Biological Sciences Center, Department of Biochemistry, Universidade Estadual de Maringá, Maringá, PR, Brazil.
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16
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Kolotylo V, Piwowarek K, Kieliszek M. Microbiological transglutaminase: Biotechnological application in the food industry. Open Life Sci 2023; 18:20220737. [PMID: 37791057 PMCID: PMC10543708 DOI: 10.1515/biol-2022-0737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/31/2023] [Accepted: 09/03/2023] [Indexed: 10/05/2023] Open
Abstract
Microbial transglutaminases (mTGs) belong to the family of global TGs, isolated and characterised by various bacterial strains, with the first being Streptomyces mobaraensis. This literature review also discusses TGs of animal and plant origin. TGs catalyse the formation of an isopeptide bond, cross-linking the amino and acyl groups. Due to its broad enzymatic activity, TG is extensively utilised in the food industry. The annual net growth in the utilisation of enzymes in the food processing industry is estimated to be 21.9%. As of 2020, the global food enzymes market was valued at around $2.3 billion USD (mTG market was estimated to be around $200 million USD). Much of this growth is attributed to the applications of mTG, benefiting both producers and consumers. In the food industry, TG enhances gelation and modifies emulsification, foaming, viscosity, and water-holding capacity. Research on TG, mainly mTG, provides increasing insights into the wide range of applications of this enzyme in various industrial sectors and promotes enzymatic processing. This work presents the characteristics of TGs, their properties, and the rationale for their utilisation. The review aims to provide theoretical foundations that will assist researchers worldwide in building a methodological framework and furthering the advancement of biotechnology research.
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Affiliation(s)
- Vitaliy Kolotylo
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences – SGGW, Nowoursynowska 159 C, 02-776Warsaw, Poland
| | - Kamil Piwowarek
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences – SGGW, Nowoursynowska 159 C, 02-776Warsaw, Poland
| | - Marek Kieliszek
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences – SGGW, Nowoursynowska 159 C, 02-776Warsaw, Poland
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17
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Bourne CM, Wallisch P, Dacek MM, Gardner TJ, Pierre S, Vogt K, Corless BC, Bah MA, Romero-Pichardo JE, Charles A, Kurtz KG, Tan DS, Scheinberg DA. Host Interactions with Engineered T-cell Micropharmacies. Cancer Immunol Res 2023; 11:1253-1265. [PMID: 37379366 PMCID: PMC10472090 DOI: 10.1158/2326-6066.cir-22-0879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/08/2023] [Accepted: 06/27/2023] [Indexed: 06/30/2023]
Abstract
Genetically engineered, cytotoxic, adoptively transferred T cells localize to antigen-positive cancer cells inside patients, but tumor heterogeneity and multiple immune escape mechanisms have prevented the eradication of most solid tumor types. More effective, multifunctional engineered T cells are in development to overcome the barriers to the treatment of solid tumors, but the interactions of these highly modified cells with the host are poorly understood. We previously engineered prodrug-activating enzymatic functions into chimeric antigen receptor (CAR) T cells, endowing them with a killing mechanism orthogonal to conventional T-cell cytotoxicity. These drug-delivering cells, termed Synthetic Enzyme-Armed KillER (SEAKER) cells, demonstrated efficacy in mouse lymphoma xenograft models. However, the interactions of an immunocompromised xenograft with such complex engineered T cells are distinct from those in an immunocompetent host, precluding an understanding of how these physiologic processes may affect the therapy. Herein, we expanded the repertoire of SEAKER cells to target solid-tumor melanomas in syngeneic mouse models using specific targeting with T-cell receptor (TCR)-engineered T cells. We demonstrate that SEAKER cells localized specifically to tumors, and activated bioactive prodrugs, despite host immune responses. We additionally show that TCR-engineered SEAKER cells were efficacious in immunocompetent hosts, demonstrating that the SEAKER platform is applicable to many adoptive cell therapies.
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Affiliation(s)
- Christopher M. Bourne
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Patrick Wallisch
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Pharmacology Program, Weill Cornell Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Megan M. Dacek
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Pharmacology Program, Weill Cornell Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Thomas J. Gardner
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Stephanie Pierre
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kristen Vogt
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Broderick C. Corless
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Pharmacology Program, Weill Cornell Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mamadou A. Bah
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jesus E. Romero-Pichardo
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Angel Charles
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Keifer G. Kurtz
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Pharmacology Program, Weill Cornell Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Derek S. Tan
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David A. Scheinberg
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Pharmacology Program, Weill Cornell Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York
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18
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Li X, Jing X, Yu Z, Huang Y. Diverse Antibacterial Treatments beyond Antibiotics for Diabetic Foot Ulcer Therapy. Adv Healthc Mater 2023; 12:e2300375. [PMID: 37141030 DOI: 10.1002/adhm.202300375] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/06/2023] [Indexed: 05/05/2023]
Abstract
Diabetic foot ulcer (DFU), a common complication of diabetes, has become a great burden to both patients and the society. The delayed wound closure of ulcer sites resulting from vascular damage and neutrophil dysfunction facilitates bacterial infection. Once drug resistance occurs or bacterial biofilm is formed, conventional therapy tends to fail and amputation is unavoidable. Therefore, effective antibacterial treatment beyond antibiotics is of utmost importance to accelerate the wound healing process and prevent amputation. Considering the complexity of multidrug resistance, biofilm formation, and special microenvironments (such as hyperglycemia, hypoxia, and abnormal pH value) at the infected site of DFU, several antibacterial agents and different mechanisms have been explored to achieve the desired outcome. The present review focuses on the recent progress of antibacterial treatments, including metal-based medications, natural and synthesized antimicrobial peptides, antibacterial polymers, and sensitizer-based therapy. This review provides a valuable reference for the innovation of antibacterial material design for DFU therapy.
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Affiliation(s)
- Xiaoyuan Li
- Faculty of Chemistry, Northeast Normal University, Renmin Street, Changchun, 130024, P. R. China
| | - Xin Jing
- Faculty of Chemistry, Northeast Normal University, Renmin Street, Changchun, 130024, P. R. China
| | - Ziqian Yu
- Faculty of Chemistry, Northeast Normal University, Renmin Street, Changchun, 130024, P. R. China
| | - Yubin Huang
- Faculty of Chemistry, Northeast Normal University, Renmin Street, Changchun, 130024, P. R. China
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19
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Chamanmalik MI, Antony AM, Yelamaggad CV, Patil SA, Patil SA. Biogenic Silver Nanoparticles/Mg-Al Layered Double Hydroxides with Peroxidase-like Activity for Mercury Detection and Antibacterial Activity. Molecules 2023; 28:5754. [PMID: 37570724 PMCID: PMC10421139 DOI: 10.3390/molecules28155754] [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] [Received: 06/30/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Over the past decade, the attention of researchers has been drawn to materials with enzyme-like properties to substitute natural enzymes. The ability of nanomaterials to mimic enzymes makes them excellent enzyme mimics; nevertheless, there is a wide berth for improving their activity and providing a platform to heighten their potential. Herein, we report a green and facile route for Tectona grandis leaves extract-assisted synthesis of silver nanoparticles (Ag NPs) decorated on Mg-Al layered double hydroxides (Mg-Al-OH@TGLE-AgNPs) as a nanocatalyst. The Mg-Al-OH@TGLE-AgNPs nanocatalyst was well characterized, and the average crystallite size of the Ag NPs was found to be 7.92 nm. The peroxidase-like activity in the oxidation of o-phenylenediamine in the presence of H2O2 was found to be an intrinsic property of the Mg-Al-OH@TGLE-AgNPs nanocatalyst. In addition, the use of the Mg-Al-OH@TGLE-AgNPs nanocatalyst was extended towards the quantification of Hg2+ ions which showed a wide linearity in the concentration range of 80-400 μM with a limit of detection of 0.2 nM. Additionally, the synergistic medicinal property of Ag NPs and the phytochemicals present in the Tectona grandis leaves extract demonstrated notable antibacterial activity for the Mg-Al-OH@TGLE-AgNPs nanocatalyst against Gram-negative Escherichia coli and Gram-positive Bacillus cereus.
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Affiliation(s)
- Masira I. Chamanmalik
- Centre for Nano and Material Sciences, Jain Global Campus, Jain (Deemed-to-be University), Kanakapura, Bangalore 562112, India; (M.I.C.); (A.M.A.)
| | - Arnet Maria Antony
- Centre for Nano and Material Sciences, Jain Global Campus, Jain (Deemed-to-be University), Kanakapura, Bangalore 562112, India; (M.I.C.); (A.M.A.)
| | - C. V. Yelamaggad
- Centre for Nano and Soft Matter Sciences, Survey No. 7, Shivanapura, Bangalore 562162, India;
| | - Shivaputra A. Patil
- Pharmaceutical Sciences Department, College of Pharmacy, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064, USA
| | - Siddappa A. Patil
- Centre for Nano and Material Sciences, Jain Global Campus, Jain (Deemed-to-be University), Kanakapura, Bangalore 562112, India; (M.I.C.); (A.M.A.)
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20
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Egbune EO, Ezedom T, Orororo OC, Egbune OU, Avwioroko OJ, Aganbi E, Anigboro AA, Tonukari NJ. Solid-state fermentation of cassava (Manihot esculenta Crantz): a review. World J Microbiol Biotechnol 2023; 39:259. [PMID: 37493900 DOI: 10.1007/s11274-023-03706-0] [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] [Received: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 07/27/2023]
Abstract
Solid-state fermentation (SSF) is a promising technology for producing value-added products from cassava (Manihot esculenta Crantz). In this process, microorganisms are grown on cassava biomass without the presence of free-flowing liquid. Compared to other processing methods, SSF has several advantages, such as lower costs, reduced water usage, and higher product yields. By enhancing the content of bioactive compounds like antioxidants and phenolic compounds, SSF can also improve the nutritional value of cassava-based products. Various products, including enzymes, organic acids, and biofuels, have been produced using SSF of cassava. Additionally, SSF can help minimize waste generated during cassava processing by utilizing cassava waste as a substrate, which can reduce environmental pollution. The process has also been explored for the production of feed and food products such as tempeh and cassava flour. However, optimizing the process conditions, selecting suitable microbial strains, and developing cost-effective production processes are essential for the successful commercialization of SSF of cassava.
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Affiliation(s)
- Egoamaka O Egbune
- Department of Biochemistry, Faculty of Science, Delta state University, P.M.B. 1, Abraka, Nigeria.
- Tonukari Biotechnology Laboratory, Sapele, Delta state, Nigeria.
| | - Theresa Ezedom
- Department of Medical Biochemistry, Faculty of Basic Medical Sciences, Delta State University, P.M.B. 1, Abraka, Nigeria
| | - Osuvwe C Orororo
- Department of Medical Biochemistry, Faculty of Basic Medical Sciences, Delta State University, P.M.B. 1, Abraka, Nigeria
| | - Olisemeke U Egbune
- Department of Human Physiology, Faculty of Basic Medical Sciences, University of Jos, Jos, Plateau State, Nigeria
| | - Oghenetega J Avwioroko
- Department of Biochemistry, Faculty of Basic Medical Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Eferhire Aganbi
- Department of Biochemistry, Faculty of Science, Delta state University, P.M.B. 1, Abraka, Nigeria
- Georgia State University, J. Mack Robinson College of Business, 3348 Peachtree Rd NE, Atlanta, GA, 30326, USA
| | - Akpovwehwee A Anigboro
- Department of Biochemistry, Faculty of Science, Delta state University, P.M.B. 1, Abraka, Nigeria
| | - Nyerhovwo J Tonukari
- Department of Biochemistry, Faculty of Science, Delta state University, P.M.B. 1, Abraka, Nigeria
- Tonukari Biotechnology Laboratory, Sapele, Delta state, Nigeria
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21
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Vélez MA, Wolf VI, Espariz M, Acciarri G, Magni C, Hynes E, Perotti MC. Study of volatile compounds profiles in milk matrices using Enterococcus faecalis EstA and Rhizomucor miehei lipase. Food Res Int 2023; 169:112861. [PMID: 37254435 DOI: 10.1016/j.foodres.2023.112861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 02/02/2023] [Accepted: 04/17/2023] [Indexed: 06/01/2023]
Abstract
The use of esterase/lipase enzymes of different origins in food industry is a widely employed strategy to enhance the formation of characteristic aromatic compounds derived from fat and diversify flavour. In the present work, we studied EstA enzyme of Enterococcus faecalis and a high purity Rhizomucor miehei lipase (Palatase). EstA was obtained recombinantly in Escherichia coli BL21 (DE3), and optimum esterase activity was detected at pH 6.75 and 40 °C. We evaluated the effect of the enzymes on milk mixtures prepared with different fat contents (2.8 and 6%) and structure (native or homogenized) on volatile compounds profiles. The milk fat structure before and after the application of low homogenization was characterized by dynamic light dispersion and microscopy. Native milk fat mixtures presented particles of 4.6 μm and 184 nm and homogenized mixtures had particles of 1.4 μm and 258 nm; microscopy images were in concordance with these results. Fifteen volatile compounds were identified, including ketones, esters, alcohols, and acids. We showed the key role of milk fat levels and microstructure in the nature of the volatile compounds produced by the R. miehei enzyme. Both in native or homogenized states, the highest content of fat favored a higher production of acids whereas the lowest fat level favored a higher esters production along with a more balanced volatile profile. For EstA enzyme, results showed a limited action on fat, as biosynthesis of esters only increased with the highest fat level homogenized.
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Affiliation(s)
- María A Vélez
- Instituto de Lactología Industrial (INLAIN, Universidad Nacional del Litoral/CONICET), Facultad de Ingeniería Química, Santiago del Estero 2829, S3000AOM, Santa Fe, Argentina.
| | - Verónica I Wolf
- Instituto de Lactología Industrial (INLAIN, Universidad Nacional del Litoral/CONICET), Facultad de Ingeniería Química, Santiago del Estero 2829, S3000AOM, Santa Fe, Argentina
| | - Martín Espariz
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Suipacha 590, 2000, Rosario, Santa Fe, Argentina
| | - Giuliana Acciarri
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Suipacha 590, 2000, Rosario, Santa Fe, Argentina
| | - Christian Magni
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Suipacha 590, 2000, Rosario, Santa Fe, Argentina
| | - Erica Hynes
- Instituto de Lactología Industrial (INLAIN, Universidad Nacional del Litoral/CONICET), Facultad de Ingeniería Química, Santiago del Estero 2829, S3000AOM, Santa Fe, Argentina
| | - María C Perotti
- Instituto de Lactología Industrial (INLAIN, Universidad Nacional del Litoral/CONICET), Facultad de Ingeniería Química, Santiago del Estero 2829, S3000AOM, Santa Fe, Argentina
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22
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Sorour AA, Olama ZA, El-Naggar MY, Ali SM. Bioprocess development for extraction and purification of cellulases from Aspergillus niger 3ASZ using statistical experimental design techniques. Int J Biol Macromol 2023; 242:124759. [PMID: 37150365 DOI: 10.1016/j.ijbiomac.2023.124759] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/09/2023]
Abstract
The amount of cellulosic materials is large and may lead to environmental pollution, so they can be converted into useful materials for use in food or energy. Statistical design (Plackett-Burman and Box-Behnken) was the main topic of this study and was used to optimize the effect of environmental factors on cellulase production by Aspergillus niger. Cellulase production using Plackett-Burman was 6.86-fold higher than the production of cellulase using the basal medium. B0X-Benken showed an increase in the cellulase production equal to 18 times compared to the basal medium, where the cellulase produced had an activity equal to 79.4 U/mL/min. Ammonium sulfate precipitation was applied to the crude enzyme, followed by sequential fractionation with an Amicon system. The Amicon was used to demonstrate the final volume, total enzyme activity, specific activity, purification fold, and yield of cellulase (partially purified enzyme). Numerous cellulolytic enzymes are abundant in Aspergillus species. All of the data showed that Aspergillus sp. might be a reliable source of industrially and economically useful cellulases. By statistically calculating the relevance of a large number of elements in one experiment using a multifactorial statistical design, time may be saved while still maintaining the validity of each component.
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Affiliation(s)
- Aman A Sorour
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Egypt
| | - Zakia A Olama
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Egypt
| | - Moustafa Y El-Naggar
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Egypt
| | - Safaa M Ali
- Nucleic Acid Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, Alexandria, Egypt.
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23
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Bourne CM, Wallisch P, Dacek M, Gardner T, Pierre S, Vogt K, Corless BC, Bah MA, Romero Pichardo J, Charles A, Kurtz KG, Tan DS, Scheinberg DA. Host-cell Interactions of Engineered T cell Micropharmacies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535717. [PMID: 37205431 PMCID: PMC10187158 DOI: 10.1101/2023.04.05.535717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Genetically engineered, cytotoxic, adoptive T cells localize to antigen positive cancer cells inside patients, but tumor heterogeneity and multiple immune escape mechanisms have prevented the eradication of most solid tumor types. More effective, multifunctional engineered T cells are in development to overcome the barriers to the treatment of solid tumors, but the interactions of these highly modified cells with the host are poorly understood. We previously engineered prodrug-activating enzymatic functions into chimeric antigen receptor (CAR) T cells, endowing them with an orthogonal killing mechanism to conventional T-cell cytotoxicity. These drug-delivering cells, termed Synthetic Enzyme-Armed KillER (SEAKER) cells, demonstrated efficacy in mouse lymphoma xenograft models. However, the interactions of an immunocompromised xenograft with such complex engineered T cells are distinct from those in an immunocompetent host, precluding an understanding of how these physiologic processes may affect the therapy. Here, we also expand the repertoire of SEAKER cells to target solid-tumor melanomas in syngeneic mouse models using specific targeting with TCR-engineered T cells. We demonstrate that SEAKER cells localize specifically to tumors, and activate bioactive prodrugs, despite host immune responses. We additionally show that TCR-engineered SEAKER cells are efficacious in immunocompetent hosts, demonstrating that the SEAKER platform is applicable to many adoptive cell therapies.
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Affiliation(s)
- Christopher M. Bourne
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA 10065
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA 10065
| | - Patrick Wallisch
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA 10065
- Pharmacology Program, Weill Cornell Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA, 10021
| | - Megan Dacek
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA 10065
- Pharmacology Program, Weill Cornell Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA, 10021
| | - Thomas Gardner
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA 10065
| | - Stephanie Pierre
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA 10065
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kristen Vogt
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA 10065
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA, 10065
| | - Broderick C. Corless
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA 10065
- Pharmacology Program, Weill Cornell Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA, 10021
| | - Mamadou A. Bah
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA 10065
| | - Jesus Romero Pichardo
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA 10065
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Angel Charles
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA 10065
| | - Keifer G. Kurtz
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA 10065
- Pharmacology Program, Weill Cornell Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA, 10021
| | - Derek S. Tan
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA 10065
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA, 10065
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA, 10065
| | - David A. Scheinberg
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA 10065
- Pharmacology Program, Weill Cornell Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA, 10021
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA, 10065
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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24
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Nandhakumar P, Bhatia A, Lee NS, Yoon YH, Yang H. Rapid nanocatalytic reaction using antibody-conjugated gold nanoparticles for simple and sensitive detection of parathyroid hormone. Int J Biol Macromol 2023; 241:124574. [PMID: 37100334 DOI: 10.1016/j.ijbiomac.2023.124574] [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: 02/27/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 04/28/2023]
Abstract
Biomolecule-conjugated metal nanoparticles (NPs) have been primarily used as colorimetric labels in affinity-based bioassays for point-of-care testing. A facile electrochemical detection scheme using a rapid nanocatalytic reaction of a metal NP label is required to achieve more quantitative and sensitive point-of-care testing. Moreover, all the involved components should be stable in their dried form and solution. This study developed a stable component set that allows for rapid and simple nanocatalytic reactions combined with electrochemical detection and applied it for the sensitive detection of parathyroid hormone (PTH). The component set consists of an indium-tin oxide (ITO) electrode, ferrocenemethanol (FcMeOH), antibody-conjugated Au NPs, and ammonia borane (AB). Despite being a strong reducing agent, AB is selected because it is stable in its dried form and solution. The slow direct reaction between FcMeOH+ and AB provides a low electrochemical background, and the rapid nanocatalytic reaction allows for a high electrochemical signal. Under optimal conditions, PTH could be quantified in a wide range of concentrations in artificial serum, with a detection limit of ~0.5 pg/mL. Clinical validation of the developed PTH immunosensor using real serum samples indicates that this novel electrochemical detection scheme is promising for quantitative and sensitive immunoassays for point-of-care testing.
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Affiliation(s)
- Ponnusamy Nandhakumar
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Aman Bhatia
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Nam-Sihk Lee
- EONE Laboratories, Incheon 22014, Republic of Korea
| | | | - Haesik Yang
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea.
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25
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Munawar A, Shaheen M, Ramzan S, Masih SA, Jabeen F, Younis T, Aslam M. DIVERISTY and enzymatic potential of indigenous bacteria from unexplored contaminted soils in Faisalabad. Heliyon 2023; 9:e15256. [PMID: 37095930 PMCID: PMC10122040 DOI: 10.1016/j.heliyon.2023.e15256] [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: 02/03/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/26/2023] Open
Abstract
Bacteria residing in contaminated waste soil degrade and utilize organic and inorganic material as a source of nutrients as well as reduce environmental contamination through their enzymatic machinery. This enzymatic potential of indigenous bacteria can be exploited at industrial level through detailed screening, characterization, optimization and purification. In present study, diversity and enzymatic potential of indigenous bacteria was investigated through qualitative and quantitative screening methods from unexplored contaminated soil waste sites in Faisalabad. Shannon diversity (H') index revealed that twenty-eight soil samples from four contaminated sites were highly diverse of amylase, protease and lipase producing bacteria. Maximum protease producing bacteria were detected in fruit waste (1.929 × 107), whereas amylase and lipase producing bacteria were found in industrial (1.475 × 107) and (5.38 × 106), in household waste soil samples. Most of the indigenous bacterial isolates showed potential for multiple enzymes. An isolate OC5 exhibited capability for amylase production and optimization at a wider range of cultural conditions; pH (6-8), temperature (25 °C, 37 °C, 45 °C), incubation time (24-72 h), and NaCl concentrations 0.5-13%, using (1%) starch and lactose as substrates. An isolate OC5 was identified by molecular identification and phylogenetic analysis showed 99% sequence similarity with Bacillus spp. ANOVA was used to analyzed all data statistically. This study enhances the importance of initial screening and reporting of industrially potent indigenous bacteria from unexplored contaminated waste soils. In future, indigenous bacteria in contaminated wastes may be good candidates to solve various environmental pollution problems.
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Affiliation(s)
- Ayesha Munawar
- Department of Zoology, Government College University, Faisalabad, 38000, Pakistan
| | - Musrat Shaheen
- Department of Zoology, Government College University, Faisalabad, 38000, Pakistan
- Corresponding author.
| | - Sobia Ramzan
- Department of Zoology, Government College University, Faisalabad, 38000, Pakistan
| | - Somi Akram Masih
- Department of Zoology, Government College University, Faisalabad, 38000, Pakistan
| | - Faiza Jabeen
- Department of Zoology, University of Education, Lahore, 54000, Pakistan
| | - Tahira Younis
- Department of Biochemistry and Biotechnology, The Women University, Multan, Pakistan
| | - Maryam Aslam
- Department of Zoology, Government College University, Faisalabad, 38000, Pakistan
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26
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Bulka NR, Barbosa-Tessmann IP. Characterization of an Amylolytic Enzyme from Massilia timonae of the GH13_19 Subfamily with Mixed Maltogenic and CGTase Activity. Appl Biochem Biotechnol 2023; 195:2028-2056. [PMID: 36401066 DOI: 10.1007/s12010-022-04226-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2022] [Indexed: 11/20/2022]
Abstract
This work reports the characterization of an amylolytic enzyme from the bacteria Massilia timonae CTI-57. A gene encoding this protein was expressed from the pTrcHis2B plasmid in Escherichia coli BL21 Star™ (DE3). The purified protein had 64 kDa, and its modeled structure showed a monomer with the conserved α-amylases structure composed of the domain A with the characteristic (β/α)8-barrel, the small domain B, and the domain C with an antiparallel beta-sheet. Phylogenetic analysis demonstrated that the expressed protein belongs to the GH13_19 subfamily of glycoside hydrolases. The ions Ca2+, Mn2+, Na+, Mg2+, Mo6+, and K+ did activate the purified enzyme, while EDTA and the ions Fe2+, Hg2+, Zn2+, and Cu2+ were strong inhibitors. SDS was also a strong inhibitor. The enzyme's optimal pH and temperature were 7.0 and 45 °C, respectively, and its Tm was 62.2 °C. The KM of the purified enzyme for starch was 13 mg/mL, and the Vmax was 0.24 μmol of reducing sugars released per min. The characterized enzyme presented higher specificity for maltodextrin and starch and produced maltose as the main starch hydrolysis product. This is the first characterized maltose-forming amylolytic enzyme from the GH13_19 subfamily. The purified enzyme produced β-cyclodextrin from starch and maltodextrin and could be considered a cyclodextrin glucanotransferase (CGTase). This is the first report of a GH13_19 subfamily enzyme with CGTase activity.
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Affiliation(s)
- Nathalia Rodrigues Bulka
- Department of Biochemistry, State University of Maringá, Av. Colombo, 5790, Maringá, PR, 87020-900, Brazil
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27
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Dhanasekaran S, Selvadoss PP, Manoharan SS. Anti-Fungal Potential of Structurally Diverse FDA-Approved Therapeutics Targeting Secreted Aspartyl Proteinase (SAP) of Candida albicans: an In Silico Drug Repurposing Approach. Appl Biochem Biotechnol 2023; 195:1983-1998. [PMID: 36401722 DOI: 10.1007/s12010-022-04207-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2022] [Indexed: 11/21/2022]
Abstract
In recent years, candidiasis attains major clinical importance due to its unique pathogenic strategy, which distinguishes it from other nosocomial infections. Secreted aspartyl proteinases (SAPs) is a hydrolytic enzyme secreted by Candida species that mediate versatile biological activity including hyphal formation, adherence, biofilm formation, phenotypic adaptation, etc. Emerging clinical evidence strongly suggested that conventional anti-fungal agent's are often prone to high level of resistance upon repeated exposure. Drug repurposing is an ideal strategy that shall impose the additional clinical benefits of the already approved molecules. Hence, through this realistic pathway, the potential of the suitable lead candidates will be explored in order to prolong the life span of existing molecules thereby need for newer therapeutics shall be avoided. The main aim of the present investigation is to determine the enzyme inhibitory potential of certain FDA-approved antibiotics and to validate its efficacy against the virulent enzyme secreted aspartyl proteinase (SAP) of Candida albicans via the AutoDock simulation program. The outcome of in silico dynamic simulations depicts that the drugs such as gentamicin, clindamycin, meropenem, metronidazole, and aztreonam emphasize superior binding affinity in terms of demonstrating considerable interaction with the core catalytic residues (Asp 32, Asp86, Asp 218, Gly220, Thr 221, and Thr 222). Data further indicates that the drug gentamicin exhibited best binding affinity of - 14.16 kcal/mol followed by meropenem (- 9.20 kcal/mol), clindamycin (- 9.00 kcal/mol), ciprofloxacin (- 8.95 kcal/mol), and imipenem (- 8.00 kcal/mol). In conclusion, repurposed antibiotics like gentamicin, clindamycin, meropenem, metronidazole, and aztreonam shall be considered an alternate drug of choice for the clinical management of drug resistant candida infections in the near future.
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Affiliation(s)
- Sivaraman Dhanasekaran
- Pandit Deendayal Energy University, Knowledge Corridor, Raisan Village, PDPU Road, Gandhinagar, Gujarat, 382426, India.
| | - Pradeep Pushparaj Selvadoss
- Pandit Deendayal Energy University, Knowledge Corridor, Raisan Village, PDPU Road, Gandhinagar, Gujarat, 382426, India
| | - Solomon Sundar Manoharan
- Pandit Deendayal Energy University, Knowledge Corridor, Raisan Village, PDPU Road, Gandhinagar, Gujarat, 382426, India
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28
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Ghattavi S, Homaei A. Marine enzymes: Classification and application in various industries. Int J Biol Macromol 2023; 230:123136. [PMID: 36621739 DOI: 10.1016/j.ijbiomac.2023.123136] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/23/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023]
Abstract
Oceans are regarded as a plentiful and sustainable source of biological compounds. Enzymes are a group of marine biomaterials that have recently drawn more attention because they are produced in harsh environmental conditions such as high salinity, extensive pH, a wide temperature range, and high pressure. Hence, marine-derived enzymes are capable of exhibiting remarkable properties due to their unique composition. In this review, we overviewed and discussed characteristics of marine enzymes as well as the sources of marine enzymes, ranging from primitive organisms to vertebrates, and presented the importance, advantages, and challenges of using marine enzymes with a summary of their applications in a variety of industries. Current biotechnological advancements need the study of novel marine enzymes that could be applied in a variety of ways. Resources of marine enzyme can benefit greatly for biotechnological applications duo to their biocompatible, ecofriendly and high effectiveness. It is beneficial to use the unique characteristics offered by marine enzymes to either develop new processes and products or improve existing ones. As a result, marine-derived enzymes have promising potential and are an excellent candidate for a variety of biotechnology applications and a future rise in the use of marine enzymes is to be anticipated.
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Affiliation(s)
- Saba Ghattavi
- Fisheries Department, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran.
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29
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Pedezzi R, Evangelista DE, da Rosa Garzon NG, de Oliveira Simões FA, de Oliveira AHC, Polikarpov I, Cabral H. Biochemical and biophysical properties of a recombinant serine peptidase from Purpureocillium lilacinum. Biophys Chem 2023; 296:106978. [PMID: 36827753 DOI: 10.1016/j.bpc.2023.106978] [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: 11/22/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023]
Abstract
The industrial uses of peptidases have already been consolidated; however, their range of applications is increasing. Thus, the biochemical characterization of new peptidases could increase the range of their biotechnological applications. In silico analysis identified a gene encoding a putative serine peptidase from Purpureocillium lilacinum (Pl_SerPep), annotated as a cuticle-degrading enzyme. The Pl_SerPep gene product was expressed as a recombinant in a Komagataella phaffii (previously Pichia pastoris) expression system. The enzyme (rPl_SerPep) showed optimal pH and temperature of 8.0 and 60 °C, respectively. Moreover, rPl_SerPep has a higher thermal stability than the cuticle-degrading enzymes described elsewhere. The structural analysis indicated a conformational change in the rPl_SerPep secondary structure, which would allow an increase in catalytic activity at 60 °C. Komagataella phaffii secretes rPl_SerPep with the pro peptide in its inactive form. Low-resolution small-angle X-ray scattering (SAXS) analysis showed little mobility of the pro peptide portion, which indicates the apparent stability of the inactive form of the enzyme. The presence of 20 mM guanidine in the reaction resulted in the maintenance of activity, which was apparently a consequence of pro peptide structure flexibilization.
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Affiliation(s)
- Rafael Pedezzi
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, Brazil
| | - Danilo Elton Evangelista
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Sãocarlense 400, São Carlos 13566-590, SP, Brazil
| | - Nathalia Gonsales da Rosa Garzon
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, Brazil
| | - Flávio Antônio de Oliveira Simões
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, Brazil
| | | | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Sãocarlense 400, São Carlos 13566-590, SP, Brazil
| | - Hamilton Cabral
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, Brazil.
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Othman AM, Elshafei AM, Elsayed MA, Ibrahim GE, Hassan MM, Mehanna NS. Biochemical characterization and insights into the potency of the acidic Aspergillus niger NRC114 purified α-galactosidase in removing raffinose family oligosaccharides from soymilk yogurt. BMC Biotechnol 2023; 23:3. [PMID: 36721204 PMCID: PMC9887927 DOI: 10.1186/s12896-023-00773-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/20/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Because humans lack α-galactosidase, foods containing certain oligosaccharides from the raffinose family, such as soybeans and other legumes, may disrupt digestion and cause flatulence. RESULTS Aspergillus niger NRC114 α-galactosidase was purified using protein precipitation, gel filtration, and ion exchange chromatography steps, which resulted in a 123-fold purification. The purified enzyme was found to be 64 kDa using the SDS-PAGE approach. The optimum pH and temperature of the purified α-galactosidase were detected at pH 3.5 and 60 ºC, respectively. The pure enzyme exhibited potent acidic pH stability at pH 3.0 and pH 4.0 for 2 h, and it retained its full activity at 50 ºC and 60 ºC for 120 min and 90 min, respectively. The enzyme was activated using 2.5 mM of K+, Mg2+, Co2+, or Zn2+ by 14%, 23%, 28%, and 11%, respectively. The Km and Vmax values of the purified enzyme were calculated to be 0.401 µM and 14.65 μmol min-1, respectively. The soymilk yogurt showed an increase in its total phenolic content and total flavonoids after enzyme treatment, as well as several volatile compounds that were detected and identified using GC-MS analysis. HPLC analysis clarified the enzymatic action in the hydrolysis of raffinose family oligosaccharides. CONCLUSION The findings of this study indicate the importance of A. niger NRC114 α-galactosidase enzyme for future studies, especially its applications in a variety of biological fields.
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Affiliation(s)
- Abdelmageed M. Othman
- grid.419725.c0000 0001 2151 8157Microbial Chemistry Department, Biotechnology Research Institute, National Research Centre, 33 El Bohouth St., Dokki 12622 Giza, Egypt
| | - Ali M. Elshafei
- grid.419725.c0000 0001 2151 8157Microbial Chemistry Department, Biotechnology Research Institute, National Research Centre, 33 El Bohouth St., Dokki 12622 Giza, Egypt
| | - Maysa A. Elsayed
- grid.419725.c0000 0001 2151 8157Microbial Chemistry Department, Biotechnology Research Institute, National Research Centre, 33 El Bohouth St., Dokki 12622 Giza, Egypt
| | - Gamil E. Ibrahim
- grid.419725.c0000 0001 2151 8157Chemistry of Flavor and Aroma Department, Food Industries and Nutrition Research Institute, National Research Centre, 33 El Bohouth St., Dokki 12622 Giza, Egypt
| | - Mohamed M. Hassan
- grid.419725.c0000 0001 2151 8157Microbial Chemistry Department, Biotechnology Research Institute, National Research Centre, 33 El Bohouth St., Dokki 12622 Giza, Egypt
| | - Nayra S. Mehanna
- grid.419725.c0000 0001 2151 8157Dairy Sciences Department, Food Industries and Nutrition Research Institute, National Research Centre, 33 El Bohouth St., Dokki 12622 Giza, Egypt
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Rabbani G, Ahmad E, Ahmad A, Khan RH. Structural features, temperature adaptation and industrial applications of microbial lipases from psychrophilic, mesophilic and thermophilic origins. Int J Biol Macromol 2023; 225:822-839. [PMID: 36402388 DOI: 10.1016/j.ijbiomac.2022.11.146] [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: 06/10/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Microbial lipases are very prominent biocatalysts because of their ability to catalyze a wide variety of reactions in aqueous and non-aqueous media. Here microbial lipases from different origins (psychrophiles, mesophiles, and thermophiles) have been reviewed. This review emphasizes an update of structural diversity in temperature adaptation and industrial applications, of psychrophilic, mesophilic, and thermophilic lipases. The microbial origins of lipases are logically dynamic, proficient, and also have an extensive range of industrial uses with the manufacturing of altered molecules. It is therefore of interest to understand the molecular mechanisms of adaptation to temperature in occurring lipases. However, lipases from extremophiles (psychrophiles, and thermophiles) are widely used to design biotransformation reactions with higher yields, fewer byproducts, or useful side products and have been predicted to catalyze those reactions also, which otherwise are not possible with the mesophilic lipases. Lipases as a multipurpose biological catalyst have given a favorable vision in meeting the needs of several industries such as biodiesel, foods, and drinks, leather, textile, detergents, pharmaceuticals, and medicals.
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Affiliation(s)
- Gulam Rabbani
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202 002, India; Department of Medical Biotechnology, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea.
| | - Ejaz Ahmad
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, United States of America
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202 002, India.
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Cantwell C, Song X, Li X, Zhang B. Prediction of adsorption capacity and biodegradability of polybrominated diphenyl ethers in soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:12207-12222. [PMID: 36109482 DOI: 10.1007/s11356-022-22996-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Polybrominated diphenyl ethers (PBDEs) are widely used brominated flame retardants with strong toxicity concerns. Understanding the behaviors of PBDEs in soil is essential to evaluate their environmental impact. However, the limited, incoherent, and inaccurate data has challenged predicting the adsorption capacity and biodegradability of all 209 PBDE congeners in the soil. Moreover, there are minimal studies regarding the interactions between adsorption and biodegradation behaviors of PBDEs in the soil. Herein, in this study, we adopted quantitative structure-property relationship (QSAR) modeling to predict the adsorption behavior of 209 PBDE congeners by estimating their organic carbon-water partition coefficient (KOC) values. In addition, the biodegradability of commonly occurring PBDE congeners was evaluated by analyzing their affinity to extracellular enzymes responsible for biodegradation using molecular docking. The results highlight that the degree of bromination plays a significant role in both the absorption and biodegradation of PBDEs in the soil due to compound stability and molecular geometry. Our findings help to advance the knowledge on PBDE behaviors in the soil and facilitate PBDE remediation associated with a soil environment.
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Affiliation(s)
- Cuirin Cantwell
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, A1B 3X5, Canada
| | - Xing Song
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, A1B 3X5, Canada
| | - Xixi Li
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, A1B 3X5, Canada
| | - Baiyu Zhang
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, A1B 3X5, Canada.
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Ng YK, Ikeno S, Kadhim Almansoori AK, Muhammad I, Abdul Rahim R. Characterization of Sphingobacterium sp. Ab3 Lipase and Its Coexpression with LEA Peptides. Microbiol Spectr 2022; 10:e0142221. [PMID: 36314920 PMCID: PMC9769720 DOI: 10.1128/spectrum.01422-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 09/23/2022] [Indexed: 12/24/2022] Open
Abstract
Sphingobacterium sp. is a yellowish Gram-negative bacterium that is usually characterized by high concentrations of sphingophospholipids as lipid components. As microbial enzymes have been in high demand in industrial fields in the past few decades, this study hopes to provide significant information on lipase activities of Sphingobacterium sp., since limited studies have been conducted on the Sphingobacterium sp. lipase. A microbe from one collected Artic soil sample, ARC4, was identified as psychrotolerant Sphingobacterium sp., and it could grow in temperatures ranging from 0°C to 24°C. The expression of Sphingobacterium sp. lipase was successfully performed through an efficient approach of utilizing mutated group 3 late embryogenesis abundant (G3LEA) proteins developed from Polypedilum vanderplanki. Purified enzyme was characterized using a few parameters, such as temperature, pH, metal ion cofactors, organic solvents, and detergents. The expressed enzyme is reported to be cold adapted and has the capability to work efficiently under neutral pH (pH 5.0 to 7.0), cofactors like Na+ ion, and the water-like solvent methanol. Addition of nonionic detergents greatly enhanced the activity of purified enzyme. IMPORTANCE The mechanism of action of LEA proteins has remained unknown to many; in this study we reveal their presence and improved protein expression due to the molecular shielding effect reported by others. This paper should be regarded as a useful example of using such proteins to influence an existing expression system to produce difficult-to-express proteins.
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Affiliation(s)
- You Kiat Ng
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Shinya Ikeno
- Department of Biological Functions and Engineering, Graduate School of Life Science and System Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | | | - Ibrahim Muhammad
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
- Department of Science Lab. Technology, Ramat Polytechnic Maiduguri, Maiduguri, Nigeria
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Matinja AI, Kamarudin NHA, Leow ATC, Oslan SN, Ali MSM. Cold-Active Lipases and Esterases: A Review on Recombinant Overexpression and Other Essential Issues. Int J Mol Sci 2022; 23:ijms232315394. [PMID: 36499718 PMCID: PMC9740821 DOI: 10.3390/ijms232315394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/21/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
Cold environments characterised by diverse temperatures close to or below the water freezing point dominate about 80% of the Earth's biosphere. One of the survival strategies adopted by microorganisms living in cold environments is their expression of cold-active enzymes that enable them to perform an efficient metabolic flux at low temperatures necessary to thrive and reproduce under those constraints. Cold-active enzymes are ideal biocatalysts that can reduce the need for heating procedures and improve industrial processes' quality, sustainability, and cost-effectiveness. Despite their wide applications, their industrial usage is still limited, and the major contributing factor is the lack of complete understanding of their structure and cold adaptation mechanisms. The current review looked at the recombinant overexpression, purification, and recent mechanism of cold adaptation, various approaches for purification, and three-dimensional (3D) crystal structure elucidation of cold-active lipases and esterase.
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Affiliation(s)
- Adamu Idris Matinja
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Department of Biochemistry, Faculty of Science, Bauchi State University, Gadau 751105, Nigeria
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Correspondence:
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Forsythe NL, Tan MF, Vinciguerra D, Woodford J, Stieg AZ, Maynard HD. Noncovalent Enzyme Nanogels via a Photocleavable Linkage. Macromolecules 2022; 55:9925-9933. [PMID: 36438597 PMCID: PMC9686129 DOI: 10.1021/acs.macromol.2c01334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/12/2022] [Indexed: 11/06/2022]
Abstract
Enzyme nanogels (ENGs) offer a convenient method to protect therapeutic proteins from in vivo stressors. Current methodologies to prepare ENGs rely on either covalent modification of surface residues or the noncovalent assembly of monomers at the protein surface. In this study, we report a new method for the preparation of noncovalent ENGs that utilizes a heterobifunctional, photocleavable monomer as a hybrid approach. Initial covalent modification with this monomer established a polymerizable handle at the protein surface, followed by radical polymerization with poly(ethylene glycol) methacrylate monomer and ethylene glycol dimethacrylate crosslinker in solution. Final photoirradiation cleaved the linkage between the polymer and protein to afford the noncovalent ENGs. The enzyme phenylalanine ammonia lyase (PAL) was utilized as a model protein yielding well-defined nanogels 80 nm in size by dynamic light scattering (DLS) and 76 nm by atomic force microscopy. The stability of PAL after exposure to trypsin or low pH was assessed and was found to be more stable in the noncovalent nanogel compared to PAL alone. This approach may be useful for the stabilization of active enzymes.
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Affiliation(s)
- Neil L. Forsythe
- Department
of Chemistry and Biochemistry, University
of California, 607 Charles
E. Young Drive East, Los Angeles, California 90095, United States
| | - Mikayla F. Tan
- Department
of Chemistry and Biochemistry, University
of California, 607 Charles
E. Young Drive East, Los Angeles, California 90095, United States
| | - Daniele Vinciguerra
- California
NanoSystems Institute, 570 Westwood Plaza Building 114, Los Angeles, California 90095, United States
| | - Jacquelin Woodford
- Department
of Chemistry and Biochemistry, University
of California, 607 Charles
E. Young Drive East, Los Angeles, California 90095, United States
| | - Adam Z. Stieg
- California
NanoSystems Institute, 570 Westwood Plaza Building 114, Los Angeles, California 90095, United States
| | - Heather D. Maynard
- Department
of Chemistry and Biochemistry, University
of California, 607 Charles
E. Young Drive East, Los Angeles, California 90095, United States,California
NanoSystems Institute, 570 Westwood Plaza Building 114, Los Angeles, California 90095, United States,
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de Francisco Martínez P, Morgante V, González-Pastor JE. Isolation of novel cold-tolerance genes from rhizosphere microorganisms of Antarctic plants by functional metagenomics. Front Microbiol 2022; 13:1026463. [DOI: 10.3389/fmicb.2022.1026463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
The microorganisms that thrive in Antarctica, one of the coldest environments on the planet, have developed diverse adaptation mechanisms to survive in these extreme conditions. Through functional metagenomics, in this work, 29 new genes related to cold tolerance have been isolated and characterized from metagenomic libraries of microorganisms from the rhizosphere of two Antarctic plants. Both libraries were hosted in two cold-sensitive strains of Escherichia coli: DH10B ΔcsdA and DH10B ΔcsdA Δrnr. The csdA gene encodes a DEAD-box RNA helicase and rnr gene encodes an exoribonuclease, both essential for cold-adaptation. Cold-tolerance tests have been carried out in solid and liquid media at 15°C. Among the cold-tolerance genes identified, 12 encode hypothetical and unknown proteins, and 17 encode a wide variety of different proteins previously related to other well-characterized ones involved in metabolism reactions, transport and membrane processes, or genetic information processes. Most of them have been connected to cold-tolerance mechanisms. Interestingly, 13 genes had no homologs in E. coli, thus potentially providing entirely new adaptation strategies for this bacterium. Moreover, ten genes also conferred resistance to UV-B radiation, another extreme condition in Antarctica.
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Zarrin M, Shialy Z. Molecular analysis of acid-stable alpha-amylase (asAA) gene in Aspergillus niger using PCR-RFLP. Biomedicine (Taipei) 2022. [DOI: 10.51248/.v42i5.1726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Introduction and Aim: Amylase is an important enzyme with vast applications in various industries such as food and therapeutic industries. Aspergillus niger is commercially engaged in the making of alpha-amylase. Acid-stable alpha -amylase is mostly produced with microorganisms such as Bacillus and Aspergillus. The aim of this research was the molecular investigation of the acid-stable alpha-amylase (alpha-sAA) gene in A. niger.
Materials and Methods: Sixty-three A. niger isolates were evaluated in this study. PCR method was performed for amplification of a 347 bp DNA band of the alpha-sAA gene. The Hpa II Restriction endonuclease was used for the digestion of PCR fragments.
Results: A 347 bp DNA fragment was recovered from 49 out of 63 (78%) isolates. After cutting the PCR products with the HpalphaII enzyme, 81.6% of isolates showed the expected band and 18.4% presented different restriction endonuclease patterns.
Conclusion: The results demonstrated the PCR-RFLP technique performed in this research was a valuable tool for analysis of the alpha-sAA gene in A. niger isolates.
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Veerana M, Yu NN, Bae SJ, Kim I, Kim ES, Ketya W, Lee HY, Kim NY, Park G. Enhancement of Fungal Enzyme Production by Radio-Frequency Electromagnetic Fields. J Fungi (Basel) 2022; 8:1187. [PMID: 36354954 PMCID: PMC9695996 DOI: 10.3390/jof8111187] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/06/2022] [Accepted: 11/08/2022] [Indexed: 08/17/2023] Open
Abstract
Enzyme production by microorganisms on an industrial scale has demonstrated technical bottlenecks, such as low efficiency in enzyme expression and extracellular secretion. In this study, as a potential tool for overcoming these technical limits, radio-frequency electromagnetic field (RF-EMF) exposure was examined for its possibility to enhance production of an enzyme, α-amylase, in a filamentous fungus, Aspergillus oryzae. The RF-EMF perfectly resonated at 2 GHz with directivity radiation pattern and peak gain of 0.5 dB (0.01 Watt). Total protein concentration and activity of α-amylase measured in media were about 1.5-3-fold higher in the RF-EMF exposed (10 min) sample than control (no RF-EMF) during incubation (the highest increase after 16 h). The level of α-amylase mRNA in cells was approximately 2-8-fold increased 16 and 24 h after RF-EMF exposure for 10 min. An increase in vesicle accumulation within fungal hyphae and the transcription of some genes involved in protein cellular trafficking was observed in RF-EMF-exposed samples. Membrane potential was not changed, but the intracellular Ca2+ level was elevated after RF-EMF exposure. Our results suggest that RF-EMF can increase the extracellular level of fungal total proteins and α-amylase activity and the intracellular level of Ca2+.
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Affiliation(s)
- Mayura Veerana
- Radio-Frequency Integrated Circuit (RFIC) Center, Kwangwoon University, Seoul 01897, Korea
- Plasma Bioscience Research Center, Department of Plasma-Bio Display, Kwangwoon University, Seoul 01897, Korea
| | - Nan-Nan Yu
- Plasma Bioscience Research Center, Department of Plasma-Bio Display, Kwangwoon University, Seoul 01897, Korea
| | - Si-Jin Bae
- Radio-Frequency Integrated Circuit (RFIC) Center, Kwangwoon University, Seoul 01897, Korea
- Department of Electronics Engineering, Kwangwoon University, Seoul 01897, Korea
| | - Ikhwan Kim
- Radio-Frequency Integrated Circuit (RFIC) Center, Kwangwoon University, Seoul 01897, Korea
- Department of Electronics Engineering, Kwangwoon University, Seoul 01897, Korea
| | - Eun-Seong Kim
- Radio-Frequency Integrated Circuit (RFIC) Center, Kwangwoon University, Seoul 01897, Korea
| | - Wirinthip Ketya
- Plasma Bioscience Research Center, Department of Plasma-Bio Display, Kwangwoon University, Seoul 01897, Korea
| | - Hak-Yong Lee
- Radio-Frequency Integrated Circuit (RFIC) Center, Kwangwoon University, Seoul 01897, Korea
| | - Nam-Young Kim
- Radio-Frequency Integrated Circuit (RFIC) Center, Kwangwoon University, Seoul 01897, Korea
- Department of Electronics Engineering, Kwangwoon University, Seoul 01897, Korea
| | - Gyungsoon Park
- Plasma Bioscience Research Center, Department of Plasma-Bio Display, Kwangwoon University, Seoul 01897, Korea
- Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Korea
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Rahman MA, Heme UH, Parvez MAK. In silico functional annotation of hypothetical proteins from the Bacillus paralicheniformis strain Bac84 reveals proteins with biotechnological potentials and adaptational functions to extreme environments. PLoS One 2022; 17:e0276085. [PMID: 36228026 PMCID: PMC9560612 DOI: 10.1371/journal.pone.0276085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/28/2022] [Indexed: 11/26/2022] Open
Abstract
Members of the Bacillus genus are industrial cell factories due to their capacity to secrete significant quantities of biomolecules with industrial applications. The Bacillus paralicheniformis strain Bac84 was isolated from the Red Sea and it shares a close evolutionary relationship with Bacillus licheniformis. However, a significant number of proteins in its genome are annotated as functionally uncharacterized hypothetical proteins. Investigating these proteins' functions may help us better understand how bacteria survive extreme environmental conditions and to find novel targets for biotechnological applications. Therefore, the purpose of our research was to functionally annotate the hypothetical proteins from the genome of B. paralicheniformis strain Bac84. We employed a structured in-silico approach incorporating numerous bioinformatics tools and databases for functional annotation, physicochemical characterization, subcellular localization, protein-protein interactions, and three-dimensional structure determination. Sequences of 414 hypothetical proteins were evaluated and we were able to successfully attribute a function to 37 hypothetical proteins. Moreover, we performed receiver operating characteristic analysis to assess the performance of various tools used in this present study. We identified 12 proteins having significant adaptational roles to unfavorable environments such as sporulation, formation of biofilm, motility, regulation of transcription, etc. Additionally, 8 proteins were predicted with biotechnological potentials such as coenzyme A biosynthesis, phenylalanine biosynthesis, rare-sugars biosynthesis, antibiotic biosynthesis, bioremediation, and others. Evaluation of the performance of the tools showed an accuracy of 98% which represented the rationality of the tools used. This work shows that this annotation strategy will make the functional characterization of unknown proteins easier and can find the target for further investigation. The knowledge of these hypothetical proteins' potential functions aids B. paralicheniformis strain Bac84 in effectively creating a new biotechnological target. In addition, the results may also facilitate a better understanding of the survival mechanisms in harsh environmental conditions.
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Affiliation(s)
- Md. Atikur Rahman
- Institute of Microbiology, Friedrich Schiller University Jena, Thuringia, Germany
| | - Uzma Habiba Heme
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Thuringia, Germany
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Anand U, Vaishnav A, Sharma SK, Sahu J, Ahmad S, Sunita K, Suresh S, Dey A, Bontempi E, Singh AK, Proćków J, Shukla AK. Current advances and research prospects for agricultural and industrial uses of microbial strains available in world collections. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156641. [PMID: 35700781 DOI: 10.1016/j.scitotenv.2022.156641] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms are an important component of the ecosystem and have an enormous impact on human lives. Moreover, microorganisms are considered to have desirable effects on other co-existing species in a variety of habitats, such as agriculture and industries. In this way, they also have enormous environmental applications. Hence, collections of microorganisms with specific traits are a crucial step in developing new technologies to harness the microbial potential. Microbial culture collections (MCCs) are a repository for the preservation of a large variety of microbial species distributed throughout the world. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are vital for the safeguarding and circulation of biological resources, as well as for the progress of the life sciences. Ex situ conservation of microorganisms tagged with specific traits in the collections is the crucial step in developing new technologies to harness their potential. Type strains are mainly used in taxonomic study, whereas reference strains are used for agricultural, biotechnological, pharmaceutical research and commercial work. Despite the tremendous potential in microbiological research, little effort has been made in the true sense to harness the potential of conserved microorganisms. This review highlights (1) the importance of available global microbial collections for man and (2) the use of these resources in different research and applications in agriculture, biotechnology, and industry. In addition, an extensive literature survey was carried out on preserved microorganisms from different collection centres using the Web of Science (WoS) and SCOPUS. This review also emphasizes knowledge gaps and future perspectives. Finally, this study provides a critical analysis of the current and future roles of microorganisms available in culture collections for different sustainable agricultural and industrial applications. This work highlights target-specific potential microbial strains that have multiple important metabolic and genetic traits for future research and use.
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Affiliation(s)
- Uttpal Anand
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Anukool Vaishnav
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh 281406, India; Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland; Plant-Soil Interaction Group, Agroscope (Reckenholz), Reckenholzstrasse 191, 8046 Zürich, Switzerland
| | - Sushil K Sharma
- National Agriculturally Important Microbial Culture Collection (NAIMCC), ICAR-National Bureau of Agriculturally Important Microorganisms (ICAR-NBAIM), Mau 275 103, Uttar Pradesh, India.
| | - Jagajjit Sahu
- GyanArras Academy, Gothapatna, Malipada, Bhubaneswar, Odisha 751029, India
| | - Sarfaraz Ahmad
- Department of Botany, Jai Prakash University, Saran, Chhapra 841301, Bihar, India
| | - Kumari Sunita
- Department of Botany, Faculty of Science, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh 273009, India
| | - S Suresh
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal 462 003, Madhya Pradesh, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, West Bengal, India
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123 Brescia, Italy
| | - Amit Kishore Singh
- Department of Botany, Bhagalpur National College, (A Constituent unit of Tilka Manjhi Bhagalpur University), Bhagalpur 812007, Bihar, India
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Kożuchowska 5b, 51-631 Wrocław, Poland.
| | - Awadhesh Kumar Shukla
- Department of Botany, K.S. Saket P.G. College, Ayodhya (affiliated to Dr. Rammanohar Lohia Avadh University, Ayodhya) 224123, Uttar Pradesh, India.
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Solanki MK, Solanki AC, Rai S, Srivastava S, Kashyap BK, Divvela PK, Kumar S, Yandigeri MS, Kashyap PL, Shrivastava AK, Ali B, Khan S, Jaremko M, Qureshi KA. Functional interplay between antagonistic bacteria and Rhizoctonia solani in the tomato plant rhizosphere. Front Microbiol 2022; 13:990850. [PMID: 36225362 PMCID: PMC9548980 DOI: 10.3389/fmicb.2022.990850] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/18/2022] [Indexed: 12/28/2022] Open
Abstract
Microbial interactions with plant roots play an imperial role in tomato plant growth and defense against the Rhizoctonia solani. This study performed a field experiment with two antagonistic bacteria (Pseudomonas and Bacillus) inoculated in healthy and Rhizoctonia solani treated soil in tomato rhizosphere to understand the metabolic pattern and microbial function during plant disease suppression. In the present study, we assessed soil and microbial enzymes, bacterial and fungal cell forming unit (CFU), and carbon utilization profiling through Bio-Eco plates of rhizoplane samples. Antagonist bacteria and pathogen interaction significantly (p < 0.05) influenced the bacterial count, soil enzymes (chitinase and glucanase), and bacterial function (siderophore and chitinase production). These results indicated that these variables had an imperial role in disease suppression during plant development. Furthermore, the metabolic profiling showed that carbon source utilization enhanced under fruit development and ripening stages. These results suggested that carbon sources were essential in plant/pathogen/antagonist interaction. Substrates like β-methyl-D-glucoside, D-mannitol, D-galacturonic acid, N-acetyl-D-glucosamine, and phenylethylamine strongly connect with the suppuration of root rot disease. These carbon sources may help to propagate a healthy microbial community to reduce the pathogen invasion in the plant root system, and these carbon sources can be stimulators of antagonists against pathogens in the future.
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Affiliation(s)
- Manoj Kumar Solanki
- Faculty of Natural Sciences, Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | | | - Shalini Rai
- Department of Biotechnology, Society of Higher Education and Practical Application (SHEPA), Varanasi, UP, India
| | - Supriya Srivastava
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah, Saudi Arabia
| | - Brijendra Kumar Kashyap
- Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi, UP, India
| | | | - Sudheer Kumar
- Indian Institute of Wheat and Barley Research (ICAR), Karnal, HR, India
| | - Mahesh S. Yandigeri
- National Bureau of Agricultural Insect Resources (ICAR), Bengaluru, KA, India
- *Correspondence: Mahesh S. Yandigeri,
| | - Prem Lal Kashyap
- Indian Institute of Wheat and Barley Research (ICAR), Karnal, HR, India
| | | | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shahid Khan
- Department of Agriculture, University of Swabi, Swabi, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture Swat, Peshawar, Pakistan
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kamal Ahmad Qureshi
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah, Saudi Arabia
- Kamal Ahmad Qureshi,
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Cold-Active Enzymes and Their Potential Industrial Applications-A Review. Molecules 2022; 27:molecules27185885. [PMID: 36144621 PMCID: PMC9501442 DOI: 10.3390/molecules27185885] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
More than 70% of our planet is covered by extremely cold environments, nourishing a broad diversity of microbial life. Temperature is the most significant parameter that plays a key role in the distribution of microorganisms on our planet. Psychrophilic microorganisms are the most prominent inhabitants of the cold ecosystems, and they possess potential cold-active enzymes with diverse uses in the research and commercial sectors. Psychrophiles are modified to nurture, replicate, and retain their active metabolic activities in low temperatures. Their enzymes possess characteristics of maximal activity at low to adequate temperatures; this feature makes them more appealing and attractive in biotechnology. The high enzymatic activity of psychrozymes at low temperatures implies an important feature for energy saving. These enzymes have proven more advantageous than their mesophilic and thermophilic counterparts. Therefore, it is very important to explore the efficiency and utility of different psychrozymes in food processing, pharmaceuticals, brewing, bioremediation, and molecular biology. In this review, we focused on the properties of cold-active enzymes and their diverse uses in different industries and research areas. This review will provide insight into the areas and characteristics to be improved in cold-active enzymes so that potential and desired enzymes can be made available for commercial purposes.
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Jain N, Radhakrishnan A, Kuppusamy G. Review on nutraceuticals: phase transition from preventive to protective care. JOURNAL OF COMPLEMENTARY & INTEGRATIVE MEDICINE 2022; 19:553-570. [PMID: 35436045 DOI: 10.1515/jcim-2022-0026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Nutraceuticals are essential for healthcare which is an alternative medicine that has gained popularity in recent years. Nutraceuticals consist of nutrients, herbals, and dietary supplements, which make them useful in preserving and promoting health, fighting illness, and improving overall quality of life. Its success or failure will be determined by its rapid expansion, research advances, lack of standards, marketing enthusiasm, quality assurance, and regulations. Nutraceuticals have been used in different regions under different names/categories. however, globally there are no stringent pharmaceutical standards for nutraceutical health products till date, but slowly regulators are paying attention on it. Nutraceuticals can be broadly classified according to it clinical significance, source and therapeutic effects. Nutraceuticals and functional foods have grown to be a multibillion-dollar business worldwide in recent years and personalization is the emerging approach to deliver the best therapeutic effect in future. This review carries extensive information about nutraceutical history, classification, regulatory aspects and industrial perspective.
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Affiliation(s)
- Nishakumari Jain
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamilnadu, India
| | - Arun Radhakrishnan
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamilnadu, India
| | - Gowthamarajan Kuppusamy
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamilnadu, India
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Rabapane KJ, Ijoma GN, Matambo TS. Insufficiency in functional genomics studies, data, and applications: A case study of bio-prospecting research in ruminant microbiome. Front Genet 2022; 13:946449. [PMID: 36118848 PMCID: PMC9472250 DOI: 10.3389/fgene.2022.946449] [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: 05/17/2022] [Accepted: 07/21/2022] [Indexed: 12/02/2022] Open
Abstract
Over the last two decades, biotechnology has advanced at a rapid pace, propelled by the incorporation of bio-products into various aspects of pharmaceuticals, industry, and the environment. These developments have sparked interest in the bioprospecting of microorganisms and their products in a variety of niche environments. Furthermore, the use of omics technologies has greatly aided our analyses of environmental samples by elucidating the microbial ecological framework, biochemical pathways, and bio-products. However, the more often overemphasis on taxonomic identification in most research publications, as well as the data associated with such studies, is detrimental to immediate industrial and commercial applications. This review identifies several factors that contribute to the complexity of sequence data analysis as potential barriers to the pragmatic application of functional genomics, utilizing recent research on ruminants to demonstrate these limitations in the hopes of broadening our horizons and drawing attention to this gap in bioprospecting studies for other niche environments as well. The review also aims to emphasize the importance of routinely incorporating functional genomics into environmental metagenomics analyses in order to improve solutions that drive rapid industrial biocatalysis developments from derived outputs with the aim of achieving potential benefits in energy-use reduction and environmental considerations for current and future applications.
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45
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A Two-Step Cross-Linked Hydrogel Immobilization Strategy for Diacetylchitobiose Deacetylase. Catalysts 2022. [DOI: 10.3390/catal12090932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Free enzymes often face economic problems due to their non-recyclability, which limits their applications for industrial manufacturing. Organic biopolymers are frequently used to fabricate hydrogel for enzyme immobilization due to their advantages of non-toxicity, biocompatibility, biodegradability, and flexibility. However, for highly thermostable enzymes, simple cross-linking causes either low immobilizing efficiency or low thermal stability. Herein, we developed a novel enzyme immobilization strategy with two-step cross-linked gelatin hydrogel for thermostable enzymes working at high temperature. The hydrogel was firstly “soft cross-linked” to immobilize most enzyme molecules and then “hard cross-linked” to gain strong thermal stability. We selected the enzyme diacetylchitobiose deacetylase (Dac), which was firstly derived from hyperthermophilic bacteria, to demonstrate the advantages of our method. With the optimized fabrication steps, our hydrogel showed ~87% Dac immobilization efficiency and excellent stability against heating, dehydrating, long-time storing, and massive recycling. Importantly, our hydrogel showed ~85.0% relative enzyme activity at 80 °C and retained ~65.8% activity after 10 rounds of catalysis. This strategy showed high immobilizing efficiency and strong thermal stability and we believe it could improve the industrial potential for those enzymes.
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Escudeiro P, Henry CS, Dias RP. Functional characterization of prokaryotic dark matter: the road so far and what lies ahead. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100159. [PMID: 36561390 PMCID: PMC9764257 DOI: 10.1016/j.crmicr.2022.100159] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/18/2022] [Accepted: 08/05/2022] [Indexed: 12/25/2022] Open
Abstract
Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the "microbial dark matter" (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications.
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Affiliation(s)
- Pedro Escudeiro
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
| | - Christopher S. Henry
- Argonne National Laboratory, Lemont, Illinois, USA,University of Chicago, Chicago, Illinois, USA
| | - Ricardo P.M. Dias
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal,iXLab - Innovation for National Biological Resilience, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal,Corresponding author.
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Golgeri M DB, Mulla SI, Bagewadi ZK, Tyagi S, Hu A, Sharma S, Bilal M, Bharagava RN, Ferreira LFR, Gurumurthy DM, Nadda AK. A systematic review on potential microbial carbohydrases: current and future perspectives. Crit Rev Food Sci Nutr 2022; 64:438-455. [PMID: 35930295 DOI: 10.1080/10408398.2022.2106545] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Various studies have shown that the microbial proteins are often more stable than belongs to other sources like plant and animal origin. Hence, the interest in microbial enzymes has gained much attention due to many potential applications like bioenergy, biofuel production, biobleaching, bioconversion and so on. Additionally, recent trends revealed that the interest in isolating novel microbes from harsh environments have been the main focus of many scientists for various applications. Basically, industrially important enzymes can be categorized into mainly three groups: carbohydrases, proteases, and lipases. Among those, the enzymes especially carbohydrases involved in production of sugars. Carbohydrases include amylases, xylanases, pectinases, cellulases, chitinases, mannases, laccases, ligninases, lactase, glucanase, and glucose oxidase. Thus, here, an approach has been made to highlight five enzymes namely amylase, cellulase, laccase, pectinase, and xylanase from different sources with special emphasis on their properties, mechanism, applications, production optimization, purification, molecular approaches for its enhanced and stable production, and also biotechnological perspectives of its future development. Also, green and sustainable catalytic conversion strategies using nanoparticles of these enzymes have also been discussed. This review will provide insight into the carbohydrases importance and their usefulness that will help to the researchers working in this field.
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Affiliation(s)
- Dilshad Begum Golgeri M
- Department of Biochemistry, School of Allied Health Sciences, REVA University, Bangalore, India
- Department of Biochemistry, Indian Academy Degree College-Autonomous Kalyanagar, Bangalore, India
| | - Sikandar I Mulla
- Department of Biochemistry, School of Allied Health Sciences, REVA University, Bangalore, India
| | - Zabin K Bagewadi
- Department of Biotechnology, KLE Technological University, Hubballi, Karnataka, India
| | - Swati Tyagi
- IRRI- South Asia Regional centre, Varanasi, Uttar Pradesh, India
| | - Anyi Hu
- Institute of Urban Environment Chinese Academy of Sciences, CAS Key Laboratory of Urban Pollutant Conversion, Xiamen, China
| | - Swati Sharma
- University Institute of Biotechnology (UIBT), Chandigarh University, Mohali, Punjab, India
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Ram Naresh Bharagava
- Department of Microbiology (DM), School for Environmental Sciences (SES), Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, Uttar Pradesh, India
| | | | | | - Ashok Kumar Nadda
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, India
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Cao Y, Li W, Pei R. Exploring the catalytic mechanism of multivalent G-quadruplex/hemin DNAzymes by modulating the position and spatial orientation of connected G-quadruplexes. Anal Chim Acta 2022; 1221:340105. [DOI: 10.1016/j.aca.2022.340105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/06/2022] [Accepted: 06/18/2022] [Indexed: 11/15/2022]
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49
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Direct utilization of peach wastes for enhancements of lignocellulolytic enzymes productions by Pleurotus eryngii under solid-state fermentation conditions. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02356-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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50
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Cloning, expression and characterization of PURase gene from Pseudomonas sp. AKS31. Arch Microbiol 2022; 204:498. [PMID: 35849211 DOI: 10.1007/s00203-022-03110-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/02/2022]
Abstract
Polyurethane (PUR) is a soil and aquatic contaminant throughout the world. Towards bioremediation, in a previous study, a soil bacterium, Pseudomonas sp. AKS31, capable of efficiently degrading PUR was isolated. Polyurethanase (PURase) enzyme is capable of cleaving the ester bond of PUR and is considered as a key regulator of PUR biodegradation. Hence, for a high yield, easy purification, and further characterization, the aim of this study was to clone and overexpress the PURase gene of this isolate. The current study also investigated structural aspects of this enzyme through predictive bioinformatics analyses. In this context, the PURase gene of the isolate was cloned and expressed in E. coli using pET28(a)+ vector. The obtained recombinant protein was found insoluble. Therefore, first, the protein was made soluble with urea and purified using nickel-NTA beads. The purified enzyme exhibited substantial activities when tested on the LA-PUR plate. Bioinformatics-based analysis of the protein revealed the presence of a lipase serine active site and indicated that this PURase belongs to the Family 1.3 lipase. Hence, the present study shows that active PURase can be produced in large quantities using a prokaryotic expression system and thus, provides an effective strategy for in-vitro PUR-degradation.
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