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Bhatt HB, Sani RK, Amoozegar MA, Singh SP. Editorial: Extremozymes: characteristics, structure, protein engineering and applications. Front Microbiol 2024; 15:1423463. [PMID: 38779500 PMCID: PMC11109424 DOI: 10.3389/fmicb.2024.1423463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Affiliation(s)
- Hitarth B. Bhatt
- Department of Microbiology, Faculty of Science, Atmiya University, Rajkot, Gujarat, India
| | - Rajesh K. Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Satya P. Singh
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, India
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Ali M, Greenig M, Oeller M, Atkinson M, Xu X, Sormanni P. Automated optimization of the solubility of a hyper-stable α-amylase. Open Biol 2024; 14:240014. [PMID: 38745462 DOI: 10.1098/rsob.240014] [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: 01/18/2024] [Accepted: 03/27/2024] [Indexed: 05/16/2024] Open
Abstract
Most successes in computational protein engineering to date have focused on enhancing one biophysical trait, while multi-trait optimization remains a challenge. Different biophysical properties are often conflicting, as mutations that improve one tend to worsen the others. In this study, we explored the potential of an automated computational design strategy, called CamSol Combination, to optimize solubility and stability of enzymes without affecting their activity. Specifically, we focus on Bacillus licheniformis α-amylase (BLA), a hyper-stable enzyme that finds diverse application in industry and biotechnology. We validate the computational predictions by producing 10 BLA variants, including the wild-type (WT) and three designed models harbouring between 6 and 8 mutations each. Our results show that all three models have substantially improved relative solubility over the WT, unaffected catalytic rate and retained hyper-stability, supporting the algorithm's capacity to optimize enzymes. High stability and solubility embody enzymes with superior resilience to chemical and physical stresses, enhance manufacturability and allow for high-concentration formulations characterized by extended shelf lives. This ability to readily optimize solubility and stability of enzymes will enable the rapid and reliable generation of highly robust and versatile reagents, poised to contribute to advancements in diverse scientific and industrial domains.
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Affiliation(s)
- Montader Ali
- Yusuf Hamied Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, UK
| | - Matthew Greenig
- Yusuf Hamied Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, UK
| | - Marc Oeller
- Yusuf Hamied Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, UK
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry , Martinsried 82152, Germany
| | - Misha Atkinson
- Yusuf Hamied Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, UK
| | - Xing Xu
- Yusuf Hamied Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, UK
| | - Pietro Sormanni
- Yusuf Hamied Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, UK
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3
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Shrestha S, Goswami S, Banerjee D, Garcia V, Zhou E, Olmsted CN, Majumder ELW, Kumar D, Awasthi D, Mukhopadhyay A, Singer SW, Gladden JM, Simmons BA, Choudhary H. Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries. CHEMSUSCHEM 2024:e202301460. [PMID: 38669480 DOI: 10.1002/cssc.202301460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/14/2024] [Indexed: 04/28/2024]
Abstract
The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.
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Affiliation(s)
- Shilva Shrestha
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Shubhasish Goswami
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Valentina Garcia
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Elizabeth Zhou
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
| | - Charles N Olmsted
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Erica L-W Majumder
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Deepak Kumar
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Deepika Awasthi
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Hemant Choudhary
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA 94550, United States
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4
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Ivanov YD, Shumov ID, Kozlov AF, Valueva AA, Ershova MO, Ivanova IA, Ableev AN, Tatur VY, Lukyanitsa AA, Ivanova ND, Ziborov VS. Atomic Force Microscopy Study of the Long-Term Effect of the Glycerol Flow, Stopped in a Coiled Heat Exchanger, on Horseradish Peroxidase. MICROMACHINES 2024; 15:499. [PMID: 38675310 PMCID: PMC11052087 DOI: 10.3390/mi15040499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
Glycerol is employed as a functional component of heat-transfer fluids, which are of use in both bioreactors and various biosensor devices. At the same time, flowing glycerol was reported to cause considerable triboelectric effects. Herein, by using atomic force microscopy (AFM), we have revealed the long-term effect of glycerol flow, stopped in a ground-shielded coiled heat exchanger, on horseradish peroxidase (HRP) adsorption on mica. Namely, the solution of HRP was incubated in the vicinity of the side of the cylindrical coil with stopped glycerol flow, and then HRP was adsorbed from this solution onto a mica substrate. This incubation has been found to markedly increase the content of aggregated enzyme on mica-as compared with the control enzyme sample. We explain the phenomenon observed by the influence of triboelectrically induced electromagnetic fields of non-trivial topology. The results reported should be further considered in the development of flow-based heat exchangers of biosensors and bioreactors intended for operation with enzymes.
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Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Maria O. Ershova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Alexander N. Ableev
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Vadim Y. Tatur
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (A.A.L.); (N.D.I.)
| | - Andrei A. Lukyanitsa
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (A.A.L.); (N.D.I.)
- Faculty of Computational Mathematics and Cybernetics, Moscow State University, 119991 Moscow, Russia
| | - Nina D. Ivanova
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (A.A.L.); (N.D.I.)
- Moscow State Academy of Veterinary Medicine and Biotechnology Named after Skryabin, 109472 Moscow, Russia
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
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5
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Kuddus M, Roohi, Bano N, Sheik GB, Joseph B, Hamid B, Sindhu R, Madhavan A. Cold-active microbial enzymes and their biotechnological applications. Microb Biotechnol 2024; 17:e14467. [PMID: 38656876 PMCID: PMC11042537 DOI: 10.1111/1751-7915.14467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/26/2024] Open
Abstract
Microorganisms known as psychrophiles/psychrotrophs, which survive in cold climates, constitute majority of the biosphere on Earth. Their capability to produce cold-active enzymes along with other distinguishing characteristics allows them to survive in the cold environments. Due to the relative ease of large-scale production compared to enzymes from plants and animals, commercial uses of microbial enzyme are alluring. The ocean depths, polar, and alpine regions, which make up over 85% of the planet, are inhabited to cold ecosystems. Microbes living in these regions are important for their metabolic contribution to the ecosphere as well as for their enzymes, which may have potential industrial applications. Cold-adapted microorganisms are a possible source of cold-active enzymes that have high catalytic efficacy at low and moderate temperatures at which homologous mesophilic enzymes are not active. Cold-active enzymes can be used in a variety of biotechnological processes, including food processing, additives in the detergent and food industries, textile industry, waste-water treatment, biopulping, environmental bioremediation in cold climates, biotransformation, and molecular biology applications with great potential for energy savings. Genetically manipulated strains that are suitable for producing a particular cold-active enzyme would be crucial in a variety of industrial and biotechnological applications. The potential advantage of cold-adapted enzymes will probably lead to a greater annual market than for thermo-stable enzymes in the near future. This review includes latest updates on various microbial source of cold-active enzymes and their biotechnological applications.
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Affiliation(s)
- Mohammed Kuddus
- Department of Biochemistry, College of MedicineUniversity of HailHailSaudi Arabia
| | - Roohi
- Protein Research Laboratory, Department of BioengineeringIntegral UniversityLucknowIndia
| | - Naushin Bano
- Protein Research Laboratory, Department of BioengineeringIntegral UniversityLucknowIndia
| | | | - Babu Joseph
- Department of Clinical Laboratory Sciences, College of Applied Medical SciencesShaqra UniversityShaqraSaudi Arabia
| | - Burhan Hamid
- Center of Research for DevelopmentUniversity of KashmirSrinagarIndia
| | - Raveendran Sindhu
- Department of Food TechnologyTKM Institute of TechnologyKollamKeralaIndia
| | - Aravind Madhavan
- School of BiotechnologyAmrita Vishwa Vidyapeetham, AmritapuriKollamKeralaIndia
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6
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Wang X, Zong Y, Zhou X, Xu L, He W, Quan S. Artificial Intelligence-Powered Construction of a Microbial Optimal Growth Temperature Database and Its Impact on Enzyme Optimal Temperature Prediction. J Phys Chem B 2024; 128:2281-2292. [PMID: 38437173 DOI: 10.1021/acs.jpcb.3c06526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Accurate prediction of enzyme optimal temperature (Topt) is crucial for identifying enzymes suitable for catalytic functions under extreme bioprocessing conditions. The optimal growth temperature (OGT) of microorganisms serves as a key indicator for estimating enzyme Topt, reflecting an evolutionary temperature balance between enzyme-catalyzed reactions and the organism's growth environments. Existing OGT databases, collected from culture collection centers, often fall short as culture temperature does not precisely represent the OGT. Models trained on such databases yield inadequate accuracy in enzyme Topt prediction, underscoring the need for a high-quality OGT database. Herein, we developed AI-based models to extract the OGT information from the scientific literature, constructing a comprehensive OGT database with 1155 unique organisms and 2142 OGT values. The top-performing model, BioLinkBERT, demonstrated exceptional information extraction ability with an EM score of 91.00 and an F1 score of 91.91 for OGT. Notably, applying this OGT database in enzyme Topt prediction achieved an R2 value of 0.698, outperforming the R2 value of 0.686 obtained using culture temperature. This emphasizes the superiority of the OGT database in predicting the enzyme Topt and underscores its pivotal role in identifying enzymes with optimal catalytic temperatures.
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Affiliation(s)
- Xiaotao Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), East China University of Science and Technology, Shanghai 200237, China
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yuwei Zong
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xuanjie Zhou
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Li Xu
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wei He
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), East China University of Science and Technology, Shanghai 200237, China
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), East China University of Science and Technology, Shanghai 200237, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 201203, China
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7
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Akram F, Fatima T, Shabbir I, Haq IU, Ibrar R, Mukhtar H. Abridgement of Microbial Esterases and Their Eminent Industrial Endeavors. Mol Biotechnol 2024:10.1007/s12033-024-01108-7. [PMID: 38461181 DOI: 10.1007/s12033-024-01108-7] [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: 12/02/2023] [Accepted: 02/05/2024] [Indexed: 03/11/2024]
Abstract
Esterases are hydrolases that contribute to the hydrolysis of ester bonds into both water-soluble acyl esters and emulsified glycerol-esters containing short-chain acyl groups. They have garnered significant attention from biotechnologists and organic chemists due to their immense commercial value. Esterases, with their diverse and significant properties, have become highly sought after for various industrial applications. Synthesized ubiquitously by a wide range of living organisms, including animals, plants, and microorganisms, these enzymes have found microbial esterases to be the preferred choice in industrial settings. The cost-effective production of microbial esterases ensures higher yields, unaffected by seasonal variations. Their applications span diverse sectors, such as food manufacturing, leather tanneries, paper and pulp production, textiles, detergents, cosmetics, pharmaceuticals, biodiesel synthesis, bioremediation, and waste treatment. As the global trend shifts toward eco-friendly and sustainable practices, industrial processes are evolving with reduced waste generation, lower energy consumption, and the utilization of biocatalysts derived from renewable and unconventional raw materials. This review explores the background, structural characteristics, thermostability, and multifaceted roles of bacterial esterases in crucial industries, aiming to optimize and analyze their properties for continued successful utilization in diverse industrial processes. Additionally, recent advancements in esterase research are overviewed, showcasing novel techniques, innovations, and promising areas for further exploration.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan.
| | - Taseer Fatima
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Ifrah Shabbir
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
- Pakistan Academy of Sciences, Islamabad, Pakistan
| | - Ramesha Ibrar
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Hamid Mukhtar
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
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Salmanizadeh H, Beheshti-Maal K, Nayeri H, Torabi LR. Optimization of xylanase production by Pichia kudriavzevii and Candida tropicalis isolated from the wood product workshop. Braz J Microbiol 2024; 55:155-168. [PMID: 37957443 DOI: 10.1007/s42770-023-01171-3] [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: 06/22/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Enzymatic compounds can be found abundantly and provide numerous advantages in microbial organisms. Xylanases are used in various pharmaceutical, food, livestock, poultry, and paper industries. This study aimed to investigate xylanase-producing yeasts, xylose concentration curve and their enzymatic activity under various factors including carbon and nitrogen sources, temperature, and pH. Enzyme activity was evaluated under different conditions before, during, and after purification. The yeast strains were obtained from the wood product workshop and were subsequently cultivated on YPD (yeast extract peptone dextrose) medium. Additionally, the growth curve of the yeast and its molecular identification were conducted. The optimization and design process of xylan isolated from corn wood involved the use of Taguchi software to test different parameters like carbon and nitrogen sources, temperature, and pH, with the goal of determining the most optimal conditions for enzyme production. In addition, the Taguchi method was utilized to conduct a multifactorial optimization of xylanase enzyme activity. The isolated species were partially purified using ammonium sulfate precipitation and dialysis bag techniques. The results indicated that 3 species (8S, 18S, and 16W) after molecular identification based on 18S rRNA gene sequencing were identified as Candida tropicalis SBN-IAUF-1, Candida tropicalis SBN-IAUF-3, and Pichia kudriavzevii SBN-IAUF-2, respectively. The optimal parameters for wheat carbon source and peptone nitrogen source were found at 50 °C and pH 9.0 through single-factor optimization. By using the Taguchi approach, the best combination for highest activity was rice-derived carbon source and peptone nitrogen source at 50 °C and pH 6.0. The best conditions for xylanase enzyme production in single-factor optimization of wheat bran were 2135.6 U/mL, peptone 4475.25 U/mL, temperature 50 °C 1868 U/mL, and pH 9.0 2002.4 U/mL. Among the tested yeast, Candida tropicalis strain SBN-IAUF-1 to the access number MZ816946.1 in NCBI was found to be the best xylanase product. The highest ratio of enzyme production at the end of the delayed phase and the beginning of the logarithmic phase was concluded by comparing the growth ratio of 8S, 16W, and 18S yeasts with the level of enzymatic activity. This is the first report on the production of xylan polymer with a relative purity of 80% in Iran. The extracellular xylanases purified from the yeast species of C. tropicalis were introduced as a desirable biocatalyst due to their high enzymatic activity for the degradation of xylan polymers.
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Affiliation(s)
- Hoda Salmanizadeh
- Department of Microbiology, Falavarjan Branch, Islamic Azad University, Falavarjan, Isfahan, Iran
| | - Keivan Beheshti-Maal
- Department of Microbiology, Falavarjan Branch, Islamic Azad University, Falavarjan, Isfahan, Iran.
| | - Hashem Nayeri
- Department of Biochemistry, Falavarjan Branch, Islamic Azad University, Falavarjan, Isfahan, Iran
| | - Ladan Rahimzadeh Torabi
- Department of Microbiology, Falavarjan Branch, Islamic Azad University, Falavarjan, Isfahan, Iran
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Li L, Liu X, Bai Y, Yao B, Luo H, Tu T. High-Throughput Screening Techniques for the Selection of Thermostable Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3833-3845. [PMID: 38285533 DOI: 10.1021/acs.jafc.3c07554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
The acquisition of a thermostable enzyme is an indispensable prerequisite for its successful implementation in industrial applications and the development of novel functionalities. Various protein engineering approaches, including rational design, semirational design, and directed evolution, have been employed to enhance thermostability. However, all of these approaches require sensitive and reliable high-throughput screening (HTS) technologies to efficiently and rapidly identify variants with improved properties. While numerous reviews focus on modification strategies for enhancing enzyme thermostability, there is a dearth of literature reviewing HTS methods specifically aimed at this objective. Herein, we present a comprehensive overview of various HTS methods utilized for modifying enzyme thermostability across different screening platforms. Additionally, we highlight significant recent examples that demonstrate the successful application of these methods. Furthermore, we address the technical challenges associated with HTS technologies used for screening thermostable enzyme variants and discuss valuable perspectives to promote further advancements in this field. This review serves as an authoritative reference source offering theoretical support for selecting appropriate screening strategies tailored to specific enzymes with the aim of improving their thermostability.
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Affiliation(s)
- Lanxue Li
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingguo Bai
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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10
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Fujikawa T, Sasamoto T, Zhao F, Yamagishi A, Akanuma S. Comparative analysis of reconstructed ancestral proteins with their extant counterparts suggests primitive life had an alkaline habitat. Sci Rep 2024; 14:398. [PMID: 38172176 PMCID: PMC10764835 DOI: 10.1038/s41598-023-50828-4] [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: 05/22/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024] Open
Abstract
To understand the origin and early evolution of life it is crucial to establish characteristics of the primordial environment that facilitated the emergence and evolution of life. One important environmental factor is the pH of the primordial environment. Here, we assessed the pH-dependent thermal stabilities of previously reconstructed ancestral nucleoside diphosphate kinases and ribosomal protein uS8s. The selected proteins were likely to be present in ancient organisms such as the last common ancestor of bacteria and that of archaea. We also assessed the thermal stability of homologous proteins from extant acidophilic, neutralophilic, and alkaliphilic microorganisms as a function of pH. Our results indicate that the reconstructed ancestral proteins are more akin to those of extant alkaliphilic bacteria, which display greater stability under alkaline conditions. These findings suggest that the common ancestors of bacterial and archaeal species thrived in an alkaline environment. Moreover, we demonstrate the reconstruction method employed in this study is a valuable technique for generating alkali-tolerant proteins that can be used in a variety of biotechnological and environmental applications.
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Affiliation(s)
- Takayuki Fujikawa
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan
| | - Takahiro Sasamoto
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Fangzheng Zhao
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan.
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11
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Coker JA. 'All About' Extremophiles. Fac Rev 2023; 12:27. [PMID: 38027090 PMCID: PMC10630985 DOI: 10.12703/r/12-27] [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: 12/01/2023] Open
Abstract
Despite common perception, most of Earth is what is often referred to as an 'extreme environment.' Yet to the organisms that call these places home, it is simply that (home). They have adapted to thrive in these environments and, in the process, have evolved many unique adaptations at the molecular- and 'omic-level. Scientists' interest in these organisms has typically been in how they and their products can be harnessed for biotechnological applications and the environments where they are found, while the general public's veers more toward a fascination with their deviation from the 'norm'. However, these organisms have so much more to tell us about Life and the myriad ways there are to perform 'simple' biological processes.
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Affiliation(s)
- James A Coker
- Center for Biotechnology Education, Advanced Academic Programs, Krieger School of Arts and Sciences, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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12
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Kaličanin N, Balaž AM, Prodanović O, Prodanović R. Heterologous Expression and Partial Characterization of a Putative Opine Dehydrogenase from a Metagenomic Sequence of Desulfohalobium retbaense. Chembiochem 2023; 24:e202300414. [PMID: 37531452 DOI: 10.1002/cbic.202300414] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/13/2023] [Accepted: 08/01/2023] [Indexed: 08/04/2023]
Abstract
The aim of this research was to prove the function of the putative opine dehydrogenase from Desulfohalobium retbaense and to characterize the enzyme in terms of functional and kinetic parameters. A putative opine dehydrogenase was identified from a metagenomic library by a sequence-based technique search of the metagenomic library, and afterward was successfully heterologously produced in Escherichia coli. In order to examine its potential for applications in the synthesis of secondary amines, first the substrate specificity of the enzyme towards different amino donors and amino acceptors was determined. The highest affinity was observed towards small amino acids, preferentially L-alanine, and when it comes to α-keto acids, pyruvate proved to be a preferential amino acceptor. The highest activity was observed at pH 6.5 in the absence of salts. The enzyme showed remarkable stability in a wide range of experimental conditions, such as broad pH stability (from 6.0-11.0 after 30 min incubation in buffers at a certain pH), stability in the presence of NaCl up to 3.0 M for 24 h, it retained 80 % of the initial activity after 1 h incubation at 45 °C, and 65 % of the initial activity after 24 h incubation in 30 % dimethyl sulfoxide.
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Affiliation(s)
- Nevena Kaličanin
- University of Belgrade-Institute of Chemistry Technology and Metallurgy National Institute of the Republic of Serbia, Njegoševa 12, 11000, Belgrade, Serbia
| | - Ana Marija Balaž
- University of Belgrade-Institute of Chemistry Technology and Metallurgy National Institute of the Republic of Serbia, Njegoševa 12, 11000, Belgrade, Serbia
- Department of Otorhinolaryngology Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-University, Marchioninistr. 15, 81377, Munich, Germany
| | - Olivera Prodanović
- University of Belgrade-Institute for Multidisciplinary Research, Kneza Višeslava 1, 11030, Belgrade, Serbia
| | - Radivoje Prodanović
- Department of Biochemistry, University of Belgrade-Faculty of Chemistry, Studentski trg 12-16, 11000, Belgrade, Serbia
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13
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Slavić MŠ, Kojić M, Margetić A, Stanisavljević N, Gardijan L, Božić N, Vujčić Z. Highly stable and versatile α-amylase from Anoxybacillus vranjensis ST4 suitable for various applications. Int J Biol Macromol 2023; 249:126055. [PMID: 37524287 DOI: 10.1016/j.ijbiomac.2023.126055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/02/2023]
Abstract
α-Amylase from the thermophilic bacterial strain Anoxybacillus vranjensis ST4 (AVA) was cloned into the pMALc5HisEk expression vector and successfully expressed and purified from the Escherichia coli ER2523 host strain. AVA belongs to the GH13_5 subfamily of glycoside hydrolases and has 7 conserved sequence regions (CSRs) distributed in three distinct domains (A, B, C). In addition, there is a starch binding domain (SBD) from the CBM20 family of carbohydrate binding modules (CBMs). AVA is a monomer of 66 kDa that achieves maximum activity at 60-80 °C and is active and stable over a wide pH range (4.0-9.0). AVA retained 50 % of its activity after 31 h of incubation at 60 °C and was resistant to a large number of denaturing agents. It hydrolyzed starch granules very efficiently, releasing maltose, maltotriose and maltopentaose as the main products. The hydrolysis rates of raw corn, wheat, horseradish, and potato starch, at a concentration of 10 %, were 87.8, 85.9, 93.0, and 58 %, respectively, at pH 8.5 over a 3 h period. This study showed that the high level of expression as well as the properties of this highly stable and versatile enzyme show all the prerequisites for successful application in industry.
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Affiliation(s)
- Marinela Šokarda Slavić
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, Department of Chemistry, Belgrade, Republic of Serbia.
| | - Milan Kojić
- Institute of Virology, Vaccines and Sera "Torlak", Belgrade, Republic of Serbia; University of Belgrade, Institute of Molecular Genetics and Genetic Engineering (IMGGE), Belgrade, Republic of Serbia
| | - Aleksandra Margetić
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, Department of Chemistry, Belgrade, Republic of Serbia
| | - Nemanja Stanisavljević
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering (IMGGE), Belgrade, Republic of Serbia
| | - Lazar Gardijan
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering (IMGGE), Belgrade, Republic of Serbia
| | - Nataša Božić
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, Department of Chemistry, Belgrade, Republic of Serbia
| | - Zoran Vujčić
- University of Belgrade, Faculty of Chemistry, Department of Biochemistry, Belgrade, Republic of Serbia
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14
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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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15
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Senba H, Saito D, Kimura Y, Tanaka S, Doi M, Takenaka S. Heterologous expression and characterization of salt-tolerant β-glucosidase from xerophilic Aspergillus chevalieri for hydrolysis of marine biomass. Arch Microbiol 2023; 205:310. [PMID: 37596383 DOI: 10.1007/s00203-023-03648-z] [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: 05/30/2023] [Revised: 07/03/2023] [Accepted: 08/04/2023] [Indexed: 08/20/2023]
Abstract
A salt-tolerant exo-β-1,3-glucosidase (BGL_MK86) was cloned from the xerophilic mold Aspergillus chevalieri MK86 and heterologously expressed in A. oryzae. Phylogenetic analysis suggests that BGL_MK86 belongs to glycoside hydrolase family 5 (aryl-phospho-β-D-glucosidase, BglC), and exhibits D-glucose tolerance. Recombinant BGL_MK86 (rBGL_MK86) exhibited 100-fold higher expression than native BGL_MK86. rBGL_MK86 was active over a wide range of NaCl concentrations [0%-18% (w/v)] and showed increased substrate affinity for p-nitrophenyl-β-D-glucopyranoside (pNPBG) and turnover number (kcat) in the presence of NaCl. The enzyme was stable over a broad pH range (5.5-9.5). The optimum reaction pH and temperature for hydrolysis of pNPBG were 5.5 and 45 °C, respectively. rBGL_MK86 acted on the β-1,3-linked glucose dimer laminaribiose, but not β-1,4-linked or β-1,6-linked glucose dimers (cellobiose or gentiobiose). It showed tenfold higher activity toward laminarin (a linear polymer of β-1,3 glucan) from Laminaria digitata than laminarin (β-1,3/β-1,6 glucan) from Eisenia bicyclis, likely due to its inability to act on β-1,6-linked glucose residues. The β-glucosidase retained hydrolytic activity toward crude laminarin preparations from marine biomass in moderately high salt concentrations. These properties indicate wide potential applications of this enzyme in saccharification of salt-bearing marine biomass.
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Affiliation(s)
- Hironori Senba
- Division of Agrobioscience, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-Ku, Kobe, 657-8501, Japan
- General Research Laboratory, Ozeki Corporation, 4-9 Imazu, Nishinomiya, Hyogo, 663-8227, Japan
| | - Daisuke Saito
- Division of Agrobioscience, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-Ku, Kobe, 657-8501, Japan
| | - Yukihiro Kimura
- Division of Agrobioscience, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-Ku, Kobe, 657-8501, Japan
| | - Shinichi Tanaka
- Marutomo Co., Ltd., 1696 Kominato, Iyo, Ehime, 799-3192, Japan
| | - Mikiharu Doi
- Marutomo Co., Ltd., 1696 Kominato, Iyo, Ehime, 799-3192, Japan
| | - Shinji Takenaka
- Division of Agrobioscience, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-Ku, Kobe, 657-8501, Japan.
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16
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Boukid F, Ganeshan S, Wang Y, Tülbek MÇ, Nickerson MT. Bioengineered Enzymes and Precision Fermentation in the Food Industry. Int J Mol Sci 2023; 24:10156. [PMID: 37373305 DOI: 10.3390/ijms241210156] [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: 05/20/2023] [Revised: 06/06/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Enzymes have been used in the food processing industry for many years. However, the use of native enzymes is not conducive to high activity, efficiency, range of substrates, and adaptability to harsh food processing conditions. The advent of enzyme engineering approaches such as rational design, directed evolution, and semi-rational design provided much-needed impetus for tailor-made enzymes with improved or novel catalytic properties. Production of designer enzymes became further refined with the emergence of synthetic biology and gene editing techniques and a plethora of other tools such as artificial intelligence, and computational and bioinformatics analyses which have paved the way for what is referred to as precision fermentation for the production of these designer enzymes more efficiently. With all the technologies available, the bottleneck is now in the scale-up production of these enzymes. There is generally a lack of accessibility thereof of large-scale capabilities and know-how. This review is aimed at highlighting these various enzyme-engineering strategies and the associated scale-up challenges, including safety concerns surrounding genetically modified microorganisms and the use of cell-free systems to circumvent this issue. The use of solid-state fermentation (SSF) is also addressed as a potentially low-cost production system, amenable to customization and employing inexpensive feedstocks as substrate.
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Affiliation(s)
- Fatma Boukid
- ClonBio Group Ltd., 6 Fitzwilliam Pl, D02 XE61 Dublin, Ireland
| | | | - Yingxin Wang
- Saskatchewan Food Industry Development Centre, Saskatoon, SK S7M 5V1, Canada
| | | | - Michael T Nickerson
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
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17
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Tincu (Iurciuc) CE, Bouhadiba B, Atanase LI, Stan CS, Popa M, Ochiuz L. An Accessible Method to Improve the Stability and Reusability of Porcine Pancreatic α-Amylase via Immobilization in Gellan-Based Hydrogel Particles Obtained by Ionic Cross-Linking with Mg 2+ Ions. Molecules 2023; 28:4695. [PMID: 37375250 PMCID: PMC10302431 DOI: 10.3390/molecules28124695] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Amylase is an enzyme used to hydrolyze starch in order to obtain different products that are mainly used in the food industry. The results reported in this article refer to the immobilization of α-amylase in gellan hydrogel particles ionically cross-linked with Mg2+ ions. The obtained hydrogel particles were characterized physicochemically and morphologically. Their enzymatic activity was tested using starch as a substrate in several hydrolytic cycles. The results showed that the properties of the particles are influenced by the degree of cross-linking and the amount of immobilized α-amylase enzyme. The temperature and pH at which the immobilized enzyme activity is maximum were T = 60 °C and pH = 5.6. The enzymatic activity and affinity of the enzyme to the substrate depend on the particle type, and this decreases for particles with a higher cross-linking degree owing to the slow diffusion of the enzyme molecules inside the polymer's network. By immobilization, α-amylase is protected from environmental factors, and the obtained particles can be quickly recovered from the hydrolysis medium, thus being able to be reused in repeated hydrolytic cycles (at least 11 cycles) without a substantial decrease in enzymatic activity. Moreover, α-amylase immobilized in gellan particles can be reactivated via treatment with a more acidic medium.
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Affiliation(s)
- Camelia Elena Tincu (Iurciuc)
- Department of Natural and Synthetic Polymers, “Cristofor Simionescu” Faculty of Chemical Engineering and Protection of the Environment, “Gheorghe Asachi” Technical University, 73, Prof. Dr. Docent Dimitrie Mangeron Street, 700050 Iași, Romania; (C.E.T.)
- Department of Pharmaceutical Technology, Faculty of Pharmacy, “Grigore T. Popa” University of Medicine and Pharmacy, 16, University Street, 700115 Iaşi, Romania
| | - Brahim Bouhadiba
- Laboratory of Engineering of Industrial Safety and Sustainable Development LISIDD, Institute of Maintenance and Industrial Safety, University of Oran 2, Mohammed Benahmed, Oran 31000, Algeria
| | - Leonard Ionut Atanase
- Faculty of Dental Medicine, “Apollonia” University of Iasi, 11, Pacurari Street, 700511 Iași, Romania
- Academy of Romanian Scientists, 050045 Bucharest, Romania
| | - Corneliu Sergiu Stan
- Department of Natural and Synthetic Polymers, “Cristofor Simionescu” Faculty of Chemical Engineering and Protection of the Environment, “Gheorghe Asachi” Technical University, 73, Prof. Dr. Docent Dimitrie Mangeron Street, 700050 Iași, Romania; (C.E.T.)
| | - Marcel Popa
- Department of Natural and Synthetic Polymers, “Cristofor Simionescu” Faculty of Chemical Engineering and Protection of the Environment, “Gheorghe Asachi” Technical University, 73, Prof. Dr. Docent Dimitrie Mangeron Street, 700050 Iași, Romania; (C.E.T.)
- Academy of Romanian Scientists, 050045 Bucharest, Romania
| | - Lăcrămioara Ochiuz
- Department of Pharmaceutical Technology, Faculty of Pharmacy, “Grigore T. Popa” University of Medicine and Pharmacy, 16, University Street, 700115 Iaşi, Romania
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18
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Schultz J, Modolon F, Peixoto RS, Rosado AS. Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles. Front Microbiol 2023; 14:1167718. [PMID: 37333658 PMCID: PMC10272570 DOI: 10.3389/fmicb.2023.1167718] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/09/2023] [Indexed: 06/20/2023] Open
Abstract
More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth's microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed "microbial dark matter." Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology.
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Affiliation(s)
- Júnia Schultz
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Flúvio Modolon
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Silva Peixoto
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandre Soares Rosado
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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19
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Lukhele T, Msagati TAM. Evaluating the microcystin-LR-degrading potential of bacteria growing in extreme and polluted environments. Arch Microbiol 2023; 205:213. [PMID: 37129688 PMCID: PMC10154260 DOI: 10.1007/s00203-023-03554-4] [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: 02/15/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
Inhabitants of extreme and polluted environments are attractive as candidates for environmental bioremediation. Bacteria growing in oil refinery effluents, tannery dumpsite soils, car wash effluents, salt pans and hot springs were screened for microcystin-LR biodegradation potentials. Using a colorimetric BIOLOG MT2 assay; Arthrobacter sp. B105, Arthrobacter junii, Plantibacter sp. PDD-56b-14, Acinetobacter sp. DUT-2, Salinivibrio sp. YH4, Bacillus sp., Bacillus thuringiensis and Lysinibacillus boronitolerans could grow in the presence of microcystin-LR at 1, 10 and 100 µg L-1. Most bacteria grew optimally at 10 µg L-1 microcystin-LR under alkaline pH (8 and 9). The ability of these bacteria to use MC-LR as a growth substrate depicts their ability to metabolize the toxin, which is equivalent to its degradation. Through PCR screening, these bacteria were shown to lack the mlr genes implying possible use of a unique microcystin-LR degradation pathway. The study highlights the wide environmental and taxonomic distribution of microcystin-LR degraders.
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Affiliation(s)
- Thabile Lukhele
- Institute for Nanotechnology and Water Sustainability, College of Science Engineering and Technology, University of South Africa, Florida Science Campus, Johannesburg, South Africa.
| | - Titus Alfred Makudali Msagati
- Institute for Nanotechnology and Water Sustainability, College of Science Engineering and Technology, University of South Africa, Florida Science Campus, Johannesburg, South Africa
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20
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Benítez-Mateos AI, Paradisi F. Halomonas elongata: a microbial source of highly stable enzymes for applied biotechnology. Appl Microbiol Biotechnol 2023; 107:3183-3190. [PMID: 37052635 PMCID: PMC10160191 DOI: 10.1007/s00253-023-12510-7] [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: 02/15/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/14/2023]
Abstract
Extremophilic microorganisms, which are resistant to extreme levels of temperature, salinity, pH, etc., have become popular tools for biotechnological applications. Due to their availability and cost-efficacy, enzymes from extremophiles are getting the attention of researchers and industries in the field of biocatalysis to catalyze diverse chemical reactions in a selective and sustainable manner. In this mini-review, we discuss the advantages of Halomonas elongata as moderate halophilic bacteria to provide suitable enzymes for biotechnology. While enzymes from H. elongata are more resistant to the presence of salt compared to their mesophilic counterparts, they are also easier to produce in heterologous hosts compared with more extremophilic microorganisms. Herein, a set of different enzymes (hydrolases, transferases, and oxidoreductases) from H. elongata are showcased, highlighting their interesting properties as more efficient and sustainable biocatalysts. With this, we aim to improve the visibility of halotolerant enzymes and their uncommon properties to integrate biocatalysis in industrial set-ups. KEYPOINTS: • Production and use of halotolerant enzymes can be easier than strong halophilic ones. • Enzymes from halotolerant organisms are robust catalysts under harsh conditions. • Halomonas elongata has shown a broad enzyme toolbox with biotechnology applications.
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Affiliation(s)
- Ana I Benítez-Mateos
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| | - Francesca Paradisi
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
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21
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García-Calvo L, Rane DV, Everson N, Humlebrekk ST, Mathiassen LF, Mæhlum AHM, Malmo J, Bruheim P. Central carbon metabolite profiling reveals vector-associated differences in the recombinant protein production host Escherichia coli BL21. FRONTIERS IN CHEMICAL ENGINEERING 2023. [DOI: 10.3389/fceng.2023.1142226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
The Gram-negative bacterium Escherichia coli is the most widely used host for recombinant protein production, both as an industrial expression platform and as a model system at laboratory scale. The recombinant protein production industry generates proteins with direct applications as biopharmaceuticals and in technological processes central to a plethora of fields. Despite the increasing economic significance of recombinant protein production, and the importance of E. coli as an expression platform and model organism, only few studies have focused on the central carbon metabolic landscape of E. coli during high-level recombinant protein production. In the present work, we applied four targeted CapIC- and LC-MS/MS methods, covering over 60 metabolites, to perform an in-depth metabolite profiling of the effects of high-level recombinant protein production in strains derived from E. coli BL21, carrying XylS/Pm vectors with different characteristics. The mass-spectrometric central carbon metabolite profiling was complemented with the study of growth kinetics and protein production in batch bioreactors. Our work shows the robustness in E. coli central carbon metabolism when introducing increased plasmid copy number, as well as the greater importance of induction of recombinant protein production as a metabolic challenge, especially when strong promoters are used.
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22
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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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23
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Suyal DC, Yadav AN, El Enshasy HA, Soni R. Editorial: Exploration of cold-adapted microorganisms for sustainable development. Front Microbiol 2023; 14:1191673. [PMID: 37125203 PMCID: PMC10133685 DOI: 10.3389/fmicb.2023.1191673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 03/31/2023] [Indexed: 05/02/2023] Open
Affiliation(s)
- Deep Chandra Suyal
- Vidyadayini Institute of Science, Management, and Technology, Bhopal, Madhya Pradesh, India
| | - Ajar Nath Yadav
- Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Sirmour, Himachal Pradesh, India
- Ajar Nath Yadav
| | - Hesham Ali El Enshasy
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), Johor Bahru, Johor, Malaysia
- Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia (UTM), Johor Bahru, Johor, Malaysia
- City of Scientific Research and Technology Applications (SRTA), New Borg El-Arab, Alexandria, Egypt
| | - Ravindra Soni
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalya, Raipur, Chhattisgarh, India
- *Correspondence: Ravindra Soni
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Leonardo IC, Barreto Crespo MT, Gaspar FB. Unveiling the complete genome sequence of Alicyclobacillus acidoterrestris DSM 3922T, a taint-producing strain. G3 GENES|GENOMES|GENETICS 2022; 12:6761305. [DOI: 10.1093/g3journal/jkac225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/26/2022] [Indexed: 11/06/2022]
Abstract
Abstract
Several species from the Alicyclobacillus genus have received much attention from the food and beverages industries. Their presence has been co-related with spoilage events of acidic food matrices, namely fruit juices and other fruit-based products, the majority attributed to Alicyclobacillus acidoterrestris. In this work, a combination of short and long reads enabled the assembly of the complete genome of A. acidoterrestris DSM 3922T, perfecting the draft genome already available (AURB00000000), and revealing the presence of one chromosome (4,222,202 bp; GC content 52.3%) as well as one plasmid (124,737 bp; GC content 46.6%). From the 4,288 genes identified, 4,004 sequences were attributed to coding sequences with proteins, with more than 80% being functionally annotated. This allowed the identification of metabolic pathways and networks and the interpretation of high-level functions with significant reliability. Furthermore, the additional genes of interest related to spore germination, off-flavor production, namely the vdc cluster, and CRISPR arrays, were identified. More importantly, this is the first complete and closed genome sequence for a taint-producing Alicyclobacillus species and thus represents a valuable reference for further comparative and functional genomic studies.
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Affiliation(s)
- Inês Carvalho Leonardo
- Food & Health Division, iBET, Instituto de Biologia Experimental e Tecnológica , Apartado 12, 2781-901 Oeiras, Portugal
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República , 2780-157 Oeiras, Portugal
| | - Maria Teresa Barreto Crespo
- Food & Health Division, iBET, Instituto de Biologia Experimental e Tecnológica , Apartado 12, 2781-901 Oeiras, Portugal
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República , 2780-157 Oeiras, Portugal
| | - Frédéric Bustos Gaspar
- Food & Health Division, iBET, Instituto de Biologia Experimental e Tecnológica , Apartado 12, 2781-901 Oeiras, Portugal
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República , 2780-157 Oeiras, Portugal
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Wen Y, Qiang J, Zhou G, Zhang X, Wang L, Shi Y. Characterization of redox and salinity-tolerant alkaline protease from Bacillus halotolerans strain DS5. Front Microbiol 2022; 13:935072. [PMID: 36060753 PMCID: PMC9434114 DOI: 10.3389/fmicb.2022.935072] [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: 05/03/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Bacillus halotolerans DS5 was isolated and identified as a halophilic microbe according to 16S rRNA analysis and the physical and chemical indices of the strain. A new alkaline protease (designated as prot DS5) from Bacillus halotolerans DS5 was produced, purified, and characterized. After 12 h incubation in the medium with 1% dextrin, 0.5% NaCl, 2% soluble starch, and 1% yeast extract (pH 7.0), it could reach the maximum enzyme activity (279.74 U/ml). The prot DS5 was stable in the pH range of 6.0–12.0 and the temperature range of 40–60°C, with maximal hydrolytic activities at pH 9 and at 50°C. In the presence of Ca2+, Mn2+, Ba2+, Mg2+, and Fe3+, protease activity was enhanced. The prot DS5 was maintained highly stable in NaCl (up to 2.5 mol/L), reducing and oxidizing agents. The prot DS5 also exhibited compatibility in other detergent ingredients, such as non-ionic and anionic surfactants. These properties of prot DS5 make this enzyme suitable for various industrial applications (e.g., detergents and leather).
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Some Clues about Enzymes from Psychrophilic Microorganisms. Microorganisms 2022; 10:microorganisms10061161. [PMID: 35744679 PMCID: PMC9227589 DOI: 10.3390/microorganisms10061161] [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: 04/30/2022] [Revised: 05/29/2022] [Accepted: 06/03/2022] [Indexed: 02/04/2023] Open
Abstract
Enzymes purified from psychrophilic microorganisms prove to be efficient catalysts at low temperatures and possess a great potential for biotechnological applications. The low-temperature catalytic activity has to come from specific structural fluctuations involving the active site region, however, the relationship between protein conformational stability and enzymatic activity is subtle. We provide a survey of the thermodynamic stability of globular proteins and their rationalization grounded in a theoretical approach devised by one of us. Furthermore, we provide a link between marginal conformational stability and protein flexibility grounded in the harmonic approximation of the vibrational degrees of freedom, emphasizing the occurrence of long-wavelength and excited vibrations in all globular proteins. Finally, we offer a close view of three enzymes: chloride-dependent α-amylase, citrate synthase, and β-galactosidase.
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