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Carbonaro M, Aulitto M, Mazurkewich S, Fraia AD, Contursi P, Limauro D, Larsbrink J, Fiorentino G. Genomic mining of Geobacillus stearothermophilus GF16 for xylose production from hemicellulose-rich biomasses using secreted enzymes. N Biotechnol 2024; 82:14-24. [PMID: 38688408 DOI: 10.1016/j.nbt.2024.04.002] [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: 03/15/2024] [Revised: 04/11/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
The valorization of lignocellulosic biomass, derived from various bio-waste materials, has received considerable attention as a sustainable approach to improve production chains while reducing environmental impact. Microbial enzymes have emerged as key players in the degradation of polysaccharides, offering versatile applications in biotechnology and industry. Among these enzymes, glycoside hydrolases (GHs) play a central role. Xylanases, in particular, are used in a wide range of applications and are essential for the production of xylose, which can be fermented into bioethanol or find use in many other industries. Currently, fungal secretomes dominate as the main reservoir of lignocellulolytic enzymes, but thermophilic microorganisms offer notable advantages in terms of enzyme stability and production efficiency. Here we present the genomic characterization of Geobacillus stearothermophilus GF16 to identify genes encoding putative enzymes involved in lignocellulose degradation. Thermostable GHs secreted by G. stearothermophilus GF16 were investigated and found to be active on different natural polysaccharides and synthetic substrates, revealing an array of inducible GH activities. In particular, the concentrated secretome possesses significant thermostable xylanase and β-xylosidase activities (5 ×103 U/L and 1.7 ×105 U/L, respectively), highlighting its potential for application in biomass valorization. We assessed the hemicellulose hydrolysis capabilities of various agri-food wastes using the concentrated secretome of the strain cultivated on xylan. An impressive 300-fold increase in xylose release compared to a commercially available cocktail was obtained with the secretome, underscoring the remarkable efficacy of this approach.
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Affiliation(s)
- Miriam Carbonaro
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Martina Aulitto
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Scott Mazurkewich
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Alessia Di Fraia
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Patrizia Contursi
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Danila Limauro
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Johan Larsbrink
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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2
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Maslać N, Cadoux C, Bolte P, Murken F, Gu W, Milton RD, Wagner T. Structural comparison of (hyper-)thermophilic nitrogenase reductases from three marine Methanococcales. FEBS J 2024; 291:3454-3480. [PMID: 38696373 DOI: 10.1111/febs.17148] [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: 08/16/2023] [Revised: 01/17/2024] [Accepted: 04/17/2024] [Indexed: 05/04/2024]
Abstract
The nitrogenase reductase NifH catalyses ATP-dependent electron delivery to the Mo-nitrogenase, a reaction central to biological dinitrogen (N2) fixation. While NifHs have been extensively studied in bacteria, structural information about their archaeal counterparts is limited. Archaeal NifHs are considered more ancient, particularly those from Methanococcales, a group of marine hydrogenotrophic methanogens, which includes diazotrophs growing at temperatures near 92 °C. Here, we structurally and biochemically analyse NifHs from three Methanococcales, offering the X-ray crystal structures from meso-, thermo-, and hyperthermophilic methanogens. While NifH from Methanococcus maripaludis (37 °C) was obtained through heterologous recombinant expression, the proteins from Methanothermococcus thermolithotrophicus (65 °C) and Methanocaldococcus infernus (85 °C) were natively purified from the diazotrophic archaea. The structures from M. thermolithotrophicus crystallised as isolated exhibit high flexibility. In contrast, the complexes of NifH with MgADP obtained from the three methanogens are superposable, more rigid, and present remarkable structural conservation with their homologues. They retain key structural features of P-loop NTPases and share similar electrostatic profiles with the counterpart from the bacterial model organism Azotobacter vinelandii. In comparison to the NifH from the phylogenetically distant Methanosarcina acetivorans, these reductases do not cross-react significantly with Mo-nitrogenase from A. vinelandii. However, they associate with bacterial nitrogenase when ADP·AlF 4 - is added to mimic a transient reactive state. Accordingly, detailed surface analyses suggest that subtle substitutions would affect optimal binding during the catalytic cycle between the NifH from Methanococcales and the bacterial nitrogenase, implying differences in the N2-machinery from these ancient archaea.
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Affiliation(s)
- Nevena Maslać
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Cécile Cadoux
- Department of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Switzerland
- National Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Switzerland
| | - Pauline Bolte
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Fenja Murken
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Wenyu Gu
- Laboratory of Microbial Physiology and Resource Biorecovery, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédéral de Lausanne, Switzerland
| | - Ross D Milton
- Department of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Switzerland
- National Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Switzerland
| | - Tristan Wagner
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
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3
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Salas-Bruggink D, Guzmán H, Espina G, Blamey JM. Recombinant Expression and Characterization of a Novel Thermo-Alkaline Lipase with Increased Solvent Stability from the Antarctic Thermophilic Bacterium Geobacillus sp. ID17. Int J Mol Sci 2024; 25:7928. [PMID: 39063171 PMCID: PMC11277018 DOI: 10.3390/ijms25147928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/10/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Lipases are enzymes that hydrolyze long-chain carboxylic esters, and in the presence of organic solvents, they catalyze organic synthesis reactions. However, the use of solvents in these processes often results in enzyme denaturation, leading to a reduction in enzymatic activity. Consequently, there is significant interest in identifying new lipases that are resistant to denaturing conditions, with extremozymes emerging as promising candidates for this purpose. Lip7, a lipase from Geobacillus sp. ID17, a thermophilic microorganism isolated from Deception Island, Antarctica, was recombinantly expressed in E. coli C41 (DE3) in functional soluble form. Its purification was achieved with 96% purity and 23% yield. Enzymatic characterization revealed Lip7 to be a thermo-alkaline enzyme, reaching a maximum rate of 3350 U mg-1 at 50 °C and pH 11.0, using p-nitrophenyl laurate substrate. Notably, its kinetics displayed a sigmoidal behavior, with a higher kinetic efficiency (kcat/Km) for substrates of 12-carbon atom chain. In terms of thermal stability, Lip7 demonstrates stability up to 60 °C at pH 8.0 and up to 50 °C at pH 11.0. Remarkably, it showed high stability in the presence of organic solvents, and under certain conditions even exhibited enzymatic activation, reaching up to 2.5-fold and 1.35-fold after incubation in 50% v/v ethanol and 70% v/v isopropanol, respectively. Lip7 represents one of the first lipases from the bacterial subfamily I.5 and genus Geobacillus with activity and stability at pH 11.0. Its compatibility with organic solvents makes it a compelling candidate for future research in biocatalysis and various biotechnological applications.
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Affiliation(s)
| | - Hardy Guzmán
- Facultad de Química y Biología, Universidad de Santiago de Chile, Alameda 3363, Santiago 9170022, Chile;
| | - Giannina Espina
- Fundación Biociencia, José Domingo Cañas 2280, Santiago 7750132, Chile;
| | - Jenny M. Blamey
- Fundación Biociencia, José Domingo Cañas 2280, Santiago 7750132, Chile;
- Facultad de Química y Biología, Universidad de Santiago de Chile, Alameda 3363, Santiago 9170022, Chile;
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Xia Y, Zhao J, Saeed M, Hussain N, Chen X, Guo Z, Yong Y, Chen H. Molecular Modification Strategies of Nitrilase for Its Potential Application in Agriculture. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:15106-15121. [PMID: 38949086 DOI: 10.1021/acs.jafc.4c03388] [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: 07/02/2024]
Abstract
Some feed source plants will produce secondary metabolites such as cyanogenic glycosides during metabolism, which will produce some poisonous nitrile compounds after hydrolysis and remain in plant tissues. The consumption of feed-source plants without proper treatment affect the health of the animals' bodies. Nitrilases can convert nitriles and have been used in industry as green biocatalysts. However, due to their bottleneck problems, their application in agriculture is still facing challenges. Acid-resistant nitrilase preparations, high-temperature resistance, antiprotease activity, strong activity, and strict reaction specificity urgently need to be developed. In this paper, the application potential of nitrilase in agriculture, especially in feed processing industry was explored, the source properties and catalytic mechanism of nitrilase were reviewed, and modification strategies for nitrilase application in agriculture were proposed to provide references for future research and application of nitrilase in agricultural and especially in the biological feed scene.
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Affiliation(s)
- Yutong Xia
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Jia Zhao
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Muhammad Saeed
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
- Department of Poultry Science, Faculty of Animal Production and Technology, The Cholistan University of Veterinary and Animal Sciences, Bahawalpur 63100, Pakistan
| | - Nazar Hussain
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Xihua Chen
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Zhongjian Guo
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Yangchun Yong
- Biofuels Institute, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Huayou Chen
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
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Galstyan V, D'Angelo P, Tarabella G, Vurro D, Djenizian T. High versatility of polyethylene terephthalate (PET) waste for the development of batteries, biosensing and gas sensing devices. CHEMOSPHERE 2024; 359:142314. [PMID: 38735489 DOI: 10.1016/j.chemosphere.2024.142314] [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: 10/29/2023] [Revised: 04/10/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
Continuously growing adoption of electronic devices in energy storage, human health and environmental monitoring systems increases demand for cost-effective, lightweight, comfortable, and highly efficient functional structures. In this regard, the recycling and reuse of polyethylene terephthalate (PET) waste in the aforementioned fields due to its excellent mechanical properties and chemical resistance is an effective solution to reduce plastic waste. Herein, we review recent advances in synthesis procedures and research studies on the integration of PET into energy storage (Li-ion batteries) and the detection of gaseous and biological species. The operating principles of such systems are described and the role of recycled PET for various types of architectures is discussed. Modifying the composition, crystallinity, surface porosity, and polar surface functional groups of PET are important factors for tuning its features as the active or substrate material in biological and gas sensors. The findings indicate that conceptually new pathways to the study are opened up for the effective application of recycled PET in the design of Li-ion batteries, as well as biochemical and catalytic detection systems. The current challenges in these fields are also presented with perspectives on the opportunities that may enable a circular economy in PET use.
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Affiliation(s)
- Vardan Galstyan
- Institute of Materials for Electronics and Magnetism, National Research Council (IMEM-CNR), Parco Area delle Scienze, 37/A, 43124, Parma, (PR), Italy; Department of Engineering "Enzo Ferrari", University of Modena and Reggio Emilia, Via Vivarelli 10, 41125, Modena, Italy.
| | - Pasquale D'Angelo
- Institute of Materials for Electronics and Magnetism, National Research Council (IMEM-CNR), Parco Area delle Scienze, 37/A, 43124, Parma, (PR), Italy
| | - Giuseppe Tarabella
- Institute of Materials for Electronics and Magnetism, National Research Council (IMEM-CNR), Parco Area delle Scienze, 37/A, 43124, Parma, (PR), Italy
| | - Davide Vurro
- Institute of Materials for Electronics and Magnetism, National Research Council (IMEM-CNR), Parco Area delle Scienze, 37/A, 43124, Parma, (PR), Italy
| | - Thierry Djenizian
- Mines Saint-Etienne, Center of Microelectronics in Provence, Department of Flexible Electronics, F-13541, Gardanne, France; Al-Farabi Kazakh National University, Center of Physical-Chemical Methods of Research and Analysis, Tole bi str., 96A, Almaty, Kazakhstan
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6
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Araújo EV, Carneiro SV, Neto DMA, Freire TM, Costa VM, Freire RM, Fechine LMUD, Clemente CS, Denardin JC, Dos Santos JCS, Santos-Oliveira R, Rocha JS, Fechine PBA. Advances in surface design and biomedical applications of magnetic nanoparticles. Adv Colloid Interface Sci 2024; 328:103166. [PMID: 38728773 DOI: 10.1016/j.cis.2024.103166] [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: 01/05/2024] [Revised: 04/13/2024] [Accepted: 04/27/2024] [Indexed: 05/12/2024]
Abstract
Despite significant efforts by scientists in the development of advanced nanotechnology materials for smart diagnosis devices and drug delivery systems, the success of clinical trials remains largely elusive. In order to address this biomedical challenge, magnetic nanoparticles (MNPs) have gained attention as a promising candidate due to their theranostic properties, which allow the simultaneous treatment and diagnosis of a disease. Moreover, MNPs have advantageous characteristics such as a larger surface area, high surface-to-volume ratio, enhanced mobility, mass transference and, more notably, easy manipulation under external magnetic fields. Besides, certain magnetic particle types based on the magnetite (Fe3O4) phase have already been FDA-approved, demonstrating biocompatible and low toxicity. Typically, surface modification and/or functional group conjugation are required to prevent oxidation and particle aggregation. A wide range of inorganic and organic molecules have been utilized to coat the surface of MNPs, including surfactants, antibodies, synthetic and natural polymers, silica, metals, and various other substances. Furthermore, various strategies have been developed for the synthesis and surface functionalization of MNPs to enhance their colloidal stability, biocompatibility, good response to an external magnetic field, etc. Both uncoated MNPs and those coated with inorganic and organic compounds exhibit versatility, making them suitable for a range of applications such as drug delivery systems (DDS), magnetic hyperthermia, fluorescent biological labels, biodetection and magnetic resonance imaging (MRI). Thus, this review provides an update of recently published MNPs works, providing a current discussion regarding their strategies of synthesis and surface modifications, biomedical applications, and perspectives.
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Affiliation(s)
- E V Araújo
- Advanced Chemistry Materials Group (GQMat)- Analytical Chemistry and Physical Chemistry Department, Federal Unversity of Ceará, - UFC, Campus do Pici, CP 12100, 60451-970 Fortaleza, CE, Brazil.
| | - S V Carneiro
- Advanced Chemistry Materials Group (GQMat)- Analytical Chemistry and Physical Chemistry Department, Federal Unversity of Ceará, - UFC, Campus do Pici, CP 12100, 60451-970 Fortaleza, CE, Brazil.
| | - D M A Neto
- Advanced Chemistry Materials Group (GQMat)- Analytical Chemistry and Physical Chemistry Department, Federal Unversity of Ceará, - UFC, Campus do Pici, CP 12100, 60451-970 Fortaleza, CE, Brazil.
| | - T M Freire
- Advanced Chemistry Materials Group (GQMat)- Analytical Chemistry and Physical Chemistry Department, Federal Unversity of Ceará, - UFC, Campus do Pici, CP 12100, 60451-970 Fortaleza, CE, Brazil.
| | - V M Costa
- Advanced Chemistry Materials Group (GQMat)- Analytical Chemistry and Physical Chemistry Department, Federal Unversity of Ceará, - UFC, Campus do Pici, CP 12100, 60451-970 Fortaleza, CE, Brazil.
| | - R M Freire
- Universidad Central de Chile, Santiago 8330601, Chile.
| | - L M U D Fechine
- Advanced Chemistry Materials Group (GQMat)- Analytical Chemistry and Physical Chemistry Department, Federal Unversity of Ceará, - UFC, Campus do Pici, CP 12100, 60451-970 Fortaleza, CE, Brazil.
| | - C S Clemente
- Department of Organic and Inorganic Chemistry, Federal University of Ceará, Fortaleza, CE 60440-900, Brazil.
| | - J C Denardin
- Physics Department and CEDENNA, University of Santiago of Chile (USACH), Santiago 9170124, Chile.
| | - J C S Dos Santos
- Engineering and Sustainable Development Institute, International Afro-Brazilian Lusophone Integration University, Campus das Auroras, Redenção 62790970, CE, Brazil; Chemical Engineering Department, Federal University of Ceará, Campus do Pici, Bloco 709, Fortaleza 60455760, CE, Brazil.
| | - R Santos-Oliveira
- Brazilian Nuclear Energy Commission, Nuclear Engineering Institute, Laboratory of Nanoradiopharmacy and Synthesis of Novel Radiopharmaceuticals, R. Helio de Almeida, 75, Rio de Janeiro 21941906, RJ, Brazil; Zona Oeste State University, Laboratory of Nanoradiopharmacy, Av Manuel Caldeira de Alvarenga, 1203, Campo Grande 23070200, RJ, Brazil.
| | - Janaina S Rocha
- Industrial Technology and Quality Center of Ceará, R. Prof. Rômulo Proença, s/n - Pici, 60440-552 Fortaleza, CE, Brazil.
| | - P B A Fechine
- Advanced Chemistry Materials Group (GQMat)- Analytical Chemistry and Physical Chemistry Department, Federal Unversity of Ceará, - UFC, Campus do Pici, CP 12100, 60451-970 Fortaleza, CE, Brazil.
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Llorent-Martínez EJ, Ruiz-Medina A, Terzic M, Sinan KI, Koyuncu I, Egi K, Nilofar N, Zengin G. Chemical composition and biological activities of Cucurbita okeechobeensis extracts from its aerial parts, seeds, and fruit shells. Arch Pharm (Weinheim) 2024; 357:e2300663. [PMID: 38408265 DOI: 10.1002/ardp.202300663] [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: 11/16/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 02/28/2024]
Abstract
The Cucurbita genus has been widely used in traditional medicinal systems across different countries. In this study, we aimed to investigate the chemical composition, antioxidant properties, enzyme inhibitory, and cytotoxic effects of methanol and aqueous extracts obtained from the aerial parts, seeds, and fruit shells of Cucurbita okeechobeensis. Antioxidant properties were assessed using various chemical methods, including radical quenching (DPPH and ABTS), reducing power (CUPRAC and FRAP), metal chelation, and phosphomolybdenum assays. The extracts' enzyme inhibitory effects were tested against cholinesterase, amylase, glucosidase, and tyrosinase, whereas different cancer cell lines were used for the cytotoxicity study. The chemical composition, evaluated by HPLC-ESI-MSn, showed that the most abundant compounds were flavonoids (mainly quercetin glycosides) followed by phenolic acids (mostly caffeic acid derivatives). The aerial parts displayed stronger antioxidant ability than the seed and fruit shells, in agreement with the highest content in phytochemicals. In addition, the methanol extracts presented the highest bioactivity and content in phytochemicals; among them, the extract of the aerial part exhibited significant cytotoxic effects on cancer cell lines and induced apoptosis. Overall, our results suggest that C. okeechobeensis is a valuable source of bioactive compounds for the pharmaceutical and nutraceutical industries.
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Affiliation(s)
| | - Antonio Ruiz-Medina
- Department of Physical and Analytical Chemistry, University of Jaén, Campus Las Lagunillas, Jaén, Spain
| | - Milena Terzic
- Faculty of Technology Novi Sad, University of Novi Sad, Novi Sad, Serbia
| | | | - Ismail Koyuncu
- Department of Medical Biochemistry, Faculty of Medicine, Harran University, Sanliurfa, Turkey
| | - Kadir Egi
- Dialysis Program, Vocational School of Health Services, Harran University, Sanliurfa, Turkey
| | - Nilofar Nilofar
- Department of Biology, Science Faculty, Selcuk University, Konya, Turkey
- Department of Pharmacy, Botanic Garden "Giardino dei Semplici", Università degli Studi "Gabriele d'Annunzio", Chieti, Italy
| | - Gokhan Zengin
- Department of Biology, Science Faculty, Selcuk University, Konya, Turkey
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Ortega-Villar R, Escalante A, Astudillo-Melgar F, Lizárraga-Mendiola L, Vázquez-Rodríguez GA, Hidalgo-Lara ME, Coronel-Olivares C. Isolation and Characterization of Thermophilic Bacteria from a Hot Spring in the State of Hidalgo, Mexico, and Geochemical Analysis of the Thermal Water. Microorganisms 2024; 12:1066. [PMID: 38930448 PMCID: PMC11205571 DOI: 10.3390/microorganisms12061066] [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: 04/17/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Hot springs worldwide can be a source of extremophilic microorganisms of biotechnological interest. In this study, samplings of a hot spring in Hidalgo, Mexico, were conducted to isolate, identify, and characterize morphologically, biochemically, and molecularly those bacterial strains with potential industrial applications. In addition, a physicochemical and geochemical examination of the hot spring was conducted to fully understand the study region and its potential connection to the strains discovered. The hot spring was classified as sulfate-calcic according to the Piper Diagram; the hydrogeochemical analysis showed the possible interactions between minerals and water. Eighteen bacterial strains were isolated with optimal growth temperatures from 50 to 55 °C. All strains are Gram-positive, the majority having a rod shape, and one a round shape, and 17 produce endospores. Hydrolysis tests on cellulose, pectin, and xylan agar plates demonstrated enzymatic activity in some of the strains. Molecular identification through the 16S rDNA gene allowed classification of 17 strains within the Phylum Firmicutes and one within Deinococcus-Thermus. The bacterial strains were associated with the genera Anoxybacillus, Bacillus, Anerunibacillus, Paenibacillus, and Deinococcus, indicating a diversity of bacterial strains with potential industrial applications.
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Affiliation(s)
- Rosangel Ortega-Villar
- Área Académica de Química, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Tulancingo Km. 4.5, Mineral de la Reforma 42184, Hidalgo, Mexico; (R.O.-V.)
| | - Adelfo Escalante
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico
| | - Fernando Astudillo-Melgar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico
| | - Liliana Lizárraga-Mendiola
- Área Académica de Ingeniería y Arquitectura, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Tulancingo Km. 4.5, Mineral de la Reforma 42184, Hidalgo, Mexico
| | - Gabriela A. Vázquez-Rodríguez
- Área Académica de Química, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Tulancingo Km. 4.5, Mineral de la Reforma 42184, Hidalgo, Mexico; (R.O.-V.)
| | | | - Claudia Coronel-Olivares
- Área Académica de Química, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Tulancingo Km. 4.5, Mineral de la Reforma 42184, Hidalgo, Mexico; (R.O.-V.)
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9
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Vishwakarma SK, Patil A, Pandey A, Arya M. Biosorption of Heavy Metal (Mn 2+) by Thermophilic Bacterial Strains Isolated from Surya Kund Hot Spring, Yamunotri, Uttarakhand. Appl Biochem Biotechnol 2024; 196:2518-2533. [PMID: 37659051 DOI: 10.1007/s12010-023-04682-9] [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] [Accepted: 08/16/2023] [Indexed: 09/05/2023]
Abstract
This investigation aimed to identify the bioremediation potential of Mn2+-resistant bacterial strains cultured from the Surya Kund hot spring, Yamunotri, Uttarakhand. In this study, eight heavy metal-resistant isolates belonging to two phyla, i.e., Firmicutes and Proteobacteria, were investigated for their Mn2+ biosorption potential. The metal tolerance potential of all the thermophilic bacterial strains was determined by MIC. Bioremediation assay of these metal-resistant strains was performed for Mn2+ through the live and dead biomass of the bacterial cell. The evaluation of the bioremediation rate of metal ions through bacteria was done by AAS. All the selected bacterial strains were evaluated with effective biosorption rates for Mn2+. Acinetobacter sp. LSN-10 (YII-1) has been showing the highest potential for the removal of Mn2+ in both live (41.202%) and dead biomass (64.721%) conditions. The bioremediation rate of dead biomass was observed quite higher in comparison to bioremediation through live bacterial cells in the maximum number of isolates. This study may provide a new eco-friendly and cost-effective approach to dealing with metal toxicity. However, further investigation is needed to identify the most effective applications and potential limitations of this method.
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Affiliation(s)
- Shailesh K Vishwakarma
- Department of Biotechnology, Hemvati Nandan Bahuguna Garhwal University, Srinagar, Uttarakhand, 246174, India
| | - Anjali Patil
- Department of Biotechnology, Hemvati Nandan Bahuguna Garhwal University, Srinagar, Uttarakhand, 246174, India
| | - Anita Pandey
- Department of Biotechnology, Graphic Era (Deemed to be) University, Dehradun, Uttarakhand, 248002, India
| | - Mamta Arya
- Department of Biotechnology, Hemvati Nandan Bahuguna Garhwal University, Srinagar, Uttarakhand, 246174, India.
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10
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Orsi E, Schada von Borzyskowski L, Noack S, Nikel PI, Lindner SN. Automated in vivo enzyme engineering accelerates biocatalyst optimization. Nat Commun 2024; 15:3447. [PMID: 38658554 PMCID: PMC11043082 DOI: 10.1038/s41467-024-46574-4] [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] [Accepted: 03/04/2024] [Indexed: 04/26/2024] Open
Abstract
Achieving cost-competitive bio-based processes requires development of stable and selective biocatalysts. Their realization through in vitro enzyme characterization and engineering is mostly low throughput and labor-intensive. Therefore, strategies for increasing throughput while diminishing manual labor are gaining momentum, such as in vivo screening and evolution campaigns. Computational tools like machine learning further support enzyme engineering efforts by widening the explorable design space. Here, we propose an integrated solution to enzyme engineering challenges whereby ML-guided, automated workflows (including library generation, implementation of hypermutation systems, adapted laboratory evolution, and in vivo growth-coupled selection) could be realized to accelerate pipelines towards superior biocatalysts.
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Affiliation(s)
- Enrico Orsi
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | | | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany.
- Department of Biochemistry, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, 10117, Berlin, Germany.
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11
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Maldonado-Ruiz K, Pedroza-Islas R, Pedraza-Segura L. Blue Biotechnology: Marine Bacteria Bioproducts. Microorganisms 2024; 12:697. [PMID: 38674641 PMCID: PMC11051736 DOI: 10.3390/microorganisms12040697] [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: 02/14/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
The ocean is the habitat of a great number of organisms with different characteristics. Compared to terrestrial microorganisms, marine microorganisms also represent a vast and largely unexplored reservoir of bioactive compounds with diverse industrial applications like terrestrial microorganisms. This review examines the properties and potential applications of products derived from marine microorganisms, including bacteriocins, enzymes, exopolysaccharides, and pigments, juxtaposing them in some cases against their terrestrial counterparts. We discuss the distinct characteristics that set marine-derived products apart, including enhanced stability and unique structural features such as the amount of uronic acid and sulfate groups in exopolysaccharides. Further, we explore the uses of these marine-derived compounds across various industries, ranging from food and pharmaceuticals to cosmetics and biotechnology. This review also presents a broad description of biotechnologically important compounds produced by bacteria isolated from marine environments, some of them with different qualities compared to their terrestrial counterparts.
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Affiliation(s)
| | - Ruth Pedroza-Islas
- Department of Chemical, Industrial and Food Engineering, Universidad Iberoamericana, Prol. Paseo de la Reforma 880, Lomas de Santa Fe, Mexico City 01210, Mexico; (K.M.-R.); (L.P.-S.)
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12
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Purcarea C, Ruginescu R, Banciu RM, Vasilescu A. Extremozyme-Based Biosensors for Environmental Pollution Monitoring: Recent Developments. BIOSENSORS 2024; 14:143. [PMID: 38534250 DOI: 10.3390/bios14030143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/04/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
Extremozymes combine high specificity and sensitivity with the ability to withstand extreme operational conditions. This work presents an overview of extremozymes that show potential for environmental monitoring devices and outlines the latest advances in biosensors utilizing these unique molecules. The characteristics of various extremozymes described so far are presented, underlining their stability and operational conditions that make them attractive for biosensing. The biosensor design is discussed based on the detection of photosynthesis-inhibiting herbicides as a case study. Several biosensors for the detection of pesticides, heavy metals, and phenols are presented in more detail to highlight interesting substrate specificity, applications or immobilization methods. Compared to mesophilic enzymes, the integration of extremozymes in biosensors faces additional challenges related to lower availability and high production costs. The use of extremozymes in biosensing does not parallel their success in industrial applications. In recent years, the "collection" of recognition elements was enriched by extremozymes with interesting selectivity and by thermostable chimeras. The perspectives for biosensor development are exciting, considering also the progress in genetic editing for the oriented immobilization of enzymes, efficient folding, and better electron transport. Stability, production costs and immobilization at sensing interfaces must be improved to encourage wider applications of extremozymes in biosensors.
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Affiliation(s)
- Cristina Purcarea
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, 060031 Bucharest, Romania
| | - Robert Ruginescu
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, 060031 Bucharest, Romania
| | - Roberta Maria Banciu
- International Centre of Biodynamics, 1B Intrarea Portocalelor, 060101 Bucharest, Romania
- Department of Analytical and Physical Chemistry, University of Bucharest, 4-12 Regina Elisabeta Blvd., 030018 Bucharest, Romania
| | - Alina Vasilescu
- International Centre of Biodynamics, 1B Intrarea Portocalelor, 060101 Bucharest, Romania
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13
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Qi C, Li L, Yu K, Lin Y, Li L. Use of ultrasound to increase the catalytic activity of α-L-rhamnosidase. Prep Biochem Biotechnol 2024:1-5. [PMID: 38477625 DOI: 10.1080/10826068.2024.2326877] [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: 03/14/2024]
Abstract
α-L-rhamnosidase (Rha) is ubiquitous in nature and has high feasibility in the food and biotechnology industries. A green and environmentally friendly method was used to improve the activity of Rha. Here, we show that the effects of ultrasound treatment on the Rha. Ultrasonic treatment at 80 W for 10 min yielded the highest enzyme activity. Treatment increased enzyme activity by 26.3% and half-life by 124 min. Further, treatment increased the catalytic efficiency of Rha and increased the substrate conversion rate by 33.88%. These results demonstrate that ultrasound increases the catalytic activity and stability of Rha. Thus, ultrasonic treatment of Rha is cost-effective on the industrial scale.
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Affiliation(s)
- Chen Qi
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
| | - Le Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
| | - Kunpeng Yu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
| | - Yanling Lin
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
| | - Lijun Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
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14
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Sadaqat B, Dar MA, Sha C, Abomohra A, Shao W, Yong YC. Thermophilic β-mannanases from bacteria: production, resources, structural features and bioengineering strategies. World J Microbiol Biotechnol 2024; 40:130. [PMID: 38460032 DOI: 10.1007/s11274-024-03912-4] [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: 12/01/2023] [Accepted: 01/29/2024] [Indexed: 03/11/2024]
Abstract
β-mannanases are pivotal enzymes that cleave the mannan backbone to release short chain mannooligosaccharides, which have tremendous biotechnological applications including food/feed, prebiotics and biofuel production. Due to the high temperature conditions in many industrial applications, thermophilic mannanases seem to have great potential to overcome the thermal impediments. Thus, structural analysis of thermostable β-mannanases is extremely important, as it could open up new avenues for genetic engineering, and protein engineering of these enzymes with enhanced properties and catalytic efficiencies. Under this scope, the present review provides a state-of-the-art discussion on the thermophilic β-mannanases from bacterial origin, their production, engineering and structural characterization. It covers broad insights into various molecular biology techniques such as gene mutagenesis, heterologous gene expression, and protein engineering, that are employed to improve the catalytic efficiency and thermostability of bacterial mannanases for potential industrial applications. Further, the bottlenecks associated with mannanase production and process optimization are also discussed. Finally, future research related to bioengineering of mannanases with novel protein expression systems for commercial applications are also elaborated.
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Affiliation(s)
- Beenish Sadaqat
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China
- Department of Biochemistry and Structural Biology, Lund University, Box 124, 22100, Lund, Sweden
| | - Mudasir A Dar
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China
| | - Chong Sha
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China
| | - Abdelfatah Abomohra
- Aquatic Ecophysiology and Phycology, Department of Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, 22609, Germany
| | - Weilan Shao
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China.
| | - Yang-Chun Yong
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China.
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15
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Zhang Y, Gao Y, Chen J, Yu F, Bao Y. Overexpression and truncation of a novel cold-adapted lipase with improved enzymatic characteristics. Protein Expr Purif 2024; 214:106376. [PMID: 37839629 DOI: 10.1016/j.pep.2023.106376] [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: 08/06/2023] [Revised: 09/18/2023] [Accepted: 09/24/2023] [Indexed: 10/17/2023]
Abstract
The novel cold-adapted lipase (Lip ZC12) derived from Psychrobacter sp. ZY124 exhibited higher catalytic activity at 20-40 °C, the whole gene was then sequenced, analyzed, and overexpressed. However, its intrinsic structural characteristics lead to a decreased affinity toward the substrate, thus limiting the improvement of catalytic efficiency. Modeling the homologous structure and simulating the binding process of Lip ZC12 with the substrate. It was found that truncated lid (lip-Δlid) could not only increase the kcat, but also significantly enhance the substrate affinity, the substrate affinity and catalytic efficiency of Lip ZC12 modified by lid truncation were significantly improved. The results revealed that the kcat/Km value of lip-Δlid was 1.6 times higher than that of free lipase. This improved catalytic performance of cold-adapted lipase, and these findings laid an important foundation for further application.
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Affiliation(s)
- Yue Zhang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.
| | - Yu Gao
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Jiahui Chen
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Fang Yu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Yongming Bao
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
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16
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Li Z, Zhong Y, Qing Z, Li Z. A circuitous route for in vitro multi-enzyme cascade production of cytidine triphosphate to overcome the thermodynamic bottleneck. BIORESOUR BIOPROCESS 2024; 11:6. [PMID: 38647971 PMCID: PMC10992187 DOI: 10.1186/s40643-023-00724-6] [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: 10/14/2023] [Accepted: 12/23/2023] [Indexed: 04/25/2024] Open
Abstract
Cytidine triphosphate (CTP), as a substance involved in the metabolism of phospholipids, proteins and nucleic acids, has precise drug effects and is a direct precursor for the synthesis of drugs such as citicoline. In this study, we established an in vitro six-enzyme cascade system to generate CTP. To avoid thermodynamic bottlenecks, we employed a circuitous and two-stage reaction strategy. Using cytidine as the key substrate, the final product CTP is obtained via the deamination and uridine phosphorylation pathways, relying on the irreversible reaction of cytidine triphosphate synthase to catalyze the amination of uridine triphosphate. Several extremophilic microbial-derived deaminases were screened and characterized, and a suitable cytidine deaminase was selected to match the first-stage reaction conditions. In addition, directed evolution modification of the rate-limiting enzyme CTP synthetase in the pathway yielded a variant that successfully relieved the product feedback inhibition, along with a 1.7-fold increase in activity over the wild type. After optimizing the reaction conditions, we finally carried out the catalytic reaction at an initial cytidine concentration of 20 mM, and the yield of CTP exceeded 82% within 10.0 h.
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Affiliation(s)
- Zonglin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
| | - Yahui Zhong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Zhoulei Qing
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai, 200237, China.
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17
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Gattupalli M, Dashora K, Mishra M, Javed Z, Tripathi GD. Microbial bioprocess performance in nanoparticle-mediated composting. Crit Rev Biotechnol 2023; 43:1193-1210. [PMID: 36510336 DOI: 10.1080/07388551.2022.2106178] [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: 02/16/2022] [Accepted: 07/10/2022] [Indexed: 12/15/2022]
Abstract
Microbial composting is one of the most cost-effective techniques for degradation, remediation, nutrition, etc. Currently, there is faster growth and development in nanotechnology in different sectors. This development leads nanoparticles (NPs) to enter into the composts in different ways. First, unintentional entry of NPs into the composts via: waste discharge, buried solid waste, surface runoff, direct disposal into wastes (consumer goods, food, pharmaceuticals, and personal care products). Second, intentional mediation of the NPs in the composting process is a novel approach developed to enhance the degradation rate of wastes and as a nutrient for plants. The presence of NPs in the composts can cause nanotoxicity. Conversely, their presence might also be beneficial, such as soil reclamations, degradation, etc. Alternatively, metal NPs are also helpful for all living organisms, including microorganisms, in various biological processes, such as DNA replication, precursor biosynthesis, respiration, oxidative stress responses, and transcription. NPs show exemplary performance in multiple fields, whereas their role in composting process is worth studying. Consequently, this article aids the understanding of the role of NPs in the composting process and how far their presence can be beneficial. This article reviews the significance of NPs in: the composting process, microbial bioprocess performance during nano composting, basic life cycle assessment (LCA) of NP-mediated composting, and mode of action of the NPs in the soil matrix. This article also sheds insight on the notion of nanozymes and highlights their biocatalytic characterization, which will be helpful in future composting research.
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Affiliation(s)
- Meghana Gattupalli
- Centre for Rural Development and Technology, Indian Institute of Technology, New Delhi, India
| | - Kavya Dashora
- Centre for Rural Development and Technology, Indian Institute of Technology, New Delhi, India
| | - Mansi Mishra
- Centre for Rural Development and Technology, Indian Institute of Technology, New Delhi, India
| | - Zoya Javed
- Centre for Rural Development and Technology, Indian Institute of Technology, New Delhi, India
| | - Gyan Datta Tripathi
- Centre for Rural Development and Technology, Indian Institute of Technology, New Delhi, India
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18
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Li M, Wang H, Yang Z, Zhang L, Zhu Y. DeepTM: A deep learning algorithm for prediction of melting temperature of thermophilic proteins directly from sequences. Comput Struct Biotechnol J 2023; 21:5544-5560. [PMID: 38034401 PMCID: PMC10681957 DOI: 10.1016/j.csbj.2023.11.006] [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: 08/23/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023] Open
Abstract
Thermally stable proteins find extensive applications in industrial production, pharmaceutical development, and serve as a highly evolved starting point in protein engineering. The thermal stability of proteins is commonly characterized by their melting temperature (Tm). However, due to the limited availability of experimentally determined Tm data and the insufficient accuracy of existing computational methods in predicting Tm, there is an urgent need for a computational approach to accurately forecast the Tm values of thermophilic proteins. Here, we present a deep learning-based model, called DeepTM, which exclusively utilizes protein sequences as input and accurately predicts the Tm values of target thermophilic proteins on a dataset consisting of 7790 thermophilic protein entries. On a test set of 1550 samples, DeepTM demonstrates excellent performance with a coefficient of determination (R2) of 0.75, Pearson correlation coefficient (P) of 0.87, and root mean square error (RMSE) of 6.24 ℃. We further analyzed the sequence features that determine the thermal stability of thermophilic proteins and found that dipeptide frequency, optimal growth temperature (OGT) of the host organisms, and the evolutionary information of the protein significantly affect its melting temperature. We compared the performance of DeepTM with recently reported methods, ProTstab2 and DeepSTABp, in predicting the Tm values on two blind test datasets. One dataset comprised 22 PET plastic-degrading enzymes, while the other included 29 thermally stable proteins of broader classification. In the PET plastic-degrading enzyme dataset, DeepTM achieved RMSE of 8.25 ℃. Compared to ProTstab2 (20.05 ℃) and DeepSTABp (20.97 ℃), DeepTM demonstrated a reduction in RMSE of 58.85% and 60.66%, respectively. In the dataset of thermally stable proteins, DeepTM (RMSE=7.66 ℃) demonstrated a 51.73% reduction in RMSE compared to ProTstab2 (RMSE=15.87 ℃). DeepTM, with the sole requirement of protein sequence information, accurately predicts the melting temperature and achieves a fully end-to-end prediction process, thus providing enhanced convenience and expediency for further protein engineering.
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Affiliation(s)
- Mengyu Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hongzhao Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zhenwu Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Longgui Zhang
- SINOPEC Beijing Research Institute of Chemical Industry, Beijing 100013, China
| | - Yushan Zhu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing 100029, China
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19
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Ma Z, Mu K, Zhu J, Xiao M, Wang L, Jiang X. Molecular dynamics simulations identify the topological weak spots of a protease CN2S8A. J Mol Graph Model 2023; 124:108571. [PMID: 37487372 DOI: 10.1016/j.jmgm.2023.108571] [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: 05/10/2023] [Revised: 07/06/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023]
Abstract
Thermophilic enzymes are highly desired in industrial applications due to their efficient catalytic activity at high temperature. However, most enzymes exhibit inferior thermostability and it remains challenging to identify the optimal sites for designing mutations to improve protein stability. To tackle this issue, we integrated topological analysis and all-atom molecular dynamics simulations to efficiently pinpoint the thermally-unstable regions in protein structures. Using a protease CN2S8A as the model, we analyzed the intramolecular hydrogen bonding interactions between adjacent secondary structure elements, and then identified the topological weak spots of CN2S8A where weak hydrogen bonding interactions were formed. To examine the role of these sites in protein structural stability, we designed three virtual mutations at different weak spots and characterized the effects of these mutations on the structural properties of CN2S8A. The results showed that all three mutations increased the protein structural stability. In conclusion, these findings provide a novel method to identify the topological weak spots of proteins, with implications in the rational design of biocatalysts with superior thermostability.
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Affiliation(s)
- Zhenyu Ma
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Kaijie Mu
- Biomedicine Discovery Institute, Monash University, Melbourne, 3500, Australia
| | - Jingyi Zhu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Min Xiao
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China.
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20
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Malesevic M, Stanisavljevic N, Matijasevic D, Curcic J, Tasic V, Tasic S, Kojic M. Metagenomic Analysis of Bacterial Community and Isolation of Representative Strains from Vranjska Banja Hot Spring, Serbia. MICROBIAL ECOLOGY 2023; 86:2344-2356. [PMID: 37222803 DOI: 10.1007/s00248-023-02242-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/15/2023] [Indexed: 05/25/2023]
Abstract
The hot spring Vranjska Banja is the hottest spring on the Balkan Peninsula with a water temperature of 63-95 °C and a pH value of 7.1, in situ. According to the physicochemical analysis, Vranjska Banja hot spring belongs to the bicarbonated and sulfated hyperthermal waters. The structures of microbial community of this geothermal spring are still largely unexplored. In order to determine and monitor the diversity of microbiota of the Vranjska Banja hot spring, a comprehensive culture-independent metagenomic analysis was conducted in parallel with a culture-dependent approach for the first time. Microbial profiling using amplicon sequencing analysis revealed the presence of phylogenetically novel taxa, ranging from species to phyla. Cultivation-based methods resulted in the isolation of 17 strains belonging to the genera Anoxybacillus, Bacillus, Geobacillus, and Hydrogenophillus. Whole-genome sequencing of five representative strains was then performed. The genomic characterization and OrthoANI analysis revealed that the Vranjska Banja hot spring harbors phylogenetically novel species of the genus Anoxybacillus, proving its uniqueness. Moreover, these isolates contain stress response genes that enable them to survive in the harsh conditions of the hot springs. The results of the in silico analysis show that most of the sequenced strains have the potential to produce thermostable enzymes (proteases, lipases, amylases, phytase, chitinase, and glucanase) and various antimicrobial molecules that can be of great importance for industrial, agricultural, and biotechnological applications. Finally, this study provides a basis for further research and understanding of the metabolic potential of these microorganisms.
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Affiliation(s)
- Milka Malesevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia.
| | - Nemanja Stanisavljevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Danka Matijasevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Jovana Curcic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Vukasin Tasic
- Faculty of Informatics and Computing, Singidunum University, Belgrade, Serbia
| | - Srdjan Tasic
- The Academy of Applied Technical and Preschool Studies, Nis, Serbia
| | - Milan Kojic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
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21
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Abellanas-Perez P, Carballares D, Fernandez-Lafuente R, Rocha-Martin J. Glutaraldehyde modification of lipases immobilized on octyl agarose beads: Roles of the support enzyme loading and chemical amination of the enzyme on the final enzyme features. Int J Biol Macromol 2023; 248:125853. [PMID: 37460068 DOI: 10.1016/j.ijbiomac.2023.125853] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023]
Abstract
Lipase B from Candida antarctica (CALB) and lipase from Thermomyces lanuginosus (TLL) have been immobilized on octyl agarose at low loading and at a loading exceeding the maximum support capacity. Then, the enzymes have been treated with glutaraldehyde and inactivated at pH 7.0 in Tris-HCl, sodium phosphate and HEPES, giving different stabilities. Stabilization (depending on the buffer) of the highly loaded biocatalysts was found, very likely as a consequence of the detected intermolecular crosslinkings. This did not occur for the lowly loaded biocatalysts. Next, the enzymes were chemically aminated and then treated with glutaraldehyde. In the case of TLL, the intramolecular crosslinkings (visible by the apparent reduction of the protein size) increased enzyme stability of the lowly loaded biocatalysts, an effect that was further increased for the highly loaded biocatalysts due to intermolecular crosslinkings. Using CALB, the intramolecular crosslinkings were less intense, and the stabilization was lower, even though the intermolecular crosslinkings were quite intense for the highly loaded biocatalyst. The stabilization detected depended on the inactivation buffer. The interactions between enzyme loading and inactivating buffer on the effects of the chemical modifications suggest that the modification and inactivation studies must be performed under the target biocatalysts and conditions.
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Affiliation(s)
| | - Diego Carballares
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain
| | | | - Javier Rocha-Martin
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid Spain.
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22
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Zhang D, Kukkar D, Kaur H, Kim KH. Recent advances in the synthesis and applications of single-atom nanozymes in food safety monitoring. Adv Colloid Interface Sci 2023; 319:102968. [PMID: 37582302 DOI: 10.1016/j.cis.2023.102968] [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: 05/17/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/17/2023]
Abstract
Nanozymes are synthetic compounds with enzyme-like tunable catalytic properties. The success of nanozymes for catalytic applications can be attributed to their small dimensions, cost-effective synthesis, appreciable stability, and scalability to molecular dimensions. The emergence of single atom nanozymes (SANzymes) has opened up new possibilities in bioanalytical applications. In this regard, this review outlines enzyme-mimicking features of SANzymes for food safety applications in relation to the key variables controlling their catalytic performance. The discussion is extended further to cover the applications of SANzymes for the monitoring of various compounds/biomaterials of significance with respect to food safety (e.g., pesticides, veterinary drug residues, foodborne pathogenic bacteria, mycotoxins/bacterial endotoxin, antioxidant residues, hydrogen peroxide residues, and heavy metal ions). Furthermore, the performance of SANzymes is evaluated in terms of various performance metrics such as limit of detection (LOD), linear dynamic range, and figure of merit (FoM). The challenges and future road map for the applications of SANzymes are also addressed along with their upscaling in the area of food safety.
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Affiliation(s)
- Daohong Zhang
- College of Food Engineering, Ludong University, Yantai, 264025, Shandong, China; Bio-Nanotechnology Research Institute, Ludong University, Yantai, 264025, Shandong, China
| | - Deepak Kukkar
- Department of Biotechnology, Chandigarh University, Gharuan, Mohali 140413, India; University Centre for Research and Development, Chandigarh University, Gharuan, Mohali 140413, India
| | - Harsimran Kaur
- Department of Biotechnology, Chandigarh University, Gharuan, Mohali 140413, India
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea.
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23
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Qiu Y, Xu H, Ji Q, Xu R, Zhu M, Dang Y, Shi X, Zhang L, Xia Y. Mutation, food-grade expression, and characterization of a lactonase for zearalenone degradation. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12638-6. [PMID: 37401996 DOI: 10.1007/s00253-023-12638-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023]
Abstract
Zearalenone (ZEN) is a mycotoxin that causes serious threats to human health. People are exposed to ZEN contamination externally and internally through many ways, while environmental-friendly strategies for efficient elimination of ZEN are urgently needed worldwide. Previous studies revealed that the lactonase Zhd101 from Clonostachys rosea can hydrolyze ZEN to low toxicity compounds. In this work, the enzyme Zhd101 was conducted with combinational mutations to enhance its application properties. The optimal mutant (V153H-V158F), named Zhd101.1, was selected and introduced into the food-grade recombinant yeast strain Kluyveromyces lactis GG799(pKLAC1-Zhd101.1), followed by induced expression and secretion into the supernatant. The enzymatic properties of this mutant were extensively examined, revealing a 1.1-fold increase in specific activity, as well as improved thermostability and pH stability, compared to the wild-type enzyme. The ZEN degradation tests and the reaction parameters optimization were carried out in both solutions and the ZEN-contaminated corns, using the fermentation supernatants of the food-grade yeast strain. Results showed that the degradation rates for ZEN by fermentation supernatants reached 96.9% under optimal reaction conditions and 74.6% in corn samples, respectively. These new results are a useful reference to zearalenone biodegradation technologies and indicated that the mutant enzyme Zhd101.1 has potential to be used in food and feed industries. KEY POINTS: • Mutated lactonase showed 1.1-fold activity, better pH stability than the wild type. • The strain K. lactis GG799(pKLAC1-Zhd101.1) and the mutant Zhd101.1 are food-grade. • ZEN degradation rates by supernatants reached 96.9% in solution and 74.6% in corns.
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Affiliation(s)
- Yangyu Qiu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Huidong Xu
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Qinyi Ji
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Rongrong Xu
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- Shandong Freda Bioeng Co., Ltd., Jinan, 250101, China
| | - Mulan Zhu
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Yali Dang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315211, China
| | - Xizhi Shi
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Lili Zhang
- Key Laboratory of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Yu Xia
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
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24
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Bidart GN, Gharabli H, Welner DH. Functional characterization of the phosphotransferase system in Parageobacillus thermoglucosidasius. Sci Rep 2023; 13:7131. [PMID: 37130962 PMCID: PMC10154347 DOI: 10.1038/s41598-023-33918-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/20/2023] [Indexed: 05/04/2023] Open
Abstract
Parageobacillus thermoglucosidasius is a thermophilic bacterium characterized by rapid growth, low nutrient requirements, and amenability to genetic manipulation. These characteristics along with its ability to ferment a broad range of carbohydrates make P. thermoglucosidasius a potential workhorse in whole-cell biocatalysis. The phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) catalyzes the transport and phosphorylation of carbohydrates and sugar derivatives in bacteria, making it important for their physiological characterization. In this study, the role of PTS elements on the catabolism of PTS and non-PTS substrates was investigated for P. thermoglucosidasius DSM 2542. Knockout of the common enzyme I, part of all PTSs, showed that arbutin, cellobiose, fructose, glucose, glycerol, mannitol, mannose, N-acetylglucosamine, N-acetylmuramic acid, sorbitol, salicin, sucrose, and trehalose were PTS-dependent on translocation and coupled to phosphorylation. The role of each putative PTS was investigated and six PTS-deletion variants could not grow on arbutin, mannitol, N-acetylglucosamine, sorbitol, and trehalose as the main carbon source, or showed diminished growth on N-acetylmuramic acid. We concluded that PTS is a pivotal factor in the sugar metabolism of P. thermoglucosidasius and established six PTS variants important for the translocation of specific carbohydrates. This study lays the groundwork for engineering efforts with P. thermoglucosidasius towards efficient utilization of diverse carbon substrates for whole-cell biocatalysis.
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Affiliation(s)
- Gonzalo N Bidart
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - Hani Gharabli
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - Ditte Hededam Welner
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark.
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25
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Liao M, Dong R, Li L, Liu X, Wang Y, Bai Y, Luo H, Yao B, Huang H, Tu T. High Production of Maltooligosaccharides in the Starch Liquefaction Process: A Study on the Hyperthermophilic Mechanism of α-Amylase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6480-6489. [PMID: 36959740 DOI: 10.1021/acs.jafc.3c00665] [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: 05/03/2023]
Abstract
The efficient production of high-value-added bioproducts from starchy substances requires α-amylases with hyperthermophilic properties for industrial starch liquefaction. In this study, two hyperthermophilic α-amylases with significant differences in thermostability, PfAmy and TeAmy, were comparatively studied through structural analysis, domain swapping, and site-directed mutagenesis, finding that three residues, His152, Cys166, and His168, located in domain B were the main contributors to hyperthermostability. The effects of these three residues were strongly synergistic, causing the optimum temperature for the mutant K152H/A166C/E168H of TeAmy to shift to 95-100 °C and stabilize at 90 °C without Ca2+. Compared to PfAmy and TeAmy, the mutant K152H/A166C/E168H, respectively, exhibited 1.7- and 2.5-times higher starch hydrolysis activity at 105 °C and pH 5.5 (10411 ± 70 U/mg) and released 1.1- and 1.7-times more maltooligosaccharides from 1% starch. This work has interpreted the hyperthermophilic mechanism of α-amylase and thereby providing a potential candidate for the efficient industrial conversion of starch to bioproducts.
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Affiliation(s)
- Min Liao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ruyue Dong
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lanxue Li
- State Key Laboratory of Animal Nutrition, 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
| | - Yaru Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yingguo Bai
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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26
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Zhang Y, Feng Z, Xiang H, Zhang X, Yang L. Characterization of Feruloyl Esterase from Klebsiella oxytoca Z28 and Its Application in the Release of Ferulic Acid from De-Starching Wheat Bran. Microorganisms 2023; 11:microorganisms11040989. [PMID: 37110412 PMCID: PMC10146132 DOI: 10.3390/microorganisms11040989] [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: 03/19/2023] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Feruloyl esterase (EC3.1.1.73; FAE) can degrade biomass to release ferulic acid (FA), which has a high application in bioprocessing, food, pharmaceutical, paper, feed, and other industrial fields. A strain of Klebsiella oxytoca Z28 with ferulic esterase activity was screened from Daqu. In addition, the FAE gene was expressed in Escherichia coli BL21 (DE3). The enzyme consists of 340 amino acids with a molecular mass of 37.7 kDa. The FAE enzyme activity was 463 U/L when the substrate was ethyl 4-hydroxy-3-methoxycinnamate and the optimum temperature and pH were 50 °C and 8.0, respectively. The enzyme had good stability at temperatures of 25-40 °C and a pH of 8.0. Ba2+, Cu2+, Mn2+, and Ca2+ had a strong inhibitory effect on the enzyme activity, and Na+ had a promotive effect on the enzyme activity. The de-starching wheat bran was degraded by KoFAE, and the FA release was up to 227.15 µg/g. This indicated that the heterologous expression of KoFAE from Klebsiella oxytoca Z28 in E. coli had a certain potential of biodegradation, which can be applied to the degradation of agricultural waste to obtain high value-added FA products.
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Affiliation(s)
- Yao Zhang
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin 644000, China
| | - Zhiping Feng
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin 644000, China
- Liquor Making Bio-Technology & Application of Key Laboratory of Sichuan Province, Sichuan University of Science & Engineering, Yibin 644000, China
| | - Hongzhu Xiang
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin 644000, China
| | - Xian Zhang
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin 644000, China
| | - Lijuan Yang
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin 644000, China
- Liquor Making Bio-Technology & Application of Key Laboratory of Sichuan Province, Sichuan University of Science & Engineering, Yibin 644000, China
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27
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Chib S, Jamwal VL, Kumar V, Gandhi SG, Saran S. Fungal production of kojic acid and its industrial applications. Appl Microbiol Biotechnol 2023; 107:2111-2130. [PMID: 36912905 DOI: 10.1007/s00253-023-12451-1] [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: 11/22/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/14/2023]
Abstract
Kojic acid has gained its importance after it was known worldwide that the substance functions primarily as skin-lightening agent. Kojic acid plays a vital role in skin care products, as it enhances the ability to prevent exposure to UV radiation. It inhibits the tyrosinase formation which suppresses hyperpigmentation in human skin. Besides cosmetics, kojic acid is also greatly used in food, agriculture, and pharmaceuticals industries. Conversely, according to Global Industry Analysts, the Middle East, Asia, and in Africa especially, the demand of whitening cream is very high, and probably the market will reach to $31.2 billion by 2024 from $17.9 billion of 2017. The important kojic acid-producing strains were mainly belongs to the genus Aspergillus and Penicillium. Due to its commercial potential, it continues to attract the attention for its green synthesis, and the studies are still widely conducted to improve kojic acid production. Thus, the present review is focused on the current production processes, gene regulation, and limitation of its commercial production, probable reasons, and possible solutions. For the first time, detailed information on the metabolic pathway and the genes involved in kojic acid production, along with illustrations of genes, are highlighted in the present review. Demand and market applications of kojic acid and its regulatory approvals for its safer use are also discussed. KEY POINTS: • Kojic acid is an organic acid that is primarily produced by Aspergillus species. • It is mainly used in the field of health care and cosmetic industries. • Kojic acid and its derivatives seem to be safe molecules for human use.
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Affiliation(s)
- Shifali Chib
- Fermentation and Microbial Biotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vijay Lakshmi Jamwal
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Infectious Disease Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Vinod Kumar
- Fermentation and Microbial Biotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sumit G Gandhi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Infectious Disease Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Saurabh Saran
- Fermentation and Microbial Biotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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28
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Ye JW, Lin YN, Yi XQ, Yu ZX, Liu X, Chen GQ. Synthetic biology of extremophiles: a new wave of biomanufacturing. Trends Biotechnol 2023; 41:342-357. [PMID: 36535816 DOI: 10.1016/j.tibtech.2022.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/12/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022]
Abstract
Microbial biomanufacturing, powered by the advances of synthetic biology, has attracted growing interest for the production of diverse products. In contrast to conventional microbes, extremophiles have shown better performance for low-cost production owing to their outstanding growth and synthesis capacity under stress conditions, allowing unsterilized fermentation processes. We review increasing numbers of products already manufactured utilizing extremophiles in recent years. In addition, genetic parts, molecular tools, and manipulation approaches for extremophile engineering are also summarized, and challenges and opportunities are predicted for non-conventional chassis. Next-generation industrial biotechnology (NGIB) based on engineered extremophiles promises to simplify biomanufacturing processes and achieve open and continuous fermentation, without sterilization, and utilizing low-cost substrates, making NGIB an attractive green process for sustainable manufacturing.
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Affiliation(s)
- Jian-Wen Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China; Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yi-Na Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China; Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xue-Qing Yi
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhuo-Xuan Yu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xu Liu
- PhaBuilder Biotech Company, Shunyi District, Zhaoquan Ying, Beijing 101309, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; Ministry of Education (MOE) Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, China.
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29
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Daddaoua A, Álvarez C, Oggerin M, Rodriguez N, Duque E, Amils R, Armengaud J, Segura A, Ramos JL. Rio Tinto as a niche for acidophilus enzymes of industrial relevance. Microb Biotechnol 2023; 16:1069-1086. [PMID: 36748404 PMCID: PMC10128141 DOI: 10.1111/1751-7915.14192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/06/2022] [Indexed: 02/08/2023] Open
Abstract
Lignocellulosic residues are amongst the most abundant waste products on Earth. Therefore, there is an increasing interest in the utilization of these residues for bioethanol production and for biorefineries to produce compounds of industrial interest. Enzymes that breakdown cellulose and hemicellulose into oligomers and monosaccharides are required in these processes and cellulolytic enzymes with optimum activity at a low pH area are desirable for industrial processes. Here, we explore the fungal biodiversity of Rıo Tinto, the largest acidic ecosystem on Earth, as far as the secretion of cellulolytic enzymes is concerned. Using colorimetric and industrial substrates, we show that a high proportion of the fungi present in this extremophilic environment secrete a wide range of enzymes that are able to hydrolyze cellulose and hemicellulose at acidic pH (4.5-5). Shotgun proteomic analysis of the secretomes of some of these fungi has identified different cellulases and hemicellulolytic enzymes as well as a number of auxiliary enzymes. Supplementation of pre-industrial cocktails from Myceliophtora with Rio Tinto secretomes increased the amount of monosaccharides released from corn stover or sugar cane straw. We conclude that the Rio Tinto fungi display a good variety of hydrolytic enzymes with high industrial potential.
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Affiliation(s)
- Abdelali Daddaoua
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Consolación Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis (CSIC-US), Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, CIC Cartuja, Seville, Spain
| | - Monika Oggerin
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Nuria Rodriguez
- Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, Spain
| | - Estrella Duque
- Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.,Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, Spain
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - Ana Segura
- Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
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30
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Cloning, Expression and Characterization of an Alginate Lyase in Bacillus subtilis WB600. FERMENTATION 2023. [DOI: 10.3390/fermentation9020144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The aim of this study was to further broaden the heterologous expression of alginate lyase from Vibrio alginolyticus in a Bacillus subtilis expression vector. A B. subtilis WB600/pP43NMK-alg62 strain was constructed. (NH4)2SO4 precipitation and Ni-affinity chromatography were performed to purify the enzyme. We then characterized the enzyme. Its molecular weight was 57.64 kDa, and it worked optimally at 30 °C with a pH of 8.0. Ca2+ markedly enhanced the enzymatic activity of Alg62 while Cu2+ and Ni2+ inhibited its activity. Alg62 had a wide range of substrate specificity, showing high activity toward sodium alginate and polyG. Following optimization of the fermentation process, the optimal conditions for the recombinant expression of Alg62 were as follows: temperature of 37 °C, pH of 7.0, medium consisting of glycerol 15 g/L, yeast powder 25 g/L and K+ 1.5 mmol/L. At these optimal conditions, enzyme activity reached 318.21 U/mL, which was 1.54 times higher than the initial enzyme activity.
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31
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Dixit M, Chhabra D, Shukla P. Optimization of endoglucanase-lipase-amylase enzyme consortium from Thermomyces lanuginosus VAPS25 using Multi-Objective genetic algorithm and their bio-deinking applications. BIORESOURCE TECHNOLOGY 2023; 370:128467. [PMID: 36509307 DOI: 10.1016/j.biortech.2022.128467] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
In this study, the enzyme consortium of endoglucanase, lipase, and amylase was obtained and optimized using artificial intelligence-based tools. After optimization using a multi-objective genetic algorithm and artificial neural network, the enzyme activity was 8.8 IU/g, 153.68 U/g, and 19.2 IU/g for endoglucanase, lipase, and amylase, respectively, using Thermomyces lanuginosus VAPS25. The highest enzyme activity was obtained at parameters 77.69% moisture content, 52.7 °C temperature, 98 h, and 3.1 eucalyptus leaves: wheat bran ratio. The endoglucanase-lipase-amylase (END-LIP-AMY) enzyme consortium showed reliable characteristics in terms of catalytic activity at 50-80 °C and pH 6.0-9.0. The increase in deinking efficiency of 27.8% and 11.1% were obtained compared to control for mixed office waste and old newspaper, respectively, using the enzyme consortium. The surface chemical composition and fiber morphology of deinked pulp was investigated using Attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) and Scanning electron microscopy (SEM).
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Affiliation(s)
- Mandeep Dixit
- Department of Microbiology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Deepak Chhabra
- Department of Mechanical Engineering, University Institute of Engineering & Technology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Pratyoosh Shukla
- Department of Microbiology, Maharshi Dayanand University, Rohtak-124001, Haryana, India; Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India.
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32
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Tamburino R, Marcolongo L, Sannino L, Ionata E, Scotti N. Plastid Transformation: New Challenges in the Circular Economy Era. Int J Mol Sci 2022; 23:ijms232315254. [PMID: 36499577 PMCID: PMC9736159 DOI: 10.3390/ijms232315254] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
In a circular economy era the transition towards renewable and sustainable materials is very urgent. The development of bio-based solutions, that can ensure technological circularity in many priority areas (e.g., agriculture, biotechnology, ecology, green industry, etc.), is very strategic. The agricultural and fishing industry wastes represent important feedstocks that require the development of sustainable and environmentally-friendly industrial processes to produce and recover biofuels, chemicals and bioactive molecules. In this context, the replacement, in industrial processes, of chemicals with enzyme-based catalysts assures great benefits to humans and the environment. In this review, we describe the potentiality of the plastid transformation technology as a sustainable and cheap platform for the production of recombinant industrial enzymes, summarize the current knowledge on the technology, and display examples of cellulolytic enzymes already produced. Further, we illustrate several types of bacterial auxiliary and chitinases/chitin deacetylases enzymes with high biotechnological value that could be manufactured by plastid transformation.
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Affiliation(s)
- Rachele Tamburino
- CNR-IBBR, Institute of Biosciences and BioResources, 80055 Naples, Italy
| | | | - Lorenza Sannino
- CNR-IBBR, Institute of Biosciences and BioResources, 80055 Naples, Italy
| | - Elena Ionata
- CNR-IRET, Research Institute on Terrestrial Ecosystems, 80131 Naples, Italy
| | - Nunzia Scotti
- CNR-IBBR, Institute of Biosciences and BioResources, 80055 Naples, Italy
- Correspondence:
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33
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McCord JP, Kohanov ZA, Lowell AN. Thermorubin Biosynthesis Initiated by a Salicylate Synthase Suggests an Unusual Conversion of Phenols to Pyrones. ACS Chem Biol 2022; 17:3169-3177. [PMID: 36255735 DOI: 10.1021/acschembio.2c00606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Thermorubin is a tetracyclic naphthoisocoumarin natural product that demands investigation due to its novel mechanism of bacterial protein synthesis inhibition and its unusual structural features. In this work, we describe the identification of the biosynthetic cluster responsible for thermorubin from the sequenced Laceyella sacchari producer species and its confirmation via heterologous production in Escherichia coli. Based on an in-depth annotation of the cluster, we propose a biosynthetic pathway that accounts for the formation of the unique, nonterminal pyrone. Additionally, the expression and use of salicylate synthase TheO enabled testing of the stability properties of this extremophile-derived enzyme. TheO displayed rapid kinetics and a remarkably robust secondary structure, converting chorismate to salicylate with a KM of 109 ± 12 μM, kcat of 9.17 ± 0.36 min-1, and catalytic efficiency (kcat/KM) of 84 ± 9 nM-1 min-1, and retained significant activity up to 50 °C. These studies serve as the basis for continued biosynthetic investigations and bioinspired synthetic approaches.
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Affiliation(s)
- Jennifer P McCord
- Department of Chemistry, Virginia Tech (Virginia Polytechnic Institute and State University), Davidson Hall Rm. 480, 1040 Drillfield Dr., Blacksburg, Virginia 24061, United States
| | - Zachary A Kohanov
- Department of Chemistry, Virginia Tech (Virginia Polytechnic Institute and State University), Davidson Hall Rm. 480, 1040 Drillfield Dr., Blacksburg, Virginia 24061, United States
| | - Andrew N Lowell
- Department of Chemistry, Virginia Tech (Virginia Polytechnic Institute and State University), Davidson Hall Rm. 480, 1040 Drillfield Dr., Blacksburg, Virginia 24061, United States
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34
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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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Molinaro C, Bénéfice M, Gorlas A, Da Cunha V, Robert HML, Catchpole R, Gallais L, Forterre P, Baffou G. Life at high temperature observed in vitro upon laser heating of gold nanoparticles. Nat Commun 2022; 13:5342. [PMID: 36097020 PMCID: PMC9468142 DOI: 10.1038/s41467-022-33074-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/31/2022] [Indexed: 11/22/2022] Open
Abstract
Thermophiles are microorganisms that thrive at high temperature. Studying them can provide valuable information on how life has adapted to extreme conditions. However, high temperature conditions are difficult to achieve on conventional optical microscopes. Some home-made solutions have been proposed, all based on local resistive electric heating, but no simple commercial solution exists. In this article, we introduce the concept of microscale laser heating over the field of view of a microscope to achieve high temperature for the study of thermophiles, while maintaining the user environment in soft conditions. Microscale heating with moderate laser intensities is achieved using a substrate covered with gold nanoparticles, as biocompatible, efficient light absorbers. The influences of possible microscale fluid convection, cell confinement and centrifugal thermophoretic motion are discussed. The method is demonstrated with two species: (i) Geobacillus stearothermophilus, a motile thermophilic bacterium thriving around 65 °C, which we observed to germinate, grow and swim upon microscale heating and (ii) Sulfolobus shibatae, a hyperthermophilic archaeon living at the optimal temperature of 80 °C. This work opens the path toward simple and safe observation of thermophilic microorganisms using current and accessible microscopy tools. Studying microorganisms at high temperatures is challenging on conventional optical microscopes. Here, the authors introduce the concept of microscale laser heating over the full field of view by using gold nanoparticles as light absorbers, and study thermophile species up to 80 °C.
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A Statistical Analysis of the Sequence and Structure of Thermophilic and Non-Thermophilic Proteins. Int J Mol Sci 2022; 23:ijms231710116. [PMID: 36077513 PMCID: PMC9456548 DOI: 10.3390/ijms231710116] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Thermophilic proteins have various practical applications in theoretical research and in industry. In recent years, the demand for thermophilic proteins on an industrial scale has been increasing; therefore, the engineering of thermophilic proteins has become a hot direction in the field of protein engineering. However, the exact mechanism of thermostability of proteins is not yet known, for engineering thermophilic proteins knowing the basis of thermostability is necessary. In order to understand the basis of the thermostability in proteins, we have made a statistical analysis of the sequences, secondary structures, hydrogen bonds, salt bridges, DHA (Donor-Hydrogen-Accepter) angles, and bond lengths of ten pairs of thermophilic proteins and their non-thermophilic orthologous. Our findings suggest that polar amino acids contribute to thermostability in proteins by forming hydrogen bonds and salt bridges which provide resistance against protein denaturation. Short bond length and a wider DHA angle provide greater bond stability in thermophilic proteins. Moreover, the increased frequency of aromatic amino acids in thermophilic proteins contributes to thermal stability by forming more aromatic interactions. Additionally, the coil, helix, and loop in the secondary structure also contribute to thermostability.
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Marchisio F, Di Nardo L, Val DS, Cerminati S, Espariz M, Rasia RM, Menzella HG, Castelli ME. Characterization of a novel thermostable phospholipase C from T. kodakarensis suitable for oil degumming. Appl Microbiol Biotechnol 2022; 106:5081-5091. [PMID: 35854045 DOI: 10.1007/s00253-022-12081-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/09/2022] [Accepted: 07/13/2022] [Indexed: 11/24/2022]
Abstract
The implementation of cleaner technologies that minimize environmental pollution caused by conventional industrial processes is an increasing global trend. Hence, traditionally used chemicals have been replaced by novel enzymatic alternatives in a wide variety of industrial-scale processes. Enzymatic oil degumming, the first step of the oil refining process, exploits the conversion catalyzed by phospholipases to remove vegetable crude oils' phospholipids. This enzymatic method reduces the gums' volume and increases the overall oil yield. A thermostable phospholipase would be highly advantageous for industrial oil degumming as oil treatment at higher temperatures would save energy and increase the recovery of oil by facilitating the mixing and gums removal. A thermostable phosphatidylcholine (PC) (and phosphatidylethanolamine (PE))-specific phospholipase C from Thermococcus kodakarensis (TkPLC) was studied and completely removed PC and PE from crude soybean oil at 80 °C. Due to these characteristics, TkPLC is an interesting promising candidate for industrial-scale enzymatic oil degumming at high temperatures. KEY POINTS: • A thermostable phospholipase C from T. kodakarensis (TkPLC) has been identified. • TkPLC was recombinantly produced in Pichia pastoris and successfully purified. • TkPLC completely hydrolyzed PC and PE in soybean oil degumming assays at 80 °C.
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Affiliation(s)
- Fiorela Marchisio
- Instituto de Procesos Biotecnológicos Y Químicos (IPROBYQ), Facultad de Ciencias, Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario (UNR), CONICET. Mitre 1998, S2000FWF, Rosario, Argentina
| | - Luisina Di Nardo
- Facultad de Ciencias, Bioquímicas Y Farmacéuticas, Instituto de Biología Celular Y Molecular de Rosario (IBR), Universidad Nacional de Rosario (UNR), CONICET. Ocampo Y Esmeralda S/N, 2000, Rosario, Argentina
| | - Diego Sebastián Val
- Instituto de Procesos Biotecnológicos Y Químicos (IPROBYQ), Facultad de Ciencias, Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario (UNR), CONICET. Mitre 1998, S2000FWF, Rosario, Argentina
| | - Sebastián Cerminati
- Instituto de Procesos Biotecnológicos Y Químicos (IPROBYQ), Facultad de Ciencias, Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario (UNR), CONICET. Mitre 1998, S2000FWF, Rosario, Argentina
| | - Martín Espariz
- Instituto de Procesos Biotecnológicos Y Químicos (IPROBYQ), Facultad de Ciencias, Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario (UNR), CONICET. Mitre 1998, S2000FWF, Rosario, Argentina.,Área Estadística Y Procesamiento de Datos, Departamento de Matemática Y Estadística, Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Rodolfo Maximiliano Rasia
- Facultad de Ciencias, Bioquímicas Y Farmacéuticas, Instituto de Biología Celular Y Molecular de Rosario (IBR), Universidad Nacional de Rosario (UNR), CONICET. Ocampo Y Esmeralda S/N, 2000, Rosario, Argentina.,Plataforma Argentina de Biología Estructural Y Metabolómica (PLABEM - CONICET), Ocampo y Esmeralda s/n, 2000, Rosario, Argentina
| | - Hugo Gabriel Menzella
- Instituto de Procesos Biotecnológicos Y Químicos (IPROBYQ), Facultad de Ciencias, Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario (UNR), CONICET. Mitre 1998, S2000FWF, Rosario, Argentina
| | - María Eugenia Castelli
- Instituto de Procesos Biotecnológicos Y Químicos (IPROBYQ), Facultad de Ciencias, Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario (UNR), CONICET. Mitre 1998, S2000FWF, Rosario, Argentina.
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Pereira de Almeida A, Vargas IP, Marciano CL, Zanoelo FF, Giannesi GC, Moraes Polizeli MDLTD, Jorge JA, Furriel RDPM, Ruller R, Masui DC. Investigation of biochemical and biotechnological potential of a thermo-halo-alkali-tolerant endo-xylanase (GH11) from Humicola brevis var. thermoidea for lignocellulosic valorization of sugarcane biomass. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Wang M, Wang X, Wu Y, Wang X, Zhao J, Liu Y, Chen Z, Jiang Z, Tian W, Zhang J. Effects of thermophiles inoculation on the efficiency and maturity of rice straw composting. BIORESOURCE TECHNOLOGY 2022; 354:127195. [PMID: 35452824 DOI: 10.1016/j.biortech.2022.127195] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/14/2022] [Accepted: 04/17/2022] [Indexed: 06/14/2023]
Abstract
The present study investigated the effects of separately or simultaneously inoculating thermophilic fungus Aspergillus fumigatus Z5 and bacterium Geobacillus stearothermophilus B5 on lignocellulose degradation, enzyme activities and humification during rice straw composting. The results indicated that inoculation of Z5 accelerated the rise of temperature in the mesophilic phase, and the degradation degree of cellulose and hemicellulose was increased by 25.3% and 20.7%, respectively, due to the higher activities of lignocellulolytic enzymes. Inoculation of B5 increased 5-7 °C of the compost temperature in the thermophilic phase, and also prolonged the duration from 33 to 41 days. Inoculated simultaneously, the secreted hydrolases of Z5 generated more nutrition and promoted the growth of B5. B5 maintained and increased the compost temperature, thus presenting a better hydrolysis environment for extracellular hydrolases. Thermophilic inoculation altered the main physicochemical factors and improved efficiency and maturity in rice straw composting.
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Affiliation(s)
- Mengmeng Wang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China; Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuanqing Wang
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali lands), Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
| | - Yuncheng Wu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Xiaosong Wang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiayin Zhao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Yu Liu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Zhe Chen
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Zhongkun Jiang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Wei Tian
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China.
| | - Jibing Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
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Enzymatically triggered delignification through a novel stable laccase: A mixed in-silico /in-vitro exploration of a complex environmental microbiota. Int J Biol Macromol 2022; 211:328-341. [PMID: 35551951 DOI: 10.1016/j.ijbiomac.2022.05.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 11/23/2022]
Abstract
Laccases have been broadly applied as a multitasking biocatalyst in various industries, but their applications tend to be limited by easy deactivation, lack of adequate stability, and susceptibility under complex conditions. Identifying stable laccase as a green-biocatalyst is crucial for developing cost-effective biorefining processes. In this direction, we attempted in-silico screening a stable metagenome-derived laccase (PersiLac1) from tannery wastewater in a complex environment. The laccase exhibited high thermostability, retaining 53.19% activity after 180 min at 70 °C, and it was stable in a wide range of pH (4.0-9.0). After 33 days of storage at 50°C, pH 6.0, the enzyme retained 71.65% of its activity. Various metal ions, inhibitors, and organic solvents showed that PersiLac1 has a stable structure. The stable PersiLac1 could successfully remove lignin and phenolic from quinoa husk and rice straw. In the separate hydrolysis and fermentation process (SHF) after 72 h, hydrolysis was obtained 100% and 73.4% for quinoa husk and rice straw, and fermentation by the S. cerevisiae was be produced 41.46 g/L and 27.75g/L ethanol, respectively. Results signified that the novel lignin-degrading enzyme was confirmed to have great potential for industrial application as a green-biocatalyst based on enzymatically triggered to delignification and detoxify lignocellulosic biomass.
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Xiong N, Lv PJ, Song JW, Shen Q, Xue YP, Zheng YG. Engineering of a nitrilase through consensus sequence analysis and conserved site substitution to improve its thermostability and activity. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Mesbah NM. Industrial Biotechnology Based on Enzymes From Extreme Environments. Front Bioeng Biotechnol 2022; 10:870083. [PMID: 35480975 PMCID: PMC9036996 DOI: 10.3389/fbioe.2022.870083] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/21/2022] [Indexed: 12/22/2022] Open
Abstract
Biocatalysis is crucial for a green, sustainable, biobased economy, and this has driven major advances in biotechnology and biocatalysis over the past 2 decades. There are numerous benefits to biocatalysis, including increased selectivity and specificity, reduced operating costs and lower toxicity, all of which result in lower environmental impact of industrial processes. Most enzymes available commercially are active and stable under a narrow range of conditions, and quickly lose activity at extremes of ion concentration, temperature, pH, pressure, and solvent concentrations. Extremophilic microorganisms thrive under extreme conditions and produce robust enzymes with higher activity and stability under unconventional circumstances. The number of extremophilic enzymes, or extremozymes, currently available are insufficient to meet growing industrial demand. This is in part due to difficulty in cultivation of extremophiles in a laboratory setting. This review will present an overview of extremozymes and their biotechnological applications. Culture-independent and genomic-based methods for study of extremozymes will be presented.
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Affiliation(s)
- Noha M Mesbah
- Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
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Le Y, Sun J. CRISPR/Cas genome editing systems in thermophiles: Current status, associated challenges, and future perspectives. ADVANCES IN APPLIED MICROBIOLOGY 2022; 118:1-30. [PMID: 35461662 DOI: 10.1016/bs.aambs.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Thermophiles, offering an attractive and unique platform for a broad range of applications in biofuels and environment protections, have received a significant attention and growing interest from academy and industry. However, the exploration and exploitation of thermophilic organisms have been hampered by the lack of a powerful genome manipulation tool to improve production efficiency. At current, the clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR associated (Cas) system has been successfully exploited as a competent, simplistic, and powerful tool for genome engineering both in eukaryotes and prokaryotes. Indeed, with the significant efforts made in recent years, some thermostable Cas9 proteins have been well identified and characterized and further, some thermostable Cas9-based editing tools have been successfully established in some representative obligate thermophiles. In this regard, we reviewed the current status and its progress in CRISPR/Cas-based genome editing system towards a variety of thermophilic organisms. Despite the potentials of these progresses, multiple factors/barriers still have to be overcome and optimized for improving its editing efficiency in thermophiles. Some insights into the roles of thermostable CRISPR/Cas technologies for the metabolic engineering of thermophiles as a thermophilic microbial cell factory were also fully analyzed and discussed.
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Affiliation(s)
- Yilin Le
- Biofuels institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu, PR China.
| | - Jianzhong Sun
- Biofuels institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu, PR China.
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Nahle S, El Khoury A, Savvaidis I, Chokr A, Louka N, Atoui A. Detoxification approaches of mycotoxins: by microorganisms, biofilms and enzymes. INTERNATIONAL JOURNAL OF FOOD CONTAMINATION 2022. [DOI: 10.1186/s40550-022-00089-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
AbstractMycotoxins are generally found in food, feed, dairy products, and beverages, subsequently presenting serious human and animal health problems. Not surprisingly, mycotoxin contamination has been a worldwide concern for many research studies. In this regard, many biological, chemical, and physical approaches were investigated to reduce and/or remove contamination from food and feed products. Biological detoxification processes seem to be the most promising approaches for mycotoxins removal from food. The current review details the newest progress in biological detoxification (adsorption and metabolization) through microorganisms, their biofilms, and enzymatic degradation, finally describing the detoxification mechanism of many mycotoxins by some microorganisms. This review also reports the possible usage of microorganisms as mycotoxins’ binders in various food commodities, which may help produce mycotoxins-free food and feed.
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Cai LN, Lu T, Lin DQ, Yao SJ. Discovery of extremophilic cellobiohydrolases from marine Aspergillus niger with computational analysis. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Zhu D, Qaria MA, Zhu B, Sun J, Yang B. Extremophiles and extremozymes in lignin bioprocessing. RENEWABLE AND SUSTAINABLE ENERGY REVIEWS 2022; 157:112069. [DOI: 10.1016/j.rser.2021.112069] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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A Comparative Analysis of Weizmannia coagulans Genomes Unravels the Genetic Potential for Biotechnological Applications. Int J Mol Sci 2022; 23:ijms23063135. [PMID: 35328559 PMCID: PMC8954581 DOI: 10.3390/ijms23063135] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/11/2022] [Accepted: 03/11/2022] [Indexed: 12/20/2022] Open
Abstract
The production of biochemicals requires the use of microbial strains with efficient substrate conversion and excellent environmental robustness, such as Weizmannia coagulans species. So far, the genomes of 47 strains have been sequenced. Herein, we report a comparative genomic analysis of nine strains on the full repertoire of Carbohydrate-Active enZymes (CAZymes), secretion systems, and resistance mechanisms to environmental challenges. Moreover, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) immune system along with CRISPR-associated (Cas) genes, was also analyzed. Overall, this study expands our understanding of the strain's genomic diversity of W. coagulans to fully exploit its potential in biotechnological applications.
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Ecological and Biotechnological Relevance of Mediterranean Hydrothermal Vent Systems. MINERALS 2022. [DOI: 10.3390/min12020251] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Marine hydrothermal systems are a special kind of extreme environments associated with submarine volcanic activity and characterized by harsh chemo-physical conditions, in terms of hot temperature, high concentrations of CO2 and H2S, and low pH. Such conditions strongly impact the living organisms, which have to develop adaptation strategies to survive. Hydrothermal systems have attracted the interest of researchers due to their enormous ecological and biotechnological relevance. From ecological perspective, these acidified habitats are useful natural laboratories to predict the effects of global environmental changes, such as ocean acidification at ecosystem level, through the observation of the marine organism responses to environmental extremes. In addition, hydrothermal vents are known as optimal sources for isolation of thermophilic and hyperthermophilic microbes, with biotechnological potential. This double aspect is the focus of this review, which aims at providing a picture of the ecological features of the main Mediterranean hydrothermal vents. The physiological responses, abundance, and distribution of biotic components are elucidated, by focusing on the necto-benthic fauna and prokaryotic communities recognized to possess pivotal role in the marine ecosystem dynamics and as indicator species. The scientific interest in hydrothermal vents will be also reviewed by pointing out their relevance as source of bioactive molecules.
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Abstract
Synthetic biology applications rely on a well-characterized set of microbial strains, with an established toolbox of molecular biology methods for their genetic manipulation. Since there are no thermophiles with such attributes, most biotechnology and synthetic biology studies use organisms that grow in the mesophilic temperature range. As a result, thermophiles, a heterogenous group of microbes that thrive at high (>50 °C) temperatures, are largely overlooked, with respect to their biotechnological potential, even though they share several favorable traits. Thermophilic bacteria tend to grow at higher rates compared to their mesophilic counterparts, while their growth has lower cooling requirements and is less prone to contamination. Over the last few years, there has been renewed interest in developing tools and methods for thermophile bioengineering. In this perspective, we explain why it is a good idea to invest time and effort into developing a thermophilic synthetic biology direction, which is the state of the art, and why we think that the implementation of a thermophilic synthetic biology platform—a thermochassis—will take synthetic biology to the extremes.
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Wang Q, Wu Q, Ye T, Wang X, Qiu H, Xie J, Wang Y, Zhou S, Wu W. Reversible Regulating the Substrate Specificity of Enzymes in Microgels by a Phase Transition in Polymer Networks. ACS Macro Lett 2022; 11:26-32. [PMID: 35574802 DOI: 10.1021/acsmacrolett.1c00687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Here, we report a distinct approach for regulating the substrate specificity of enzymes immobilized in microgels by a phase transition in polymer networks. The finding is demonstrated on glucose oxidase that is immobilized in thermoresponsive poly(N-isopropylacrylamide)-based microgels. Laser light scattering and enzymatic oxidation tests indicate that the broadened specificity appears at low temperatures, at which the gel matrix is in the relatively swollen state relative to its state at microgel synthesis temperature; upon heating to the relative higher temperatures, the gel matrix is not able to shrink further that offers a tight space in which the enzyme resides to retain high glucose specificity. It is proposed that polymer phase transition in the gel matrix mainly alter protein gates that control passage of substrates into active sites, making them open or close to a certain extent that enable reversible regulating the substrate specificity. The finding is also observed on bulk gels under a rational design, making it of potential interest in enzymatic biofuel cell applications.
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Affiliation(s)
- Qiangwei Wang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, The Key Laboratory for Chemical Biology of Fujian Province, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Qingshi Wu
- College of Chemical Engineering and Materials Science, Quanzhou Normal University, Quanzhou, Fujian 362000, China
| | - Ting Ye
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, The Key Laboratory for Chemical Biology of Fujian Province, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Xiaofei Wang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, The Key Laboratory for Chemical Biology of Fujian Province, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Huijuan Qiu
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, The Key Laboratory for Chemical Biology of Fujian Province, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Jianda Xie
- School of Materials Science and Engineering, Xiamen University of Technology, Xiamen, Fujian 361024, China
| | - Yusong Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shiming Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Weitai Wu
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, The Key Laboratory for Chemical Biology of Fujian Province, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
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