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Heng S, Sutheeworapong S, Wangnai C, Champreda V, Kosugi A, Ratanakhanokchai K, Tachaapaikoon C, Ceballos RM. Hydrolysis of ionic liquid-treated substrate with an Iocasia fonsfrigidae strain SP3-1 endoglucanase. Appl Microbiol Biotechnol 2024; 108:63. [PMID: 38189956 PMCID: PMC10774164 DOI: 10.1007/s00253-023-12918-1] [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: 07/26/2023] [Revised: 12/04/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024]
Abstract
Recently, we reported the discovery of a novel endoglucanase of the glycoside hydrolase family 12 (GH12), designated IfCelS12A, from the haloalkaliphilic anaerobic bacterium Iocasia fonsfrigidae strain SP3-1, which was isolated from a hypersaline pond in the Samut Sakhon province of Thailand (ca. 2017). IfCelS12A exhibits high substrate specificity on carboxymethyl cellulose and amorphous cellulose but low substrate specificity on b-1,3;1,4-glucan. Unlike some endoglucanases of the GH12 family, IfCelS12A does not exhibit hydrolytic activity on crystalline cellulose (i.e., Avicel™). High-Pressure Liquid Chromatography (HPLC) and Thin Layer Chromatography (TLC) analyses of products resulting from IfCelS12-mediated hydrolysis indicate mode of action for this enzyme. Notably, IfCelS12A preferentially hydrolyzes cellotetraoses, cellopentaoses, and cellohexaoses with negligible activity on cellobiose or cellotriose. Kinetic analysis with cellopentaose and barely b-D-glucan as cellulosic substrates were conducted. On cellopentaose, IfCelS12A demonstrates a 16-fold increase in activity (KM = 0.27 mM; kcat = 0.36 s-1; kcat/KM = 1.34 mM-1 s-1) compared to the enzymatic hydrolysis of barley b-D-glucan (KM: 0.04 mM, kcat: 0.51 s-1, kcat/KM = 0.08 mM-1 s-1). Moreover, IfCelS12A enzymatic efficacy is stable in hypersaline sodium chlorids (NaCl) solutions (up to 10% NaCl). Specifically, IfCel12A retains notable activity after 24 h at 2M NaCl (10% saline solution). IfCelS12A used as a cocktail component with other cellulolytic enzymes and in conjunction with mobile sequestration platform technology offers additional options for deconstruction of ionic liquid-pretreated cellulosic feedstock. KEY POINTS: • IfCelS12A from an anaerobic alkaliphile Iocasia fronsfrigidae shows salt tolerance • IfCelS12A in cocktails with other enzymes efficiently degrades cellulosic biomass • IfCelS12A used with mobile enzyme sequestration platforms enhances hydrolysis.
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Affiliation(s)
- Sobroney Heng
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
- Department of Molecular and Cell Biology, University of California, Merced, CA, 95343, USA
| | - Sawannee Sutheeworapong
- Systems Biology and Bioinformatics Laboratory, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chinnapong Wangnai
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road Klong Luang, Pathumthani, 12120, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chakrit Tachaapaikoon
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
| | - Ruben Michael Ceballos
- Department of Molecular and Cell Biology, University of California, Merced, CA, 95343, USA.
- Quantitative Systems Biology Program, University of California, Merced, CA, 95343, USA.
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2
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González E, Vera F, Scott F, Guerrero C, Bolívar JM, Aroca G, Muñoz JÁ, Ladero M, Santos VE. Acidophilic heterotrophs: basic aspects and technological applications. Front Microbiol 2024; 15:1374800. [PMID: 38827148 PMCID: PMC11141062 DOI: 10.3389/fmicb.2024.1374800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/04/2024] [Indexed: 06/04/2024] Open
Abstract
Acidophiles comprise a group of microorganisms adapted to live in acidic environments. Despite acidophiles are usually associated with an autotrophic metabolism, more than 80 microorganisms capable of utilizing organic matter have been isolated from natural and man-made environments. The ability to reduce soluble and insoluble iron compounds has been described for many of these species and may be harnessed to develop new or improved mining processes when oxidative bioleaching is ineffective. Similarly, as these microorganisms grow in highly acidic media and the chances of contamination are reduced by the low pH, they may be employed to implement robust fermentation processes. By conducting an extensive literature review, this work presents an updated view of basic aspects and technological applications in biomining, bioremediation, fermentation processes aimed at biopolymers production, microbial electrochemical systems, and the potential use of extremozymes.
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Affiliation(s)
- Ernesto González
- Department of Chemical and Materials Engineering, Faculty of Chemistry, Universidad Complutense de Madrid, Madrid, Spain
- School of Biochemical Engineering, Faculty of Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Fernando Vera
- School of Biochemical Engineering, Faculty of Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Felipe Scott
- Faculty of Engineering and Applied Sciences, Universidad de Los Andes, Santiago, Chile
| | - Cecilia Guerrero
- School of Biochemical Engineering, Faculty of Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Juan M. Bolívar
- Department of Chemical and Materials Engineering, Faculty of Chemistry, Universidad Complutense de Madrid, Madrid, Spain
| | - Germán Aroca
- School of Biochemical Engineering, Faculty of Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Jesús Ángel Muñoz
- Department of Chemical and Materials Engineering, Faculty of Chemistry, Universidad Complutense de Madrid, Madrid, Spain
| | - Miguel Ladero
- Department of Chemical and Materials Engineering, Faculty of Chemistry, Universidad Complutense de Madrid, Madrid, Spain
| | - Victoria E. Santos
- Department of Chemical and Materials Engineering, Faculty of Chemistry, Universidad Complutense de Madrid, Madrid, Spain
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3
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Semba H, Horiguchi HK, Tsuboi H, Ishikawa K, Koda A. Effects of heterologous expression and N-glycosylation on the hyperthermostable endoglucanase of Pyrococcus furiosus. J Biosci Bioeng 2024; 137:329-334. [PMID: 38461105 DOI: 10.1016/j.jbiosc.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/23/2024] [Accepted: 02/18/2024] [Indexed: 03/11/2024]
Abstract
Hyperthermostable endoglucanases of glycoside hydrolase family 12 from the archaeon Pyrococcus furiosus (EGPf) catalyze the hydrolysis of β-1,4-glucosidic linkages in cellulose and β-glucan structures that contain β-1,3- and β-1,4-mixed linkages. In this study, EGPf was heterologously expressed with Aspergillus niger and the recombinant enzyme was characterized. The successful expression of EGPf resulted as N-glycosylated protein in its secretion into the culture medium. The glycosylation of the recombinant EGPf positively impacted the kinetic characterization of EGPf, thereby enhancing its catalytic efficiency. Moreover, glycosylation significantly boosted the thermostability of EGPf, allowing it to retain over 80% of its activity even after exposure to 100 °C for 5 h, with the optimal temperature being above 120 °C. Glycosylation did not affect the pH stability or salt tolerance of EGPf, although the glycosylated compound exhibited a high tolerance to ionic liquids. EGPf displayed the highest specific activity in the presence of 20% (v/v) 1-butyl-3-methylimidazolium chloride ([Bmim]Cl), reaching approximately 2.4 times greater activity than that in the absence of [Bmim]Cl. The specific activity was comparable to that without the ionic liquid even in the presence of 40% (v/v) [Bmim]Cl. Glycosylated EGPf has potential as an enzyme for saccharifying cellulose under high-temperature conditions or with ionic liquid treatment due to its exceptional thermostability and ionic liquid tolerance. These results underscore the potential of N-glycosylation as an effective strategy to further enhance both the thermostability of highly thermostable archaeal enzymes and the hydrolysis of barley cellulose in the presence of [Bmim]Cl.
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Affiliation(s)
- Hironori Semba
- General Research Laboratory, Ozeki Corporation, 4-9 Imazu Dezaike-cho, Nishinomiya, Hyogo 663-8227, Japan.
| | - Haruka Kado Horiguchi
- General Research Laboratory, Ozeki Corporation, 4-9 Imazu Dezaike-cho, Nishinomiya, Hyogo 663-8227, Japan
| | - Hirokazu Tsuboi
- General Research Laboratory, Ozeki Corporation, 4-9 Imazu Dezaike-cho, Nishinomiya, Hyogo 663-8227, Japan
| | - Kazuhiko Ishikawa
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan; Rare Sugar and Enzyme Research, Dep. I, R&D, Matsutani Chemical Industry Co. Ltd., 5-3 Kitaitami, Itami, Hyogo 664-8508, Japan
| | - Akio Koda
- General Research Laboratory, Ozeki Corporation, 4-9 Imazu Dezaike-cho, Nishinomiya, Hyogo 663-8227, Japan
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Iacono R, De Lise F, Moracci M, Cobucci-Ponzano B, Strazzulli A. Glycoside hydrolases from (hyper)thermophilic archaea: structure, function, and applications. Essays Biochem 2023; 67:731-751. [PMID: 37341134 DOI: 10.1042/ebc20220196] [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: 02/28/2023] [Revised: 04/19/2023] [Accepted: 05/31/2023] [Indexed: 06/22/2023]
Abstract
(Hyper)thermophilic archaeal glycosidases are enzymes that catalyze the hydrolysis of glycosidic bonds to break down complex sugars and polysaccharides at high temperatures. These enzymes have an unique structure that allows them to remain stable and functional in extreme environments such as hot springs and hydrothermal vents. This review provides an overview of the current knowledge and milestones on the structures and functions of (hyper)thermophilic archaeal glycosidases and their potential applications in various fields. In particular, this review focuses on the structural characteristics of these enzymes and how these features relate to their catalytic activity by discussing different types of (hyper)thermophilic archaeal glycosidases, including β-glucosidases, chitinase, cellulases and α-amylases, describing their molecular structures, active sites, and mechanisms of action, including their role in the hydrolysis of carbohydrates. By providing a comprehensive overview of (hyper)thermophilic archaeal glycosidases, this review aims to stimulate further research into these fascinating enzymes.
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Affiliation(s)
- Roberta Iacono
- Department of Biology, University of Naples "Federico II", Complesso Universitario Di Monte S. Angelo, Via Cupa Nuova Cinthia 21, Naples, 80126, Italy
| | - Federica De Lise
- Institute of Biosciences and BioResources, National Research Council of Italy, Via P. Castellino 111, Naples, 80131, Italy
| | - Marco Moracci
- Department of Biology, University of Naples "Federico II", Complesso Universitario Di Monte S. Angelo, Via Cupa Nuova Cinthia 21, Naples, 80126, Italy
- Institute of Biosciences and BioResources, National Research Council of Italy, Via P. Castellino 111, Naples, 80131, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
- NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
| | - Beatrice Cobucci-Ponzano
- Institute of Biosciences and BioResources, National Research Council of Italy, Via P. Castellino 111, Naples, 80131, Italy
| | - Andrea Strazzulli
- Department of Biology, University of Naples "Federico II", Complesso Universitario Di Monte S. Angelo, Via Cupa Nuova Cinthia 21, Naples, 80126, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
- NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
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5
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Benatti ALT, Polizeli MDLTDM. Lignocellulolytic Biocatalysts: The Main Players Involved in Multiple Biotechnological Processes for Biomass Valorization. Microorganisms 2023; 11:microorganisms11010162. [PMID: 36677454 PMCID: PMC9864444 DOI: 10.3390/microorganisms11010162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/11/2022] [Accepted: 12/26/2022] [Indexed: 01/10/2023] Open
Abstract
Human population growth, industrialization, and globalization have caused several pressures on the planet's natural resources, culminating in the severe climate and environmental crisis which we are facing. Aiming to remedy and mitigate the impact of human activities on the environment, the use of lignocellulolytic enzymes for biofuel production, food, bioremediation, and other various industries, is presented as a more sustainable alternative. These enzymes are characterized as a group of enzymes capable of breaking down lignocellulosic biomass into its different monomer units, making it accessible for bioconversion into various products and applications in the most diverse industries. Among all the organisms that produce lignocellulolytic enzymes, microorganisms are seen as the primary sources for obtaining them. Therefore, this review proposes to discuss the fundamental aspects of the enzymes forming lignocellulolytic systems and the main microorganisms used to obtain them. In addition, different possible industrial applications for these enzymes will be discussed, as well as information about their production modes and considerations about recent advances and future perspectives in research in pursuit of expanding lignocellulolytic enzyme uses at an industrial scale.
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Archaea as a Model System for Molecular Biology and Biotechnology. Biomolecules 2023; 13:biom13010114. [PMID: 36671499 PMCID: PMC9855744 DOI: 10.3390/biom13010114] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Archaea represents the third domain of life, displaying a closer relationship with eukaryotes than bacteria. These microorganisms are valuable model systems for molecular biology and biotechnology. In fact, nowadays, methanogens, halophiles, thermophilic euryarchaeota, and crenarchaeota are the four groups of archaea for which genetic systems have been well established, making them suitable as model systems and allowing for the increasing study of archaeal genes' functions. Furthermore, thermophiles are used to explore several aspects of archaeal biology, such as stress responses, DNA replication and repair, transcription, translation and its regulation mechanisms, CRISPR systems, and carbon and energy metabolism. Extremophilic archaea also represent a valuable source of new biomolecules for biological and biotechnological applications, and there is growing interest in the development of engineered strains. In this review, we report on some of the most important aspects of the use of archaea as a model system for genetic evolution, the development of genetic tools, and their application for the elucidation of the basal molecular mechanisms in this domain of life. Furthermore, an overview on the discovery of new enzymes of biotechnological interest from archaea thriving in extreme environments is reported.
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7
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Ajeje SB, Hu Y, Song G, Peter SB, Afful RG, Sun F, Asadollahi MA, Amiri H, Abdulkhani A, Sun H. Thermostable Cellulases / Xylanases From Thermophilic and Hyperthermophilic Microorganisms: Current Perspective. Front Bioeng Biotechnol 2021; 9:794304. [PMID: 34976981 PMCID: PMC8715034 DOI: 10.3389/fbioe.2021.794304] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022] Open
Abstract
The bioconversion of lignocellulose into monosaccharides is critical for ensuring the continual manufacturing of biofuels and value-added bioproducts. Enzymatic degradation, which has a high yield, low energy consumption, and enhanced selectivity, could be the most efficient and environmentally friendly technique for converting complex lignocellulose polymers to fermentable monosaccharides, and it is expected to make cellulases and xylanases the most demanded industrial enzymes. The widespread nature of thermophilic microorganisms allows them to proliferate on a variety of substrates and release substantial quantities of cellulases and xylanases, which makes them a great source of thermostable enzymes. The most significant breakthrough of lignocellulolytic enzymes lies in lignocellulose-deconstruction by enzymatic depolymerization of holocellulose into simple monosaccharides. However, commercially valuable thermostable cellulases and xylanases are challenging to produce in high enough quantities. Thus, the present review aims at giving an overview of the most recent thermostable cellulases and xylanases isolated from thermophilic and hyperthermophilic microbes. The emphasis is on recent advancements in manufacturing these enzymes in other mesophilic host and enhancement of catalytic activity as well as thermostability of thermophilic cellulases and xylanases, using genetic engineering as a promising and efficient technology for its economic production. Additionally, the biotechnological applications of thermostable cellulases and xylanases of thermophiles were also discussed.
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Affiliation(s)
- Samaila Boyi Ajeje
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yun Hu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Guojie Song
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Sunday Bulus Peter
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Richmond Godwin Afful
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Fubao Sun
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Mohammad Ali Asadollahi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Hamid Amiri
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Ali Abdulkhani
- Department of Wood and Paper Science and Technology, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Haiyan Sun
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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Amin K, Tranchimand S, Benvegnu T, Abdel-Razzak Z, Chamieh H. Glycoside Hydrolases and Glycosyltransferases from Hyperthermophilic Archaea: Insights on Their Characteristics and Applications in Biotechnology. Biomolecules 2021; 11:1557. [PMID: 34827555 PMCID: PMC8615776 DOI: 10.3390/biom11111557] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/09/2021] [Accepted: 10/16/2021] [Indexed: 01/18/2023] Open
Abstract
Hyperthermophilic Archaea colonizing unnatural habitats of extremes conditions such as volcanoes and deep-sea hydrothermal vents represent an unmeasurable bioresource for enzymes used in various industrial applications. Their enzymes show distinct structural and functional properties and are resistant to extreme conditions of temperature and pressure where their mesophilic homologs fail. In this review, we will outline carbohydrate-active enzymes (CAZymes) from hyperthermophilic Archaea with specific focus on the two largest families, glycoside hydrolases (GHs) and glycosyltransferases (GTs). We will present the latest advances on these enzymes particularly in the light of novel accumulating data from genomics and metagenomics sequencing technologies. We will discuss the contribution of these enzymes from hyperthermophilic Archaea to industrial applications and put the emphasis on newly identifed enzymes. We will highlight their common biochemical and distinct features. Finally, we will overview the areas that remain to be explored to identify novel promising hyperthermozymes.
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Affiliation(s)
- Khadija Amin
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, Lebanese University, Mitein Street, Tripoli P.O. Box 210, Lebanon; (K.A.); (Z.A.-R.)
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France; (S.T.); (T.B.)
| | - Sylvain Tranchimand
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France; (S.T.); (T.B.)
| | - Thierry Benvegnu
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France; (S.T.); (T.B.)
| | - Ziad Abdel-Razzak
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, Lebanese University, Mitein Street, Tripoli P.O. Box 210, Lebanon; (K.A.); (Z.A.-R.)
- Faculty of Sciences, Lebanese University, Rafic Hariri Campus, Beirut P.O. Box 6573, Lebanon
| | - Hala Chamieh
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, Lebanese University, Mitein Street, Tripoli P.O. Box 210, Lebanon; (K.A.); (Z.A.-R.)
- Faculty of Sciences, Lebanese University, Rafic Hariri Campus, Beirut P.O. Box 6573, Lebanon
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9
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Thermostable cellulose saccharifying microbial enzymes: Characteristics, recent advances and biotechnological applications. Int J Biol Macromol 2021; 188:226-244. [PMID: 34371052 DOI: 10.1016/j.ijbiomac.2021.08.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/19/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022]
Abstract
Cellulases play a promising role in the bioconversion of renewable lignocellulosic biomass into fermentable sugars which are subsequently fermented to biofuels and other value-added chemicals. Besides biofuel industries, they are also in huge demand in textile, detergent, and paper and pulp industries. Low titres of cellulase production and processing are the main issues that contribute to high enzyme cost. The success of ethanol-based biorefinery depends on high production titres and the catalytic efficiency of cellulases functional at elevated temperatures with acid/alkali tolerance and the low cost. In view of their wider application in various industrial processes, stable cellulases that are active at elevated temperatures in the acidic-alkaline pH ranges, and organic solvents and salt tolerance would be useful. This review provides a recent update on the advances made in thermostable cellulases. Developments in their sources, characteristics and mechanisms are updated. Various methods such as rational design, directed evolution, synthetic & system biology and immobilization techniques adopted in evolving cellulases with ameliorated thermostability and characteristics are also discussed. The wide range of applications of thermostable cellulases in various industrial sectors is described.
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10
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Medvedeva S, Brandt D, Cvirkaite-Krupovic V, Liu Y, Severinov K, Ishino S, Ishino Y, Prangishvili D, Kalinowski J, Krupovic M. New insights into the diversity and evolution of the archaeal mobilome from three complete genomes of Saccharolobus shibatae. Environ Microbiol 2021; 23:4612-4630. [PMID: 34190379 DOI: 10.1111/1462-2920.15654] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/20/2021] [Accepted: 06/28/2021] [Indexed: 12/16/2022]
Abstract
Saccharolobus (formerly Sulfolobus) shibatae B12, isolated from a hot spring in Beppu, Japan in 1982, is one of the first hyperthermophilic and acidophilic archaeal species to be discovered. It serves as a natural host to the extensively studied spindle-shaped virus SSV1, a prototype of the Fuselloviridae family. Two additional Sa. shibatae strains, BEU9 and S38A, sensitive to viruses of the families Lipothrixviridae and Portogloboviridae, respectively, have been isolated more recently. However, none of the strains has been fully sequenced, limiting their utility for studies on archaeal biology and virus-host interactions. Here, we present the complete genome sequences of all three Sa. shibatae strains and explore the rich diversity of their integrated mobile genetic elements (MGE), including transposable insertion sequences, integrative and conjugative elements, plasmids, and viruses, some of which were also detected in the extrachromosomal form. Analysis of related MGEs in other Sulfolobales species and patterns of CRISPR spacer targeting revealed a complex network of MGE distributions, involving horizontal spread and relatively frequent host switching by MGEs over large phylogenetic distances, involving species of the genera Saccharolobus, Sulfurisphaera and Acidianus. Furthermore, we characterize a remarkable case of a virus-to-plasmid transition, whereby a fusellovirus has lost the genes encoding for the capsid proteins, while retaining the replication module, effectively becoming a plasmid.
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Affiliation(s)
- Sofia Medvedeva
- Archaeal Virology Unit, Institut Pasteur, Paris, 75015, France.,Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - David Brandt
- Center for Biotechnology, Universität Bielefeld, Bielefeld, 33615, Germany
| | | | - Ying Liu
- Archaeal Virology Unit, Institut Pasteur, Paris, 75015, France
| | - Konstantin Severinov
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.,Waksman Institute, Rutgers University, Piscataway, NJ, 08854, USA.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - David Prangishvili
- Archaeal Virology Unit, Institut Pasteur, Paris, 75015, France.,Ivane Javakhishvili Tbilisi State University, Tbilisi, 0179, Georgia
| | - Jörn Kalinowski
- Center for Biotechnology, Universität Bielefeld, Bielefeld, 33615, Germany
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, 75015, France
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11
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A Computational Method to Predict Effects of Residue Mutations on the Catalytic Efficiency of Hydrolases. Catalysts 2021. [DOI: 10.3390/catal11020286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
With scientific and technological advances, growing research has focused on engineering enzymes that acquire enhanced efficiency and activity. Thereinto, computer-based enzyme modification makes up for the time-consuming and labor-intensive experimental methods and plays a significant role. In this study, for the first time, we collected and manually curated a data set for hydrolases mutation, including structural information of enzyme-substrate complexes, mutated sites and Kcat/Km obtained from vitro assay. We further constructed a classification model using the random forest algorithm to predict the effects of residue mutations on catalytic efficiency (increase or decrease) of hydrolases. This method has achieved impressive performance on a blind test set with the area under the receiver operating characteristic curve of 0.86 and the Matthews Correlation Coefficient of 0.659. Our results demonstrate that computational mutagenesis has an instructive effect on enzyme modification, which may expedite the design of engineering hydrolases.
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Suleiman M, Krüger A, Antranikian G. Biomass-degrading glycoside hydrolases of archaeal origin. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:153. [PMID: 32905355 PMCID: PMC7469102 DOI: 10.1186/s13068-020-01792-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/22/2020] [Indexed: 06/11/2023]
Abstract
During the last decades, the impact of hyperthermophiles and their enzymes has been intensively investigated for implementation in various high-temperature biotechnological processes. Biocatalysts of hyperthermophiles have proven to show extremely high thermo-activities and thermo-stabilities and are identified as suitable candidates for numerous industrial processes with harsh conditions, including the process of an efficient plant biomass pretreatment and conversion. Already-characterized archaea-originated glycoside hydrolases (GHs) have shown highly impressive features and numerous enzyme characterizations indicated that these biocatalysts show maximum activities at a higher temperature range compared to bacterial ones. However, compared to bacterial biomass-degrading enzymes, the number of characterized archaeal ones remains low. To discover new promising archaeal GH candidates, it is necessary to study in detail the microbiology and enzymology of extremely high-temperature habitats, ranging from terrestrial to marine hydrothermal systems. State-of-the art technologies such as sequencing of genomes and metagenomes and automated binning of genomes out of metagenomes, combined with classical microbiological culture-dependent approaches, have been successfully performed to detect novel promising biomass-degrading hyperthermozymes. In this review, we will focus on the detection, characterization and similarities of archaeal GHs and their unique characteristics. The potential of hyperthermozymes and their impact on high-temperature industrial applications have not yet been exhausted.
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Affiliation(s)
- Marcel Suleiman
- Institute of Technical Microbiology, University of Technology Hamburg, Hamburg, Germany
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Anna Krüger
- Institute of Technical Microbiology, University of Technology Hamburg, Hamburg, Germany
| | - Garabed Antranikian
- Institute of Technical Microbiology, University of Technology Hamburg, Hamburg, Germany
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Akram F, Haq IU. Overexpression and characterization of TnCel12B, a hyperthermophilic GH12 endo-1,4-β-glucanase cloned from Thermotoga naphthophila RKU-10 T. Anal Biochem 2020; 599:113741. [PMID: 32339490 DOI: 10.1016/j.ab.2020.113741] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 11/26/2022]
Abstract
A putative cellulolytic gene (825 bp) from Thermotoga naphthophila RKU-10T was overexpressed as an active soluble endo-1,4-β-glucanase (TnCel12B), belongs to glycoside hydrolase family 12 (GH12), in a mesophilic expression host. Heterologous expression and engineered bacterial cell mass was improved through specific strategies (induction and cultivation). Hence, intracellular activity of TnCel12B was enhanced in ZYBM9 modified medium (pH 7.0) by 8.38 and 6.25 fold with lactose (200 mM) and IPTG (0.5 mM) induction, respectively; and 6.95 fold was increased in ZYP-5052 auto-inducing medium after 8 h incubation at 26 °C (200 rev min-1). Purified TnCel12B with a molecular weight of ~32 kDa, was optimally active at 90 °C and pH 6.0; and exhibited prodigious stability over a wide range of temperature (50-85 °C) and pH (5.0-9.0) for 8 h TnCel12B displayed great resistance towards different chemical modulators, though activity was improved by Mg2+, Zn2+, Pb2+ and Ca2+. Purified TnCel12B had affinity with various substrates but peak activity was observed toward barley β-glucan (1664 U mg-1) and carboxymethyl cellulose (736 U mg-1). The values of Km, Vmax, kcat, and kcatKm-1 were found to be 4.63 mg mL-1, 916 μmol mg-1min-1, 1326.7 s-1 and 286.54 mL mg-1 s-1, respectively using CMC substrate. All noteworthy features of TnCel12B make it an appropriate industrial candidate for bioethanol production and various other potential applications.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, GC University, Lahore, 54000, Pakistan.
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, GC University, Lahore, 54000, Pakistan.
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Zayulina KS, Kochetkova TV, Piunova UE, Ziganshin RH, Podosokorskaya OA, Kublanov IV. Novel Hyperthermophilic Crenarchaeon Thermofilum adornatum sp. nov. Uses GH1, GH3, and Two Novel Glycosidases for Cellulose Hydrolysis. Front Microbiol 2020; 10:2972. [PMID: 31998263 PMCID: PMC6965361 DOI: 10.3389/fmicb.2019.02972] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 12/10/2019] [Indexed: 01/16/2023] Open
Abstract
A novel hyperthermophilic, anaerobic filamentous archaeon, Thermofilum adornatum strain 1910bT, is capable of growing with cellulose as its sole carbon and energy source. This strain was isolated from a terrestrial hot spring in Kamchatka, Russia. The isolate 1910bT grew optimally at a temperature of 80°C and a pH of 5.5-6.0, producing cell-bound inducible cellulases. During genome analysis, genes, encoding various glycosidases (GHs) involved in oligo- and polysaccharide hydrolysis and genes for the fermentation of sugars were identified. No homologs of currently known cellulase families were found among the GHs encoded by the 1910bT genome, suggesting that novel proteins are involved. To figure this out, a proteomic analysis of cells grown on cellulose or pyruvate (as a control) was performed. Both in-depth genomic and proteomic analyses revealed four proteins (Cel25, Cel30, Cel40, and Cel45) that were the most likely to be involved in the cellulose hydrolysis in this archaeon. Two of these proteins (Cel30 and Cel45) were hypothetical according to genome analysis, while the other two (Cel25 and Cel40) have GH3 and GH1 domains, respectively. The respective genes were heterologously expressed in Escherichia coli BL21 (DE3), and enzymatic activities of recombinant proteins were measured with carboxymethyl cellulose (CMC), Avicel and cellobiose as substrates. It was revealed that the Cel30 and Cel25 proteins were likely exoglucanases with side beta-glucosidase and endoglucanase activities, that Cel40 was a multifunctional glucanase capable of hydrolyzing beta-1,4-glucosides of various lengths, and that Cel45 was an endoglucanase with side exoglucanase activity. Taking into account that the cellulolytic activity of T. adornatum 1910bT surface protein fractions was inducible, that recombinant Cel25 and Cel30 were much less active than Cel40 and Cel45, and that their gene expressions were (almost) non-induced by CMC, we suggest that Cel40 and Cel45 play a major role in the degradation of cellulose, while Cel25 and Cel30 act only as accessory enzymes.
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Affiliation(s)
- Kseniya S. Zayulina
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V. Kochetkova
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Ulyana E. Piunova
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Olga A. Podosokorskaya
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya V. Kublanov
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
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Identification and characterization of an Endo-glucanase secreted from cellulolytic Escherichia coli ZH-4. BMC Biotechnol 2019; 19:63. [PMID: 31455320 PMCID: PMC6712877 DOI: 10.1186/s12896-019-0556-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 08/22/2019] [Indexed: 12/20/2022] Open
Abstract
Background In the previous study, the cellulolytic Escherichia coli ZH-4 isolated from bovine rumen was found to show extracellular cellulase activity and could degrade cellulose in the culture. The goal of this work was to identify and characterize the secreted cellulase of E. coli ZH-4. It will be helpful to re-understand E. coli and extend its application in industry. Results A secreted cellulase was confirmed to be endo-glucanase BcsZ which was encoded by bcsZ gene and located in the cellulose synthase operon bcsABZC in cellulolytic E. coli ZH-4 by western blotting. Characterization of BcsZ indicated that a broad range of pH and temperature tolerance with optima at pH 6.0 and 50 °C, respectively. The apparent Michaelis–Menten constant (Km) and maximal reaction rate (Vmax) for BcsZ were 8.86 mg/mL and 0.3 μM/min·mg, respectively. Enzyme activity of BcsZ was enhanced by Mg2+ and inhibited by Zn2+, Cu2+ and Fe3+. BcsZ could hydrolyze carboxymethylcellulose (CMC) to produce cello-oligosaccharides, cellotriose, cellobiose and glucose. Conclusions It is confirmed that extracellular cellulolytic capability of E. coli ZH-4 was attributed to BcsZ, which explained why E. coli ZH-4 can grow on cellulose. The endo-glucanase BcsZ from E. coli-ZH4 has some new characteristics which will extend the understanding of endo-glucanase. Analysis of the secretion characteristics of BcsZ provided a great reference for applying E. coli in multiple industrial fields.
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