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Kuddus M, Roohi, Bano N, Sheik GB, Joseph B, Hamid B, Sindhu R, Madhavan A. Cold-active microbial enzymes and their biotechnological applications. Microb Biotechnol 2024; 17:e14467. [PMID: 38656876 PMCID: PMC11042537 DOI: 10.1111/1751-7915.14467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/26/2024] Open
Abstract
Microorganisms known as psychrophiles/psychrotrophs, which survive in cold climates, constitute majority of the biosphere on Earth. Their capability to produce cold-active enzymes along with other distinguishing characteristics allows them to survive in the cold environments. Due to the relative ease of large-scale production compared to enzymes from plants and animals, commercial uses of microbial enzyme are alluring. The ocean depths, polar, and alpine regions, which make up over 85% of the planet, are inhabited to cold ecosystems. Microbes living in these regions are important for their metabolic contribution to the ecosphere as well as for their enzymes, which may have potential industrial applications. Cold-adapted microorganisms are a possible source of cold-active enzymes that have high catalytic efficacy at low and moderate temperatures at which homologous mesophilic enzymes are not active. Cold-active enzymes can be used in a variety of biotechnological processes, including food processing, additives in the detergent and food industries, textile industry, waste-water treatment, biopulping, environmental bioremediation in cold climates, biotransformation, and molecular biology applications with great potential for energy savings. Genetically manipulated strains that are suitable for producing a particular cold-active enzyme would be crucial in a variety of industrial and biotechnological applications. The potential advantage of cold-adapted enzymes will probably lead to a greater annual market than for thermo-stable enzymes in the near future. This review includes latest updates on various microbial source of cold-active enzymes and their biotechnological applications.
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Affiliation(s)
- Mohammed Kuddus
- Department of Biochemistry, College of MedicineUniversity of HailHailSaudi Arabia
| | - Roohi
- Protein Research Laboratory, Department of BioengineeringIntegral UniversityLucknowIndia
| | - Naushin Bano
- Protein Research Laboratory, Department of BioengineeringIntegral UniversityLucknowIndia
| | | | - Babu Joseph
- Department of Clinical Laboratory Sciences, College of Applied Medical SciencesShaqra UniversityShaqraSaudi Arabia
| | - Burhan Hamid
- Center of Research for DevelopmentUniversity of KashmirSrinagarIndia
| | - Raveendran Sindhu
- Department of Food TechnologyTKM Institute of TechnologyKollamKeralaIndia
| | - Aravind Madhavan
- School of BiotechnologyAmrita Vishwa Vidyapeetham, AmritapuriKollamKeralaIndia
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2
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Liu P, Chen Y, Ma C, Ouyang J, Zheng Z. β-Galactosidase: a traditional enzyme given multiple roles through protein engineering. Crit Rev Food Sci Nutr 2023:1-20. [PMID: 38108277 DOI: 10.1080/10408398.2023.2292282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
β-Galactosidases are crucial carbohydrate-active enzymes that naturally catalyze the hydrolysis of galactoside bonds in oligo- and disaccharides. These enzymes are commonly used to degrade lactose and produce low-lactose and lactose-free dairy products that are beneficial for lactose-intolerant people. β-galactosidases exhibit transgalactosylation activity, and they have been employed in the synthesis of galactose-containing compounds such as galactooligosaccharides. However, most β-galactosidases have intrinsic limitations, such as low transglycosylation efficiency, significant product inhibition effects, weak thermal stability, and a narrow substrate spectrum, which greatly hinder their applications. Enzyme engineering offers a solution for optimizing their catalytic performance. The study of the enzyme's structure paves the way toward explaining catalytic mechanisms and increasing the efficiency of enzyme engineering. In this review, the structure features of β-galactosidases from different glycosyl hydrolase families and the catalytic mechanisms are summarized in detail to offer guidance for protein engineering. The properties and applications of β-galactosidases are discussed. Additionally, the latest progress in β-galactosidase engineering and the strategies employed are highlighted. Based on the combined analysis of structure information and catalytic mechanisms, the ultimate goal of this review is to furnish a thorough direction for β-galactosidases engineering and promote their application in the food and dairy industries.
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Affiliation(s)
- Peng Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, People's Republic of China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Yuehua Chen
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Jia Ouyang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Zhaojuan Zheng
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
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3
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Nowak JS, Otzen DE. Helping proteins come in from the cold: 5 burning questions about cold-active enzymes. BBA ADVANCES 2023; 5:100104. [PMID: 38162634 PMCID: PMC10755280 DOI: 10.1016/j.bbadva.2023.100104] [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: 07/10/2023] [Revised: 08/21/2023] [Accepted: 09/05/2023] [Indexed: 01/03/2024] Open
Abstract
Enzymes from psychrophilic (cold-loving) organisms have attracted considerable interest over the past decades for their potential in various low-temperature industrial processes. However, we still lack large-scale commercialization of their activities. Here, we review their properties, limitations and potential. Our review is structured around answers to 5 central questions: 1. How do cold-active enzymes achieve high catalytic rates at low temperatures? 2. How is protein flexibility connected to cold-activity? 3. What are the sequence-based and structural determinants for cold-activity? 4. How does the thermodynamic stability of psychrophilic enzymes reflect their cold-active capabilities? 5. How do we effectively identify novel cold-active enzymes, and can we apply them in an industrial context? We conclude that emerging screening technologies combined with big-data handling and analysis make it reasonable to expect a bright future for our understanding and exploitation of cold-active enzymes.
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Affiliation(s)
- Jan Stanislaw Nowak
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK – 8000 Aarhus C, Denmark
| | - Daniel E. Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK – 8000 Aarhus C, Denmark
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4
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Liu Y, Zhang N, Ma J, Zhou Y, Wei Q, Tian C, Fang Y, Zhong R, Chen G, Zhang S. Advances in cold-adapted enzymes derived from microorganisms. Front Microbiol 2023; 14:1152847. [PMID: 37180232 PMCID: PMC10169661 DOI: 10.3389/fmicb.2023.1152847] [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: 01/28/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023] Open
Abstract
Cold-adapted enzymes, produced in cold-adapted organisms, are a class of enzyme with catalytic activity at low temperatures, high temperature sensitivity, and the ability to adapt to cold stimulation. These enzymes are largely derived from animals, plants, and microorganisms in polar areas, mountains, and the deep sea. With the rapid development of modern biotechnology, cold-adapted enzymes have been implemented in human and other animal food production, the protection and restoration of environments, and fundamental biological research, among other areas. Cold-adapted enzymes derived from microorganisms have attracted much attention because of their short production cycles, high yield, and simple separation and purification, compared with cold-adapted enzymes derived from plants and animals. In this review we discuss various types of cold-adapted enzyme from cold-adapted microorganisms, along with associated applications, catalytic mechanisms, and molecular modification methods, to establish foundation for the theoretical research and application of cold-adapted enzymes.
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Affiliation(s)
- Yehui Liu
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Na Zhang
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Jie Ma
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Yuqi Zhou
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Qiang Wei
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yi Fang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Rongzhen Zhong
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Guang Chen
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Sitong Zhang
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
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5
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Masnoddin M, Ling CMWV, Yusof NA. Functional Analysis of Conserved Hypothetical Proteins from the Antarctic Bacterium, Pedobacter cryoconitis Strain BG5 Reveals Protein Cold Adaptation and Thermal Tolerance Strategies. Microorganisms 2022; 10:microorganisms10081654. [PMID: 36014072 PMCID: PMC9415557 DOI: 10.3390/microorganisms10081654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/04/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
Pedobacter cryoconitis BG5 is an obligate psychrophilic bacterium that was first isolated on King George Island, Antarctica. Over the last 50 years, the West Antarctic, including King George Island, has been one of the most rapidly warming places on Earth, hence making it an excellent area to measure the resilience of living species in warmed areas exposed to the constantly changing environment due to climate change. This bacterium encodes a genome of approximately 5694 protein-coding genes. However, 35% of the gene models for this species are found to be hypothetical proteins (HP). In this study, three conserved HP genes of P. cryoconitis, designated pcbg5hp1, pcbg5hp2 and pcbg5hp12, were cloned and the proteins were expressed, purified and their functions and structures were evaluated. Real-time quantitative PCR analysis revealed that these genes were expressed constitutively, suggesting a potentially important role where the expression of these genes under an almost constant demand might have some regulatory functions in thermal stress tolerance. Functional analysis showed that these proteins maintained their activities at low and moderate temperatures. Meanwhile, a low citrate synthase aggregation at 43 °C in the presence of PCBG5HP1 suggested the characteristics of chaperone activity. Furthermore, our comparative structural analysis demonstrated that the HPs exhibited cold-adapted traits, most notably increased flexibility in their 3D structures compared to their counterparts. Concurrently, the presence of a disulphide bridge and aromatic clusters was attributed to PCBG5HP1’s unusual protein stability and chaperone activity. Thus, this suggested that the HPs examined in this study acquired strategies to maintain a balance between molecular stability and structural flexibility. Conclusively, this study has established the structure–function relationships of the HPs produced by P. cryoconitis and provided crucial experimental evidence indicating their importance in thermal stress response.
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Affiliation(s)
- Makdi Masnoddin
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia
- Preparatory Centre for Science and Technology, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia
| | | | - Nur Athirah Yusof
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia
- Correspondence:
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6
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Cold-active enzymes in the dairy industry: Insight into cold adaption mechanisms and their applications. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Arthrobacter terrae sp. nov., a psychrophilic actinobacterium with multi copies of capA gene isolated from Antarctic soil. Antonie van Leeuwenhoek 2022; 115:635-644. [PMID: 35338420 DOI: 10.1007/s10482-022-01727-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/06/2022] [Indexed: 10/18/2022]
Abstract
A Gram-staining-positive, non-spore-forming, non-flagellated, ellipsoidal, strain Z1-20 T belonging to the genus Arthrobacter was isolated from a soil sample collected from the Zhongshan station, Antarctic. Phylogenetic analysis of the 16S rRNA gene sequences and phylogenetic analysis revealed that strain Z1-20 T formed a unique single cluster in the genus Arthrobacter and shared high 16S rRNA sequence similarities of 97.1% and 96.9% with A. glacialis HLT2-12-2 T and A. psychrochitiniphilus GP3T, respectively. Values of Digital DNA-DNA hybridization (dDDH) between strain Z1-20 T against A. glacialis HLT2-12-2 T and A. psychrochitiniphilus GP3T were 20.3% and 13.8%, respectively. Average nucleotide identity (ANI) score between strain Z1-20 T against A. glacialis HLT2-12-2 T and A. psychrochitiniphilus GP3T were 72.5% and 72.1%, respectively. Genes for the synthesis of the osmoprotectant glycine betaine and higher copies of capA gene encoding cold shock protein were found in genome of Z1-20 T that may help Z1-20 T in cold-adaptation. Strain Z1-20 T comprised lysine as the diagnostic diamino acid. Based on the results of phylogenetic, phenotypic and chemotaxonomic features, strain Z1-20 T represents a novel species of a novel taxon of genus Arthrobacter, for which the name Arthrobacter terrae gen. nov., sp. nov. is proposed.
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8
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de Albuquerque TL, de Sousa M, Gomes E Silva NC, Girão Neto CAC, Gonçalves LRB, Fernandez-Lafuente R, Rocha MVP. β-Galactosidase from Kluyveromyces lactis: Characterization, production, immobilization and applications - A review. Int J Biol Macromol 2021; 191:881-898. [PMID: 34571129 DOI: 10.1016/j.ijbiomac.2021.09.133] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/30/2021] [Accepted: 09/20/2021] [Indexed: 01/06/2023]
Abstract
A review on the enzyme β-galactosidase from Kluyveromyces lactis is presented, from the perspective of its structure and mechanisms of action, the main catalyzed reactions, the key factors influencing its activity, and selectivity, as well as the main techniques used for improving the biocatalyst functionality. Particular attention was given to the discussion of hydrolysis, transglycosylation, and galactosylation reactions, which are commonly mediated by this enzyme. In addition, the products generated from these processes were highlighted. Finally, biocatalyst improvement techniques are also discussed, such as enzyme immobilization and protein engineering. On these topics, the most recent immobilization strategies are presented, emphasizing processes that not only allow the recovery of the biocatalyst but also deliver enzymes that show better resistance to high temperatures, chemicals, and inhibitors. In addition, genetic engineering techniques to improve the catalytic properties of the β-galactosidases were reported. This review gathers information to allow the development of biocatalysts based on the β-galactosidase enzyme from K. lactis, aiming to improve existing bioprocesses or develop new ones.
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Affiliation(s)
- Tiago Lima de Albuquerque
- Federal University of Ceará, Technology Center, Chemical Engineering Department, Campus do Pici, Bloco 709, 60 455 - 760 Fortaleza, Ceará, Brazil
| | - Marylane de Sousa
- Federal University of Ceará, Technology Center, Chemical Engineering Department, Campus do Pici, Bloco 709, 60 455 - 760 Fortaleza, Ceará, Brazil
| | - Natan Câmara Gomes E Silva
- Federal University of Ceará, Technology Center, Chemical Engineering Department, Campus do Pici, Bloco 709, 60 455 - 760 Fortaleza, Ceará, Brazil
| | - Carlos Alberto Chaves Girão Neto
- Federal University of Ceará, Technology Center, Chemical Engineering Department, Campus do Pici, Bloco 709, 60 455 - 760 Fortaleza, Ceará, Brazil
| | - Luciana Rocha Barros Gonçalves
- Federal University of Ceará, Technology Center, Chemical Engineering Department, Campus do Pici, Bloco 709, 60 455 - 760 Fortaleza, Ceará, Brazil
| | - Roberto Fernandez-Lafuente
- Instituto de Catálisis y Petroleoquímica - CSIC, Campus of excellence UAM-CSIC, Cantoblanco, 28049 Madrid, Spain; Center of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Maria Valderez Ponte Rocha
- Federal University of Ceará, Technology Center, Chemical Engineering Department, Campus do Pici, Bloco 709, 60 455 - 760 Fortaleza, Ceará, Brazil.
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9
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Fuchs T, Melcher F, Rerop ZS, Lorenzen J, Shaigani P, Awad D, Haack M, Prem SA, Masri M, Mehlmer N, Brueck TB. Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology. Microb Cell Fact 2021; 20:205. [PMID: 34711240 PMCID: PMC8555327 DOI: 10.1186/s12934-021-01692-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/05/2021] [Indexed: 11/30/2022] Open
Abstract
Background The oleaginous yeast Cutaneotrichosporon oleaginosus represents one of the most promising microbial platforms for resource-efficient and scalable lipid production, with the capacity to accept a wide range of carbohydrates encapsulated in complex biomass waste or lignocellulosic hydrolysates. Currently, data related to molecular aspects of the metabolic utilisation of oligomeric carbohydrates are sparse. In addition, comprehensive proteomic information for C. oleaginosus focusing on carbohydrate metabolism is not available. Results In this study, we conducted a systematic analysis of carbohydrate intake and utilisation by C. oleaginosus and investigated the influence of different di- and trisaccharide as carbon sources. Changes in the cellular growth and morphology could be observed, depending on the selected carbon source. The greatest changes in morphology were observed in media containing trehalose. A comprehensive proteomic analysis of secreted, cell wall-associated, and cytoplasmatic proteins was performed, which highlighted differences in the composition and quantity of secreted proteins, when grown on different disaccharides. Based on the proteomic data, we performed a relative quantitative analysis of the identified proteins (using glucose as the reference carbon source) and observed carbohydrate-specific protein distributions. When using cellobiose or lactose as the carbon source, we detected three- and five-fold higher diversity in terms of the respective hydrolases released. Furthermore, the analysis of the secreted enzymes enabled identification of the motif with the consensus sequence LALL[LA]L[LA][LA]AAAAAAA as a potential signal peptide. Conclusions Relative quantification of spectral intensities from crude proteomic datasets enabled the identification of new enzymes and provided new insights into protein secretion, as well as the molecular mechanisms of carbo-hydrolases involved in the cleavage of the selected carbon oligomers. These insights can help unlock new substrate sources for C. oleaginosus, such as low-cost by-products containing difficult to utilize carbohydrates. In addition, information regarding the carbo-hydrolytic potential of C. oleaginosus facilitates a more precise engineering approach when using targeted genetic approaches. This information could be used to find new and more cost-effective carbon sources for microbial lipid production by the oleaginous yeast C. oleaginosus. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01692-2.
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Affiliation(s)
- Tobias Fuchs
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Felix Melcher
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Zora Selina Rerop
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Jan Lorenzen
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Pariya Shaigani
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Dania Awad
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Martina Haack
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Sophia Alice Prem
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Mahmoud Masri
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Norbert Mehlmer
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany.
| | - Thomas B Brueck
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany.
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Zhang Y, Ding HT, Jiang WX, Zhang X, Cao HY, Wang JP, Li CY, Huang F, Zhang XY, Chen XL, Zhang YZ, Li PY. Active site architecture of an acetyl xylan esterase indicates a novel cold adaptation strategy. J Biol Chem 2021; 297:100841. [PMID: 34058201 PMCID: PMC8253974 DOI: 10.1016/j.jbc.2021.100841] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/20/2021] [Accepted: 05/26/2021] [Indexed: 11/18/2022] Open
Abstract
SGNH-type acetyl xylan esterases (AcXEs) play important roles in marine and terrestrial xylan degradation, which are necessary for removing acetyl side groups from xylan. However, only a few cold-adapted AcXEs have been reported, and the underlying mechanisms for their cold adaptation are still unknown because of the lack of structural information. Here, a cold-adapted AcXE, AlAXEase, from the Arctic marine bacterium Arcticibacterium luteifluviistationis SM1504T was characterized. AlAXEase could deacetylate xylooligosaccharides and xylan, which, together with its homologs, indicates a novel SGNH-type carbohydrate esterase family. AlAXEase showed the highest activity at 30 °C and retained over 70% activity at 0 °C but had unusual thermostability with a Tm value of 56 °C. To explain the cold adaption mechanism of AlAXEase, we next solved its crystal structure. AlAXEase has similar noncovalent stabilizing interactions to its mesophilic counterpart at the monomer level and forms stable tetramers in solutions, which may explain its high thermostability. However, a long loop containing the catalytic residues Asp200 and His203 in AlAXEase was found to be flexible because of the reduced stabilizing hydrophobic interactions and increased destabilizing asparagine and lysine residues, leading to a highly flexible active site. Structural and enzyme kinetic analyses combined with molecular dynamics simulations at different temperatures revealed that the flexible catalytic loop contributes to the cold adaptation of AlAXEase by modulating the distance between the catalytic His203 in this loop and the nucleophilic Ser32. This study reveals a new cold adaption strategy adopted by the thermostable AlAXEase, shedding light on the cold adaption mechanisms of AcXEs.
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Affiliation(s)
- Yi Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hai-Tao Ding
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Wen-Xin Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xia Zhang
- Department of Molecular Biology, Qingdao Vland Biotech Inc, Qingdao, China
| | - Hai-Yan Cao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jing-Ping Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Chun-Yang Li
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Feng Huang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China; State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
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11
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Benešová E, Šućur Z, Těšínský M, Spiwok V, Lipovová P. Transglycosylation abilities of β-d-galactosidases from GH family 2. 3 Biotech 2021; 11:168. [PMID: 33816045 DOI: 10.1007/s13205-021-02715-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
The ability to predict the transglycosylation activity of glycosidases by in silico analysis was investigated. The transglycosylation abilities of 7 different β-d-galactosidases from GH family 2 were tested experimentally using 7 different acceptors and p-nitrophenyl-β-d-galactopyranoside as a donor of galactosyl moiety. Similar transglycosylation abilities were confirmed for all enzymes originating from bacteria belonging to Enterobacteriaceae, which were able to use all tested acceptor molecules. Higher acceptor selectivity was observed for all others used bacterial strains. Structure models of all enzymes were constructed using homology modeling. Ligand-docking method was used for enzymes-transglycosylation products models construction and evaluation. Results obtained by in silico analysis were compared with results arisen out of experimental testing. The experiments confirmed that significant differences in transglycosylation abilities are caused by small differences in active sites composition of analyzed enzymes. According to obtained result, it is possible to conclude that homology modeling may serve as a quick starting point for detection or exclusion of enzymes with defined transglycosylation abilities, which can be used for subsequent synthesis of e.g., pharmaceutically interesting glycosides. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02715-w.
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Affiliation(s)
- Eva Benešová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28 Czech Republic
| | - Zoran Šućur
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28 Czech Republic
| | - Miroslav Těšínský
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28 Czech Republic
| | - Vojtěch Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28 Czech Republic
| | - Petra Lipovová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28 Czech Republic
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12
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Mangiagalli M, Lotti M. Cold-Active β-Galactosidases: Insight into Cold Adaption Mechanisms and Biotechnological Exploitation. Mar Drugs 2021; 19:md19010043. [PMID: 33477853 PMCID: PMC7832830 DOI: 10.3390/md19010043] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 01/22/2023] Open
Abstract
β-galactosidases (EC 3.2.1.23) catalyze the hydrolysis of β-galactosidic bonds in oligosaccharides and, under certain conditions, transfer a sugar moiety from a glycosyl donor to an acceptor. Cold-active β-galactosidases are identified in microorganisms endemic to permanently low-temperature environments. While mesophilic β-galactosidases are broadly studied and employed for biotechnological purposes, the cold-active enzymes are still scarcely explored, although they may prove very useful in biotechnological processes at low temperature. This review covers several issues related to cold-active β-galactosidases, including their classification, structure and molecular mechanisms of cold adaptation. Moreover, their applications are discussed, focusing on the production of lactose-free dairy products as well as on the valorization of cheese whey and the synthesis of glycosyl building blocks for the food, cosmetic and pharmaceutical industries.
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13
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Rutkiewicz M, Wanarska M, Bujacz A. Mapping the Transglycosylation Relevant Sites of Cold-Adapted β-d-Galactosidase from Arthrobacter sp. 32cB. Int J Mol Sci 2020; 21:E5354. [PMID: 32731412 PMCID: PMC7432029 DOI: 10.3390/ijms21155354] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 11/16/2022] Open
Abstract
β-Galactosidase from Arthrobacter sp. 32cB (ArthβDG) is a cold-adapted enzyme able to catalyze hydrolysis of β-d-galactosides and transglycosylation reaction, where galactosyl moiety is being transferred onto an acceptor larger than a water molecule. Mutants of ArthβDG: D207A and E517Q were designed to determine the significance of specific residues and to enable formation of complexes with lactulose and sucrose and to shed light onto the structural basis of the transglycosylation reaction. The catalytic assays proved loss of function mutation E517 into glutamine and a significant drop of activity for mutation of D207 into alanine. Solving crystal structures of two new mutants, and new complex structures of previously presented mutant E441Q enables description of introduced changes within active site of enzyme and determining the importance of mutated residues for active site size and character. Furthermore, usage of mutants with diminished and abolished enzymatic activity enabled solving six complex structures with galactose, lactulose or sucrose bounds. As a result, not only the galactose binding sites were mapped on the enzyme's surface but also the mode of lactulose, product of transglycosylation reaction, and binding within the enzyme's active site were determined and the glucopyranose binding site in the distal of active site was discovered. The latter two especially show structural details of transglycosylation, providing valuable information that may be used for engineering of ArthβDG or other analogous galactosidases belonging to GH2 family.
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Affiliation(s)
- Maria Rutkiewicz
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland;
- Macromolecular Structure and Interaction, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Marta Wanarska
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland;
| | - Anna Bujacz
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland;
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14
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Li D, Li S, Wu Y, Jin M, Zhou Y, Wang Y, Chen X, Han Y. Cloning and Characterization of a New β-Galactosidase from Alteromonas sp. QD01 and Its Potential in Synthesis of Galacto-Oligosaccharides. Mar Drugs 2020; 18:md18060312. [PMID: 32545859 PMCID: PMC7344425 DOI: 10.3390/md18060312] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/10/2020] [Accepted: 06/10/2020] [Indexed: 12/11/2022] Open
Abstract
As prebiotics, galacto-oligosaccharides (GOSs) can improve the intestinal flora and have important applications in medicine. β-galactosidases could promote the synthesis of GOSs in lactose and catalyze the hydrolysis of lactose. In this study, a new β-galactosidase gene (gal2A), which belongs to the glycoside hydrolase family 2, was cloned from marine bacterium Alteromonas sp. QD01 and expressed in Escherichia coli. The molecular weight of Gal2A was 117.07 kDa. The optimal pH and temperature of Gal2A were 8.0 and 40 °C, respectively. At the same time, Gal2A showed wide pH stability in the pH range of 6.0–9.5, which is suitable for lactose hydrolysis in milk. Most metal ions promoted the activity of Gal2A, especially Mn2+ and Mg2+. Importantly, Gal2A exhibited high transglycosylation activity, which can catalyze the formation of GOS from milk and lactose. These characteristics indicated that Gal2A may be ideal for producing GOSs and lactose-reducing dairy products.
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15
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Malecki PH, Bejger M, Rypniewski W, Vorgias CE. The Crystal Structure of a Streptomyces thermoviolaceus Thermophilic Chitinase Known for Its Refolding Efficiency. Int J Mol Sci 2020; 21:ijms21082892. [PMID: 32326166 PMCID: PMC7215727 DOI: 10.3390/ijms21082892] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 12/27/2022] Open
Abstract
Analyzing the structure of proteins from extremophiles is a promising way to study the rules governing the protein structure, because such proteins are results of structural and functional optimization under well-defined conditions. Studying the structure of chitinases addresses an interesting aspect of enzymology, because chitin, while being the world’s second most abundant biopolymer, is also a recalcitrant substrate. The crystal structure of a thermostable chitinase from Streptomyces thermoviolaceus (StChi40) has been solved revealing a β/α-barrel (TIM-barrel) fold with an α+β insertion domain. This is the first chitinase structure of the multi-chitinase system of S. thermoviolaceus. The protein is also known to refold efficiently after thermal or chemical denaturation. StChi40 is structurally close to the catalytic domain of psychrophilic chitinase B from Arthrobacter TAD20. Differences are noted in comparison to the previously examined chitinases, particularly in the substrate-binding cleft. A comparison of the thermophilic enzyme with its psychrophilic homologue revealed structural features that could be attributed to StChi40’s thermal stability: compactness of the structure with trimmed surface loops and unique disulfide bridges, one of which is additionally stabilized by S–π interactions with aromatic rings. Uncharacteristically for thermophilic proteins, StChi40 has fewer salt bridges than its mesophilic and psychrophilic homologues.
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Affiliation(s)
- Piotr H. Malecki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; (P.H.M.); (M.B.)
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; (P.H.M.); (M.B.)
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; (P.H.M.); (M.B.)
- Correspondence:
| | - Constantinos E. Vorgias
- Department of Biology, Section of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 15701 Zografou, Greece;
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16
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Rutkiewicz M, Bujacz A, Wanarska M, Wierzbicka-Wos A, Cieslinski H. Active Site Architecture and Reaction Mechanism Determination of Cold Adapted β-d-galactosidase from Arthrobacter sp. 32cB. Int J Mol Sci 2019; 20:E4301. [PMID: 31484304 PMCID: PMC6747455 DOI: 10.3390/ijms20174301] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/25/2019] [Accepted: 08/30/2019] [Indexed: 01/15/2023] Open
Abstract
ArthβDG is a dimeric, cold-adapted β-d-galactosidase that exhibits high hydrolytic and transglycosylation activity. A series of crystal structures of its wild form, as well as its ArthβDG_E441Q mutein complexes with ligands were obtained in order to describe the mode of its action. The ArthβDG_E441Q mutein is an inactive form of the enzyme designed to enable observation of enzyme interaction with its substrate. The resulting three-dimensional structures of complexes: ArthβDG_E441Q/LACs and ArthβDG/IPTG (ligand bound in shallow mode) and structures of complexes ArthβDG_E441Q/LACd, ArthβDG/ONPG (ligands bound in deep mode), and galactose ArthβDG/GAL and their analysis enabled structural characterization of the hydrolysis reaction mechanism. Furthermore, comparative analysis with mesophilic analogs revealed the most striking differences in catalysis mechanisms. The key role in substrate transfer from shallow to deep binding mode involves rotation of the F581 side chain. It is worth noting that the 10-aa loop restricting access to the active site in mesophilic GH2 βDGs, in ArthβDG is moved outward. This facilitates access of substrate to active site. Such a permanent exposure of the entrance to the active site may be a key factor for improved turnover rate of the cold adapted enzyme and thus a structural feature related to its cold adaptation.
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Affiliation(s)
- Maria Rutkiewicz
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Anna Bujacz
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland.
| | - Marta Wanarska
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Anna Wierzbicka-Wos
- Department of Microbiology, Faculty of Biology, University of Szczecin, Felczaka 3c, 71-412 Szczecin, Poland
| | - Hubert Cieslinski
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
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