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Nestl BM, Nebel BA, Resch V, Schürmann M, Tischler D. The Development and Opportunities of Predictive Biotechnology. Chembiochem 2024; 25:e202300863. [PMID: 38713151 DOI: 10.1002/cbic.202300863] [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: 12/22/2023] [Revised: 04/05/2024] [Indexed: 05/08/2024]
Abstract
Recent advances in bioeconomy allow a holistic view of existing and new process chains and enable novel production routines continuously advanced by academia and industry. All this progress benefits from a growing number of prediction tools that have found their way into the field. For example, automated genome annotations, tools for building model structures of proteins, and structural protein prediction methods such as AlphaFold2TM or RoseTTAFold have gained popularity in recent years. Recently, it has become apparent that more and more AI-based tools are being developed and used for biocatalysis and biotechnology. This is an excellent opportunity for academia and industry to accelerate advancements in the field further. Biotechnology, as a rapidly growing interdisciplinary field, stands to benefit greatly from these developments.
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Affiliation(s)
- Bettina M Nestl
- Joint working group on biotransformations of the Association for General and Applied Microbiology VAAM, the Society for Chemical Engineering, Biotechnology DECHEMA, Theodor-Heuss-Allee 25, 60486, Frankfurt, Germany
- Innophore GmbH, Am Eisernen Tor 3, 8010, Graz, Austria
| | - Bernd A Nebel
- Innophore GmbH, Am Eisernen Tor 3, 8010, Graz, Austria
| | - Verena Resch
- Innophore GmbH, Am Eisernen Tor 3, 8010, Graz, Austria
| | - Martin Schürmann
- Joint working group on biotransformations of the Association for General and Applied Microbiology VAAM, the Society for Chemical Engineering, Biotechnology DECHEMA, Theodor-Heuss-Allee 25, 60486, Frankfurt, Germany
- InnoSyn B. V., Urmonderbaan 22, 6167 RD, Geleen, The Netherlands
- SynSilico B. V., Urmonderbaan 22, 6167 RD, Geleen, The Netherlands
| | - Dirk Tischler
- Joint working group on biotransformations of the Association for General and Applied Microbiology VAAM, the Society for Chemical Engineering, Biotechnology DECHEMA, Theodor-Heuss-Allee 25, 60486, Frankfurt, Germany
- Microbial Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44780, Bochum, Germany
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Hollmann F, Sanchis J, Reetz MT. Learning from Protein Engineering by Deconvolution of Multi-Mutational Variants. Angew Chem Int Ed Engl 2024:e202404880. [PMID: 38884594 DOI: 10.1002/anie.202404880] [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: 03/11/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/18/2024]
Abstract
This review analyzes a development in biochemistry, enzymology and biotechnology that originally came as a surprise. Following the establishment of directed evolution of stereoselective enzymes in organic chemistry, the concept of partial or complete deconvolution of selective multi-mutational variants was introduced. Early deconvolution experiments of stereoselective variants led to the finding that mutations can interact cooperatively or antagonistically with one another, not just additively. During the past decade, this phenomenon was shown to be general. In some studies, molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) computations were performed in order to shed light on the origin of non-additivity at all stages of an evolutionary upward climb. Data of complete deconvolution can be used to construct unique multi-dimensional rugged fitness pathway landscapes, which provide mechanistic insights different from traditional fitness landscapes. Along a related line, biochemists have long tested the result of introducing two point mutations in an enzyme for mechanistic reasons, followed by a comparison of the respective double mutant in so-called double mutant cycles, which originally showed only additive effects, but more recently also uncovered cooperative and antagonistic non-additive effects. We conclude with suggestions for future work, and call for a unified overall picture of non-additivity and epistasis.
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Affiliation(s)
- Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, Netherlands
| | - Joaquin Sanchis
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Manfred T Reetz
- Max-Plank-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45481, Mülheim, Germany
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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Zhang X, Zhang X, Shi H, Zhang H, Zhang J, Yue C, Li D, Yao L, Tang C. Combining Flexible Region Design and Automatic Design to Enhance the Thermal Stability and Catalytic Efficiency of Leucine Dehydrogenase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38838197 DOI: 10.1021/acs.jafc.4c02152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Leucine dehydrogenase (LeuDH, EC 1.4.1.9) can reversibly catalyze the oxidative deamination of l-leucine and some other specific α-amino acids to form the corresponding α-ketoacids. This reaction has great significance in the field of food additives and the pharmaceutical industry. The LeuDH from Exiguobacterium sibiricum (EsLeuDH) has high catalytic efficiency but limited thermal stability, hindering its widespread industrial application. In this study, a mutant N5F/I12L/A352Y of EsLeuDH (referred to as M2) was developed with enhanced thermal stability and catalytic activity through rational modification. The M2 mutant exhibits a half-life at 60 °C (t1/2(60 °C)) of 975.7 min and a specific activity of 69.6 U mg-1, which is 5.4 and 2.1 times higher than those of EsLeuDH, respectively. This research may facilitate the utilization of EsLeuDH at elevated temperatures, enhancing its potential for industrial applications. The findings offer a practical and efficient approach for optimizing LeuDH and other industrial enzymes.
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Affiliation(s)
- Xiang Zhang
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Xichuan Zhang
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Hongling Shi
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Huimin Zhang
- College of Animal Science and Technology, Yangzhou University, 88 South Daxue Road, Yangzhou, Jiangsu 225009, People's Republic of China
| | - Jianhui Zhang
- Postdoctoral Innovation Training Base, She Dian Lao Jiu Co. Ltd., 2 Liquor Avenue, Nanyang, Henan 473300, People's Republic of China
| | - Chao Yue
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Dandan Li
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Lunguang Yao
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Cunduo Tang
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
- Postdoctoral Innovation Training Base, She Dian Lao Jiu Co. Ltd., 2 Liquor Avenue, Nanyang, Henan 473300, People's Republic of China
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Ren Y, Qin Z, Li C, Yuan B, Yang Y, Qu G, Sun Z. Engineering the activity and thermostability of a carboxylic acid reductase in the conversion of vanillic acid to vanillin. J Biotechnol 2024; 386:19-27. [PMID: 38521166 DOI: 10.1016/j.jbiotec.2024.03.004] [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: 02/06/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/25/2024]
Abstract
Vanillin is a valuable natural product that can be used as a fragrance and additive. Recent research in the biosynthesis of vanillin has brought attention to a key enzyme, carboxylic acid reductase (CAR), which catalyzes the reduction of vanillic acid to vanillin. Nevertheless, the biosynthesis of vanillin is hampered by the low activity and stability of CAR. As such, a rational design campaign was conducted on a well-documented carboxylic acid reductase from Segniliparus rugosus (SrCAR), using vanillic acid as the model substrate. After combined active site saturation and iterative site-specific mutagenesis, the best quadruple mutant N292H/K524S/A627L/E1121W (M3) was successfully obtained. In comparison to the wildtype SrCAR, M3 demonstrated a 4.2-fold increase in catalytic efficiency (kcat/Km), and its half-life (t1/2) was enhanced by 3.8 times up to 385.08 minutes at 40 °C. In silico docking and molecular dynamics simulation provided insights into the improved activity and stability. In the subsequent preparative-scale reaction with 100 mM (16.8 g L-1) vanillic acid, the whole cell catalysis utilizing M3 produced 10.15 g·L-1 of vanillin and 1.11 g·L-1 of vanillyl alcohol, respectively. This work demonstrates a dual improvement in the activity and thermal stability of SrCAR, thereby potentially facilitating the application of carboxylic acid reductase in the biosynthesis of vanillin.
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Affiliation(s)
- Yaoyao Ren
- Tianjin University of Science and Technology, College of Biotechnology, Tianjin 300457, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Zongmin Qin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Congcong Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Bo Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yang Yang
- Tianjin University of Science and Technology, College of Biotechnology, Tianjin 300457, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
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Zheng T, Zheng Z, Zhou H, Guo Y, Li S. The multifaceted roles of COL4A4 in lung adenocarcinoma: An integrated bioinformatics and experimental study. Comput Biol Med 2024; 170:107896. [PMID: 38217972 DOI: 10.1016/j.compbiomed.2023.107896] [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: 11/05/2023] [Revised: 12/03/2023] [Accepted: 12/23/2023] [Indexed: 01/15/2024]
Abstract
BACKGROUND Abnormal expression of collagen IV subunits has been reported in cancers, but the significance is not clear. No study has reported the significance of COL4A4 in lung adenocarcinoma (LUAD). METHODS COL4A4 expression data, single-cell sequencing data and clinical data were downloaded from public databases. A range of bioinformatics and experimental methods were adopted to analyze the association of COL4A4 expression with clinical parameters, tumor microenvironment (TME), drug resistance and immunotherapy response, and to investigate the roles and underlying mechanism of COL4A4 in LUAD. RESULTS COL4A4 is differentially expressed in most of cancers analyzed, being associated with prognosis, tumor stemness, immune checkpoint gene expression and TME parameters. In LUAD, COL4A4 expression is down-regulated and associated with various TME parameters, response to immunotherapy and drug resistance. LUAD patients with lower COL4A4 have worse prognosis. Knockdown of COL4A4 significantly inhibited the expression of cell-cycle associated genes, and the expression and activation of signaling pathways including JAK/STAT3, p38, and ERK pathways, and induced quiescence in LUAD cells. Besides, it significantly induced the expression of a range of bioactive molecule genes that have been shown to have critical roles in TME remodeling and immune regulation. CONCLUSIONS COL4A4 is implicated in the pathogenesis of cancers including LUAD. Its function may be multifaceted. It can modulate the activity of LUAD cells, TME remodeling and tumor stemness, thus affecting the pathological process of LUAD. COL4A4 may be a prognostic molecular marker and a potential therapeutic target.
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Affiliation(s)
- Tiaozhan Zheng
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, Zhuang Autonomous Region, 530021, PR China
| | - Zhiwen Zheng
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, Zhuang Autonomous Region, 530021, PR China
| | - Hanxi Zhou
- Department of Pathology, Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang Province, PR China
| | - Yiqing Guo
- Department of Pathology, Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang Province, PR China
| | - Shikang Li
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, Zhuang Autonomous Region, 530021, PR China.
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