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Wang B, Liu Y, Bai X, Tian H, Wang L, Feng M, Xia H. In vitro generation of genetic diversity for directed evolution by error-prone artificial DNA synthesis. Commun Biol 2024; 7:628. [PMID: 38789612 PMCID: PMC11126579 DOI: 10.1038/s42003-024-06340-0] [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: 10/22/2023] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Generating genetic diversity lies at the heart of directed evolution which has been widely used to engineer genetic parts and gene circuits in synthetic biology. With the ever-expanding application of directed evolution, different approaches of generating genetic diversity are required to enrich the traditional toolbox. Here we show in vitro generation of genetic diversity for directed evolution by error-prone artificial DNA synthesis (epADS). This approach comprises a three-step process which incorporates base errors randomly generated during chemical synthesis of oligonucleotides under specific conditions into the target DNA. Through this method, 200 ~ 4000 folds of diversification in fluorescent strength have been achieved in genes encoding fluorescent proteins. EpADS has also been successfully used to diversify regulatory genetic parts, synthetic gene circuits and even increase microbial tolerance to carbenicillin in a short time period. EpADS would be an alternative tool for directed evolution which may have useful applications in synthetic biology.
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Affiliation(s)
- Baowei Wang
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China.
| | - Yang Liu
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Xuelian Bai
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huijuan Tian
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Lina Wang
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Miao Feng
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China.
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Hairong Xia
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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2
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Shen L, Chen Y, Hu L, Zhang C, Liu L, Bao L, Ma J, Wang H, Xiao X, Wu L, Chen S. Development of a Highly Sensitive, Visual Platform for the Detection of Cadmium in Actual Wastewater Based on Evolved Whole-Cell Biosensors. ACS Sens 2024; 9:654-661. [PMID: 38329934 DOI: 10.1021/acssensors.3c01811] [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] [Indexed: 02/10/2024]
Abstract
A whole-cell biosensor (WCB) is a convenient and cost-effective method for detecting contaminants. However, the practical application of the cadmium WCBs has been hampered by performance deficiencies, such as low sensitivity, specificity, and responsive strength. In this study, to improve the performance of cadmium WCBs, the cadmium transcription factor (CadC) and its DNA binding site (CadO), the key sensing module of the biosensor, were successively and separately subjected to a two-step directed evolution: 6-round random mutagenesis for CadC and 2-round saturation mutagenesis for CadO. For practical application, the GFP reporter gene was replaced with the lacZ gene and a facile and rapid smartphone detection platform for actual water samples was established by optimizing the reaction systems with detergents. The results showed that the evolved cadmium fluorescent biosensor CadO66 exhibited a higher specificity and a detection limit of 0.034 μg/L, representing a 19-fold reduction compared to the wild-type cadmium biosensor. The detergent sodium dodecylbenzenesulfonate effectively enhanced the visualization of WCB B0033-lacZ. Using the fluorescent WCB CadO66 and the visual WCB B0033-lacZ to analyze the cadmium contents of the actual water samples, the results were also consistent with a graphite furnace atomic absorption spectrometer. Taken together, this study indicates that the two-step directed evolution of CadC and CadO can efficiently improve the performance of cadmium WCBs, further promoting the utilization of WCB in actual sample detection and presenting a promising and feasible method for rapid sample detection.
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Affiliation(s)
- Liang Shen
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Yiwen Chen
- Wannan Medical College, Wuhu 241002, China
| | - Liangwen Hu
- Wuhu Agricultural Products and Food Testing Center Co. Ltd., Wuhu 241000, China
| | | | | | | | - Jie Ma
- Wannan Medical College, Wuhu 241002, China
| | - Hongqiang Wang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Xiang Xiao
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Lijun Wu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Shaopeng Chen
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
- Wannan Medical College, Wuhu 241002, China
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3
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Xiong Y, Xi X, Xiang Y, Li S, Liu H, Su Y, He R, Xiong C, Xu B, Wang X, Fu L, Zhao C, Han X, Li X, Xie S, Ruan J. CRISPR-Cas9-Mediated Cytosine Base Editing Screen for the Functional Assessment of CALR Intron Variants in Japanese Encephalitis Virus Replication. Int J Mol Sci 2023; 24:13331. [PMID: 37686137 PMCID: PMC10487596 DOI: 10.3390/ijms241713331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/12/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
The Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus that causes viral encephalitis in humans, pigs and other mammals across Asia and the Western Pacific. Genetic screening tools such as CRISPR screening, DNA sequencing and RNA interference have greatly improved our understanding of JEV replication and its potential antiviral approaches. However, information on exon and intron mutations associated with JEV replication is still scanty. CRISPR-Cas9-mediated cytosine base editing can efficiently generate C: G-to-T: A conversion in the genome of living cells. One intriguing application of base editing is to screen pivotal variants for gene function that is yet to be achieved in pigs. Here, we illustrate that CRISPR-Cas9-mediated cytosine base editor, known as AncBE4max, can be used for the functional analysis of calreticulin (CALR) variants. We conducted a CRISPR-Cas9-mediated cytosine base editing screen using 457 single guide RNAs (sgRNAs) against all exons and introns of CALR to identify loss-of-function variants involved in JEV replication. We unexpectedly uncovered that two enriched sgRNAs targeted the same site in intron-2 of the CALR gene. We found that mutating four consecutive G bases in the intron-2 of the CALR gene to four A bases significantly inhibited JEV replication. Thus, we established a CRISPR-Cas9-mediated cytosine-base-editing point mutation screening technique in pigs. Our results suggest that CRISPR-mediated base editing is a powerful tool for identifying the antiviral functions of variants in the coding and noncoding regions of the CALR gene.
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Affiliation(s)
- Youcai Xiong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (Y.X.); (X.X.); (Y.X.); (S.L.); (H.L.); (Y.S.); (R.H.); (C.X.); (B.X.); (X.W.); (L.F.); (C.Z.); (X.H.); (X.L.)
| | - Xiaoning Xi
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (Y.X.); (X.X.); (Y.X.); (S.L.); (H.L.); (Y.S.); (R.H.); (C.X.); (B.X.); (X.W.); (L.F.); (C.Z.); (X.H.); (X.L.)
| | - Yue Xiang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (Y.X.); (X.X.); (Y.X.); (S.L.); (H.L.); (Y.S.); (R.H.); (C.X.); (B.X.); (X.W.); (L.F.); (C.Z.); (X.H.); (X.L.)
| | - Sheng Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (Y.X.); (X.X.); (Y.X.); (S.L.); (H.L.); (Y.S.); (R.H.); (C.X.); (B.X.); (X.W.); (L.F.); (C.Z.); (X.H.); (X.L.)
| | - Hailong Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (Y.X.); (X.X.); (Y.X.); (S.L.); (H.L.); (Y.S.); (R.H.); (C.X.); (B.X.); (X.W.); (L.F.); (C.Z.); (X.H.); (X.L.)
| | - Yinyu Su
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (Y.X.); (X.X.); (Y.X.); (S.L.); (H.L.); (Y.S.); (R.H.); (C.X.); (B.X.); (X.W.); (L.F.); (C.Z.); (X.H.); (X.L.)
| | - Ruigao He
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (Y.X.); (X.X.); (Y.X.); (S.L.); (H.L.); (Y.S.); (R.H.); (C.X.); (B.X.); (X.W.); (L.F.); (C.Z.); (X.H.); (X.L.)
| | - Chong Xiong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (Y.X.); (X.X.); (Y.X.); (S.L.); (H.L.); (Y.S.); (R.H.); (C.X.); (B.X.); (X.W.); (L.F.); (C.Z.); (X.H.); (X.L.)
| | - Bingrong Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (Y.X.); (X.X.); (Y.X.); (S.L.); (H.L.); (Y.S.); (R.H.); (C.X.); (B.X.); (X.W.); (L.F.); (C.Z.); (X.H.); (X.L.)
| | - Xinyi Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (Y.X.); (X.X.); (Y.X.); (S.L.); (H.L.); (Y.S.); (R.H.); (C.X.); (B.X.); (X.W.); (L.F.); (C.Z.); (X.H.); (X.L.)
| | - Liangliang Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (Y.X.); (X.X.); (Y.X.); (S.L.); (H.L.); (Y.S.); (R.H.); (C.X.); (B.X.); (X.W.); (L.F.); (C.Z.); (X.H.); (X.L.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
| | - Changzhi Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (Y.X.); (X.X.); (Y.X.); (S.L.); (H.L.); (Y.S.); (R.H.); (C.X.); (B.X.); (X.W.); (L.F.); (C.Z.); (X.H.); (X.L.)
| | - Xiaosong Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (Y.X.); (X.X.); (Y.X.); (S.L.); (H.L.); (Y.S.); (R.H.); (C.X.); (B.X.); (X.W.); (L.F.); (C.Z.); (X.H.); (X.L.)
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (Y.X.); (X.X.); (Y.X.); (S.L.); (H.L.); (Y.S.); (R.H.); (C.X.); (B.X.); (X.W.); (L.F.); (C.Z.); (X.H.); (X.L.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (Y.X.); (X.X.); (Y.X.); (S.L.); (H.L.); (Y.S.); (R.H.); (C.X.); (B.X.); (X.W.); (L.F.); (C.Z.); (X.H.); (X.L.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxue Ruan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (Y.X.); (X.X.); (Y.X.); (S.L.); (H.L.); (Y.S.); (R.H.); (C.X.); (B.X.); (X.W.); (L.F.); (C.Z.); (X.H.); (X.L.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
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4
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Skrekas C, Limeta A, Siewers V, David F. Targeted In Vivo Mutagenesis in Yeast Using CRISPR/Cas9 and Hyperactive Cytidine and Adenine Deaminases. ACS Synth Biol 2023; 12:2278-2289. [PMID: 37486333 PMCID: PMC10443040 DOI: 10.1021/acssynbio.2c00690] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Indexed: 07/25/2023]
Abstract
Directed evolution is a preferred strategy to improve the function of proteins such as enzymes that act as bottlenecks in metabolic pathways. Common directed evolution approaches rely on error-prone PCR-based libraries where the number of possible variants is usually limited by cellular transformation efficiencies. Targeted in vivo mutagenesis can advance directed evolution approaches and help to overcome limitations in library generation. In the current study, we aimed to develop a high-efficiency time-controllable targeted mutagenesis toolkit in the yeast Saccharomyces cerevisiae by employing the CRISPR/Cas9 technology. To that end, we fused the dCas9 protein with hyperactive variants of adenine and cytidine deaminases aiming to create an inducible CRISPR-based mutagenesis tool targeting a specific DNA sequence in vivo with extended editing windows and high mutagenesis efficiency. We also investigated the effect of guide RNA multiplexing on the mutagenesis efficiency both phenotypically and on the DNA level.
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Affiliation(s)
- Christos Skrekas
- Department
of Life Sciences, Chalmers University of
Technology, Gothenburg SE-41296, Sweden
| | - Angelo Limeta
- Department
of Life Sciences, Chalmers University of
Technology, Gothenburg SE-41296, Sweden
| | - Verena Siewers
- Department
of Life Sciences, Chalmers University of
Technology, Gothenburg SE-41296, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Florian David
- Department
of Life Sciences, Chalmers University of
Technology, Gothenburg SE-41296, Sweden
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5
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Wu F. Updated analysis to reject the laboratory-engineering hypothesis of SARS-CoV-2. ENVIRONMENTAL RESEARCH 2023; 224:115481. [PMID: 36804316 PMCID: PMC9937728 DOI: 10.1016/j.envres.2023.115481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
A clear understanding of the origin of SARS-CoV-2 is important for future pandemic preparedness. Here, I provided an updated analysis of the type IIS endonuclease maps in genomes of alphacoronavirus, betacoronavirus, and SARS-CoV-2. Scenarios to engineer SARS-CoV-2 in the laboratory and the associated workload was also discussed. The analysis clearly shows that the endonuclease fingerprint does not indicate a synthetic origin of SARS-CoV-2 and engineering a SARS-CoV-2 virus in the laboratory is extremely challenging both scientifically and financially. On the contrary, current scientific evidence does support the animal origin of SARS-CoV-2.
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Affiliation(s)
- Fuqing Wu
- Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Texas, USA; Texas Epidemic Public Health Institute, TX, USA.
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6
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Sharrock AV, Mumm JS, Bagdžiūnas G, Čėnas N, Arcus VL, Ackerley DF. The Crystal Structure of Engineered Nitroreductase NTR 2.0 and Impact of F70A and F108Y Substitutions on Substrate Specificity. Int J Mol Sci 2023; 24:ijms24076633. [PMID: 37047605 PMCID: PMC10095097 DOI: 10.3390/ijms24076633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/25/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Bacterial nitroreductase enzymes that convert prodrugs to cytotoxins are valuable tools for creating transgenic targeted ablation models to study cellular function and cell-specific regeneration paradigms. We recently engineered a nitroreductase (“NTR 2.0”) for substantially enhanced reduction of the prodrug metronidazole, which permits faster cell ablation kinetics, cleaner interrogations of cell function, ablation of previously recalcitrant cell types, and extended ablation paradigms useful for modelling chronic diseases. To provide insight into the enhanced enzymatic mechanism of NTR 2.0, we have solved the X-ray crystal structure at 1.85 Angstroms resolution and compared it to the parental enzyme, NfsB from Vibrio vulnificus. We additionally present a survey of reductive activity with eight alternative nitroaromatic substrates, to provide access to alternative ablation prodrugs, and explore applications such as remediation of dinitrotoluene pollutants. The predicted binding modes of four key substrates were investigated using molecular modelling.
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Affiliation(s)
- Abigail V. Sharrock
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jeff S. Mumm
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Gintautas Bagdžiūnas
- Institute of Biochemistry, University of Vilnius, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Narimantas Čėnas
- Institute of Biochemistry, University of Vilnius, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Vickery L. Arcus
- Te Aka Mātuatua-School of Science, University of Waikato, Hamilton 3240, New Zealand
| | - David F. Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
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7
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Nov Y. Learning Context-Dependent DNA Mutation Patterns in Error-Prone Polymerase Chain Reaction. Biochemistry 2023; 62:345-350. [PMID: 36153985 DOI: 10.1021/acs.biochem.2c00292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We present a novel statistical learning method for studying context-dependent error rates in error-prone polymerase chain reaction (PCR) experiments. We demonstrate the method by applying it to error-prone PCR sequencing data and show how it may be exploited to improve the evolvability of genes in protein engineering.
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Affiliation(s)
- Yuval Nov
- Department of Statistics, University of Haifa, Haifa 3498838, Israel
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8
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Cai Y, Zhu K, Shen L, Ma J, Bao L, Chen D, Wei L, Wei N, Liu B, Wu Y, Chen S. Evolved Biosensor with High Sensitivity and Specificity for Measuring Cadmium in Actual Environmental Samples. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:10062-10071. [PMID: 35762704 DOI: 10.1021/acs.est.2c00627] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacterial biosensors have great potential in contaminant detection for sensitivity, specificity, cost-effectiveness, and easy operation. However, the existing cadmium-responsive bacterial biosensors cannot meet the real-world detection requirements due to lack of sensitivity, specificity, and anti-interference capability. This study aimed to develop a bacterial biosensor for detecting the total and extractable cadmium in actual environmental samples. We constructed the cadmium-responsive biosensor with the regulatory element (cadmium resistance transcriptional regulatory, CadR) and the reporting element (GFP) and improved its performance by directed evolution. The mutant libraries of biosensors were generated by error-prone PCR and screened by continuous five-round fluorescence-activated cell sorting (FACS), and a bacteria variant epCadR5 with higher performance was finally isolated. Biosensor fluorescence intensity was measured by a microplate reader, and results showed that the evolved cadmium-responsive bacterial biosensor was of high sensitivity and specificity in detecting trace cadmium, with a detection limit of 0.45 μg/L, which is 6.8 times more specific to cadmium than that of the wild-type. Furthermore, microscopic qualitative analysis results showed that the bacteria could produce fluorescence response in a cadmium-contaminated soil matrix, and quantitative analysis results showed that the values of cadmium from epCadR5 bacteria were close to that from inductively coupled plasma-mass spectrometry. These results suggest that the biosensor may have a broad application prospect in the detection of cadmium-contaminated soil and water.
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Affiliation(s)
- Yeshen Cai
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Kaili Zhu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Liang Shen
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Jie Ma
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Lingzhi Bao
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Dongdong Chen
- Institute of Environmental Physics and Technology, Anhui University, Hefei 230039, China
| | - Liangchen Wei
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Nan Wei
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Binmei Liu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Yuejin Wu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Shaopeng Chen
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
- School of Public Health, Wannan Medical College, Wuhu 241002, China
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9
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Sharrock AV, Mulligan TS, Hall KR, Williams EM, White DT, Zhang L, Emmerich K, Matthews F, Nimmagadda S, Washington S, Le KD, Meir-Levi D, Cox OL, Saxena MT, Calof AL, Lopez-Burks ME, Lander AD, Ding D, Ji H, Ackerley DF, Mumm JS. NTR 2.0: a rationally engineered prodrug-converting enzyme with substantially enhanced efficacy for targeted cell ablation. Nat Methods 2022; 19:205-215. [PMID: 35132245 PMCID: PMC8851868 DOI: 10.1038/s41592-021-01364-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/29/2021] [Indexed: 11/12/2022]
Abstract
Transgenic expression of bacterial nitroreductase (NTR) enzymes sensitizes eukaryotic cells to prodrugs such as metronidazole (MTZ), enabling selective cell-ablation paradigms that have expanded studies of cell function and regeneration in vertebrates. However, first-generation NTRs required confoundingly toxic prodrug treatments to achieve effective cell ablation, and some cell types have proven resistant. Here we used rational engineering and cross-species screening to develop an NTR variant, NTR 2.0, which exhibits ~100-fold improvement in MTZ-mediated cell-specific ablation efficacy, eliminating the need for near-toxic prodrug treatment regimens. NTR 2.0 therefore enables sustained cell-loss paradigms and ablation of previously resistant cell types. These properties permit enhanced interrogations of cell function, extended challenges to the regenerative capacities of discrete stem cell niches, and novel modeling of chronic degenerative diseases. Accordingly, we have created a series of bipartite transgenic reporter/effector resources to facilitate dissemination of NTR 2.0 to the research community.
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Affiliation(s)
- Abigail V Sharrock
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Timothy S Mulligan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Kelsi R Hall
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Elsie M Williams
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - David T White
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Liyun Zhang
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Kevin Emmerich
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Frazer Matthews
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Saumya Nimmagadda
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Selena Washington
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Katherine D Le
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Danielle Meir-Levi
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Olivia L Cox
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Meera T Saxena
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
- Luminomics, Baltimore, MD, USA
| | - Anne L Calof
- Department of Anatomy and Neurobiology, University of California, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Martha E Lopez-Burks
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Arthur D Lander
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Ding Ding
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
- Centre for Biodiscovery and Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.
| | - Jeff S Mumm
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA.
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA.
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA.
- Department of Genetic Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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10
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Currin A, Parker S, Robinson CJ, Takano E, Scrutton NS, Breitling R. The evolving art of creating genetic diversity: From directed evolution to synthetic biology. Biotechnol Adv 2021; 50:107762. [PMID: 34000294 PMCID: PMC8299547 DOI: 10.1016/j.biotechadv.2021.107762] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/21/2021] [Accepted: 04/25/2021] [Indexed: 12/31/2022]
Abstract
The ability to engineer biological systems, whether to introduce novel functionality or improved performance, is a cornerstone of biotechnology and synthetic biology. Typically, this requires the generation of genetic diversity to explore variations in phenotype, a process that can be performed at many levels, from single molecule targets (i.e., in directed evolution of enzymes) to whole organisms (e.g., in chassis engineering). Recent advances in DNA synthesis technology and automation have enhanced our ability to create variant libraries with greater control and throughput. This review highlights the latest developments in approaches to create such a hierarchy of diversity from the enzyme level to entire pathways in vitro, with a focus on the creation of combinatorial libraries that are required to navigate a target's vast design space successfully to uncover significant improvements in function.
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Affiliation(s)
- Andrew Currin
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
| | - Steven Parker
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Christopher J Robinson
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Eriko Takano
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nigel S Scrutton
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Rainer Breitling
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
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11
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Röllen K, Granzin J, Remeeva A, Davari MD, Gensch T, Nazarenko VV, Kovalev K, Bogorodskiy A, Borshchevskiy V, Hemmer S, Schwaneberg U, Gordeliy V, Jaeger KE, Batra-Safferling R, Gushchin I, Krauss U. The molecular basis of spectral tuning in blue- and red-shifted flavin-binding fluorescent proteins. J Biol Chem 2021; 296:100662. [PMID: 33862085 PMCID: PMC8131319 DOI: 10.1016/j.jbc.2021.100662] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 01/09/2023] Open
Abstract
Photoactive biological systems modify the optical properties of their chromophores, known as spectral tuning. Determining the molecular origin of spectral tuning is instrumental for understanding the function and developing applications of these biomolecules. Spectral tuning in flavin-binding fluorescent proteins (FbFPs), an emerging class of fluorescent reporters, is limited by their dependency on protein-bound flavins, whose structure and hence electronic properties cannot be altered by mutation. A blue-shifted variant of the plant-derived improved light, oxygen, voltage FbFP has been created by introducing a lysine within the flavin-binding pocket, but the molecular basis of this shift remains unconfirmed. We here structurally characterize the blue-shifted improved light, oxygen, voltage variant and construct a new blue-shifted CagFbFP protein by introducing an analogous mutation. X-ray structures of both proteins reveal displacement of the lysine away from the chromophore and opening up of the structure as instrumental for the blue shift. Site saturation mutagenesis and high-throughput screening yielded a red-shifted variant, and structural analysis revealed that the lysine side chain of the blue-shifted variant is stabilized close to the flavin by a secondary mutation, accounting for the red shift. Thus, a single additional mutation in a blue-shifted variant is sufficient to generate a red-shifted FbFP. Using spectroscopy, X-ray crystallography, and quantum mechanics molecular mechanics calculations, we provide a firm structural and functional understanding of spectral tuning in FbFPs. We also show that the identified blue- and red-shifted variants allow for two-color microscopy based on spectral separation. In summary, the generated blue- and red-shifted variants represent promising new tools for application in life sciences.
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Affiliation(s)
- Katrin Röllen
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Joachim Granzin
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Mehdi D Davari
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Thomas Gensch
- IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Kirill Kovalev
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia; Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, Grenoble, France; Institute of Crystallography, RWTH Aachen University, Aachen, Germany
| | - Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Valentin Borshchevskiy
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Stefanie Hemmer
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany; IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany; DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Valentin Gordeliy
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia; Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, Grenoble, France
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany; IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Renu Batra-Safferling
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany; IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.
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12
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Alejaldre L, Lemay-St-Denis C, Perez Lopez C, Sancho Jodar F, Guallar V, Pelletier JN. Known Evolutionary Paths Are Accessible to Engineered ß-Lactamases Having Altered Protein Motions at the Timescale of Catalytic Turnover. Front Mol Biosci 2020; 7:599298. [PMID: 33330628 PMCID: PMC7716773 DOI: 10.3389/fmolb.2020.599298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/23/2020] [Indexed: 11/26/2022] Open
Abstract
The evolution of new protein functions is dependent upon inherent biophysical features of proteins. Whereas, it has been shown that changes in protein dynamics can occur in the course of directed molecular evolution trajectories and contribute to new function, it is not known whether varying protein dynamics modify the course of evolution. We investigate this question using three related ß-lactamases displaying dynamics that differ broadly at the slow timescale that corresponds to catalytic turnover yet have similar fast dynamics, thermal stability, catalytic, and substrate recognition profiles. Introduction of substitutions E104K and G238S, that are known to have a synergistic effect on function in the parent ß-lactamase, showed similar increases in catalytic efficiency toward cefotaxime in the related ß-lactamases. Molecular simulations using Protein Energy Landscape Exploration reveal that this results from stabilizing the catalytically-productive conformations, demonstrating the dominance of the synergistic effect of the E014K and G238S substitutions in vitro in contexts that vary in terms of sequence and dynamics. Furthermore, three rounds of directed molecular evolution demonstrated that known cefotaximase-enhancing mutations were accessible regardless of the differences in dynamics. Interestingly, specific sequence differences between the related ß-lactamases were shown to have a higher effect in evolutionary outcomes than did differences in dynamics. Overall, these ß-lactamase models show tolerance to protein dynamics at the timescale of catalytic turnover in the evolution of a new function.
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Affiliation(s)
- Lorea Alejaldre
- Biochemistry Department, Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec City, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
| | - Claudèle Lemay-St-Denis
- Biochemistry Department, Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec City, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
| | | | | | - Victor Guallar
- Barcelona Supercomputing Center, Barcelona, Spain
- ICREA: Institució Catalana de Recerca i Estudis Avancats, Barcelona, Spain
| | - Joelle N. Pelletier
- Biochemistry Department, Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec City, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Chemistry Department, Université de Montréal, Montréal, QC, Canada
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13
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Hall KR, Robins KJ, Williams EM, Rich MH, Calcott MJ, Copp JN, Little RF, Schwörer R, Evans GB, Patrick WM, Ackerley DF. Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active-site residues. eLife 2020; 9:59081. [PMID: 33185191 PMCID: PMC7738182 DOI: 10.7554/elife.59081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/12/2020] [Indexed: 11/17/2022] Open
Abstract
Selection for a promiscuous enzyme activity provides substantial opportunity for competition between endogenous and newly-encountered substrates to influence the evolutionary trajectory, an aspect that is often overlooked in laboratory directed evolution studies. We selected the Escherichia coli nitro/quinone reductase NfsA for chloramphenicol detoxification by simultaneously randomising eight active-site residues and interrogating ~250,000,000 reconfigured variants. Analysis of every possible intermediate of the two best chloramphenicol reductases revealed complex epistatic interactions. In both cases, improved chloramphenicol detoxification was only observed after an R225 substitution that largely eliminated activity with endogenous quinones. Error-prone PCR mutagenesis reinforced the importance of R225 substitutions, found in 100% of selected variants. This strong activity trade-off demonstrates that endogenous cellular metabolites hold considerable potential to shape evolutionary outcomes. Unselected prodrug-converting activities were mostly unaffected, emphasising the importance of negative selection to effect enzyme specialisation, and offering an application for the evolved genes as dual-purpose selectable/counter-selectable markers. In the cell, most tasks are performed by big molecules called proteins, which behave like molecular machines. Although proteins are often described as having one job each, this is not always true, and many proteins can perform different roles. Enzymes are a type of protein that facilitate chemical reactions. They are often specialised to one reaction, but they can also accelerate other side-reactions. During evolution, these side-reactions can become more useful and, as a result, the role of the enzyme may change over time. The main role of the enzyme called NfsA in Escherichia coli bacteria is thought to be to convert molecules called quinones into hydroquinones, which can protect the cell from toxic molecules produced in oxidation reactions. As a side-reaction, NfsA has the potential to protect bacteria from an antibiotic called chloramphenicol, but it generally does this with such low efficacy that the effects are negligible. Producing hydroquinones is helpful to the cell in some situations, but if bacteria are regularly exposed to chloramphenicol, NfsA’s role aiding antibiotic resistance could become more important. Over time, the enzyme could evolve to become better at neutralising chloramphenicol. Therefore, NfsA provides an opportunity to study the evolution of proteins and how bacteria adapt to antibiotics. To see how evolution might affect the activity of NfsA, Hall et al. generated 250 million E. coli with either random or targeted changes to the gene that codes for the NfsA enzyme. The resulting variants of NfsA that were most effective against chloramphenicol all had a change that eliminated the enzyme’s ability to convert quinones. This result demonstrates a key trade-off between roles for NfsA, where one must be lost for the other to improve. These results demonstrate the interplay between a protein’s different roles and provide insight into bacterial drug resistance. Additionally, the experiments showed that the bacteria with improved resistance to chloramphenicol also became more sensitive to another antibiotic, metronidazole. These findings could inform the fight against drug-resistant bacterial infections and may also be helpful in guiding the design of proteins with different roles.
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Affiliation(s)
- Kelsi R Hall
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Katherine J Robins
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand
| | - Elsie M Williams
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Michelle H Rich
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand
| | - Mark J Calcott
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Janine N Copp
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand
| | - Rory F Little
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand
| | - Ralf Schwörer
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.,Ferrier Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Gary B Evans
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.,Ferrier Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Wayne M Patrick
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
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14
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Zhang X, Xu N, Li J, Ma Z, Wei L, Liu Q, Liu J. Engineering of L-glutamate oxidase as the whole-cell biocatalyst for the improvement of α-ketoglutarate production. Enzyme Microb Technol 2020; 136:109530. [PMID: 32331723 DOI: 10.1016/j.enzmictec.2020.109530] [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: 10/27/2019] [Revised: 01/10/2020] [Accepted: 01/28/2020] [Indexed: 12/27/2022]
Abstract
L-glutamate oxidase (LGOX) catalyzes the oxidative deamination of l-glutamate to α-ketoglutarate (α-KG) with the formation of ammonia and hydrogen peroxide. Consequently, identifying a novel LGOX with high enzymatic activity is a prime target for industrial biotechnology. In this study, error-prone PCR mutagenesis of Streptomyces mobaraensis LGOX followed by high-throughput screening was performed to yield four single point mutants with improved enzymatic activity, termed F94L, S280T, I282M and H533R. Moreover, site-saturation mutagenesis at these four residues was employed, yielding two additionally improved mutants, termed I282L and H533L. Subsequently, we employed combinatorial mutagenesis of two, three and four point mutants, and the best mutant S280TH533L showed 90 % higher enzymatic activity than the wild-type control. The data also showed that the presence of these point mutations greatly enhanced enzymatic activity, but did not alter its optimum temperature and pH. Furthermore, the S280TH533L mutant had the maximal velocity (Vmax) of 231.3 μmol/mg/min and the Michaelis-Menten constant (KM) of 2.7 mM, which were the highest Vmax and lowest KM values of LGOX reported so far. Finally, we developed a whole-cell biocatalyst for α-KG production by co-expression of both S280TH533L mutant and KatE catalase. Randomized ribosome binding site (RBS) sequences were introduced to generate vectors with varying expression levels of S280TH533L and KatE, and two optimized co-expression strains were obtained after screening. The α-KG production reached a maximum titer of 181.9 g/L after 12 h conversation using the optimized whole-cell biocatalyst, with a molar conversion rate of substrate higher than 86.3 % in the absence of exogenous catalase, while the molar conversion rate of substrate using the wild-type biocatalyst was less than 30 %. Taken together, these data suggest that the engineering of LGOX has great potentials to enhance the industrial production of α-KG.
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Affiliation(s)
- Xue Zhang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, PR China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Ning Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Jialong Li
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, PR China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Zhenping Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Liang Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Qingdai Liu
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, PR China.
| | - Jun Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
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15
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Chandler PG, Broendum SS, Riley BT, Spence MA, Jackson CJ, McGowan S, Buckle AM. Strategies for Increasing Protein Stability. Methods Mol Biol 2020; 2073:163-181. [PMID: 31612442 DOI: 10.1007/978-1-4939-9869-2_10] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The stability of wild-type proteins is often a hurdle to their practical use in research, industry, and medicine. The route to engineering stability of a protein of interest lies largely with the available data. Where high-resolution structural data is available, rational design, based on fundamental principles of protein chemistry, can improve protein stability. Recent advances in computational biology and the use of nonnatural amino acids have also provided novel rational methods for improving protein stability. Likewise, the explosion of sequence and structural data available in public databases, in combination with improvements in freely available computational tools, has produced accessible phylogenetic approaches. Trawling modern sequence databases can identify the thermostable homologs of a target protein, and evolutionary data can be quickly generated using available phylogenetic tools. Grafting features from those thermostable homologs or ancestors provides stability improvement through a semi-rational approach. Further, molecular techniques such as directed evolution have shown great promise in delivering designer proteins. These strategies are well documented and newly accessible to the molecular biologist, allowing for rapid enhancements of protein stability.
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Affiliation(s)
- Peter G Chandler
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Sebastian S Broendum
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Blake T Riley
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Matthew A Spence
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Sheena McGowan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
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16
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Gionfriddo M, De Gara L, Loreto F. Directed Evolution of Plant Processes: Towards a Green (r)Evolution? TRENDS IN PLANT SCIENCE 2019; 24:999-1007. [PMID: 31604600 DOI: 10.1016/j.tplants.2019.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/11/2019] [Accepted: 08/13/2019] [Indexed: 05/13/2023]
Abstract
Directed evolution (DE) is a powerful approach for generating proteins with new chemical and physical properties. It mimics the principles of Darwinian evolution by imposing selective pressure on a large population of molecules harboring random genetic variation in DNA, such that sequences with specific desirable properties are generated and selected. We propose that combining DE and genome-editing (DE-GE) technologies represents a powerful tool to discover and integrate new traits into plants for agronomic and biotechnological gain. DE-GE has the potential to deliver a new green (r)evolution research platform that can provide novel solutions to major trait delivery aspirations for sustainable agriculture, climate-resilient crops, and improved food security and nutritional quality.
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Affiliation(s)
- Matteo Gionfriddo
- Unit of Food Science and Human Nutrition, Campus Bio-Medico, University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy; Department of Biology, Agriculture, and Food Sciences, National Research Council of Italy (CNR-DISBA), Piazzale Aldo Moro 7, 00185 Rome, Italy
| | - Laura De Gara
- Unit of Food Science and Human Nutrition, Campus Bio-Medico, University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy.
| | - Francesco Loreto
- Department of Biology, Agriculture, and Food Sciences, National Research Council of Italy (CNR-DISBA), Piazzale Aldo Moro 7, 00185 Rome, Italy; Department of Biology, University Federico II, Via Cinthia, 80126 Naples, Italy.
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17
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Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution. Nat Commun 2019; 10:3583. [PMID: 31395865 PMCID: PMC6687891 DOI: 10.1038/s41467-019-11526-w] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/15/2019] [Indexed: 02/06/2023] Open
Abstract
The majority of common variants associated with common diseases, as well as an unknown proportion of causal mutations for rare diseases, fall in noncoding regions of the genome. Although catalogs of noncoding regulatory elements are steadily improving, we have a limited understanding of the functional effects of mutations within them. Here, we perform saturation mutagenesis in conjunction with massively parallel reporter assays on 20 disease-associated gene promoters and enhancers, generating functional measurements for over 30,000 single nucleotide substitutions and deletions. We find that the density of putative transcription factor binding sites varies widely between regulatory elements, as does the extent to which evolutionary conservation or integrative scores predict functional effects. These data provide a powerful resource for interpreting the pathogenicity of clinically observed mutations in these disease-associated regulatory elements, and comprise a rich dataset for the further development of algorithms that aim to predict the regulatory effects of noncoding mutations.
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18
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Cozens C, Pinheiro VB. Darwin Assembly: fast, efficient, multi-site bespoke mutagenesis. Nucleic Acids Res 2019; 46:e51. [PMID: 29409059 PMCID: PMC5934624 DOI: 10.1093/nar/gky067] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/24/2018] [Indexed: 12/15/2022] Open
Abstract
Engineering proteins for designer functions and biotechnological applications almost invariably requires (or at least benefits from) multiple mutations to non-contiguous residues. Several methods for multiple site-directed mutagenesis exist, but there remains a need for fast and simple methods to efficiently introduce such mutations – particularly for generating large, high quality libraries for directed evolution. Here, we present Darwin Assembly, which can deliver high quality libraries of >108 transformants, targeting multiple (>10) distal sites with minimal wild-type contamination (<0.25% of total population) and which takes a single working day from purified plasmid to library transformation. We demonstrate its efficacy with whole gene codon reassignment of chloramphenicol acetyl transferase, mutating 19 codons in a single reaction in KOD DNA polymerase and generating high quality, multiple-site libraries in T7 RNA polymerase and Tgo DNA polymerase. Darwin Assembly uses commercially available enzymes, can be readily automated, and offers a cost-effective route to highly complex and customizable library generation.
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Affiliation(s)
| | - Vitor B Pinheiro
- University College London, Gower Street, London WC1E 6BT, UK.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street WC1E 7HX, UK
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19
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Chen M, Zhang X, Xing C, Zhang C, Zheng Y, Pan J, Xu J, Bai Y. Efficient Stereoselective Synthesis of Structurally Diverse γ‐ and δ‐Lactones Using an Engineered Carbonyl Reductase. ChemCatChem 2019. [DOI: 10.1002/cctc.201900382] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Meng Chen
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Xiao‐Yan Zhang
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Chen‐Guang Xing
- Xiamen Oamic Biotech. Co. Ltd 36 Longmen Road Xiamen 361026 P.R. China
| | - Chao Zhang
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Yu‐Cong Zheng
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Jiang Pan
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Jian‐He Xu
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Yun‐Peng Bai
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
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20
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Yokobayashi Y. Applications of high-throughput sequencing to analyze and engineer ribozymes. Methods 2019; 161:41-45. [PMID: 30738128 DOI: 10.1016/j.ymeth.2019.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/04/2019] [Accepted: 02/03/2019] [Indexed: 01/22/2023] Open
Abstract
A large number of catalytic RNAs, or ribozymes, have been identified in the genomes of various organisms and viruses. Ribozymes are involved in biological processes such as regulation of gene expression and viral replication, but biological roles of many ribozymes still remain unknown. Ribozymes have also inspired researchers to engineer synthetic ribozymes that function as sensors or gene switches. To gain deeper understanding of the sequence-function relationship of ribozymes and to efficiently engineer synthetic ribozymes, a large number of ribozyme variants need to be examined which was limited to hundreds of sequences by Sanger sequencing. The advent of high-throughput sequencing technologies, however, has allowed us to sequence millions of ribozyme sequences at low cost. This review focuses on the recent applications of high-throughput sequencing to both characterize and engineer ribozymes, to highlight how the large-scale sequence data can advance ribozyme research and engineering.
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Affiliation(s)
- Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan.
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21
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Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance. Proc Natl Acad Sci U S A 2018; 115:E5726-E5735. [PMID: 29871954 PMCID: PMC6016788 DOI: 10.1073/pnas.1801646115] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Antibiotic development is frequently plagued by the rapid emergence of drug resistance. However, assessing the risk of resistance development in the preclinical stage is difficult. Standard laboratory evolution approaches explore only a small fraction of the sequence space and fail to identify exceedingly rare resistance mutations and combinations thereof. Therefore, new rapid and exhaustive methods are needed to accurately assess the potential of resistance evolution and uncover the underlying mutational mechanisms. Here, we introduce directed evolution with random genomic mutations (DIvERGE), a method that allows an up to million-fold increase in mutation rate along the full lengths of multiple predefined loci in a range of bacterial species. In a single day, DIvERGE generated specific mutation combinations, yielding clinically significant resistance against trimethoprim and ciprofloxacin. Many of these mutations have remained previously undetected or provide resistance in a species-specific manner. These results indicate pathogen-specific resistance mechanisms and the necessity of future narrow-spectrum antibacterial treatments. In contrast to prior claims, we detected the rapid emergence of resistance against gepotidacin, a novel antibiotic currently in clinical trials. Based on these properties, DIvERGE could be applicable to identify less resistance-prone antibiotics at an early stage of drug development. Finally, we discuss potential future applications of DIvERGE in synthetic and evolutionary biology.
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22
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Adesioye FA, Makhalanyane TP, Vikram S, Sewell BT, Schubert WD, Cowan DA. Structural Characterization and Directed Evolution of a Novel Acetyl Xylan Esterase Reveals Thermostability Determinants of the Carbohydrate Esterase 7 Family. Appl Environ Microbiol 2018; 84:e02695-17. [PMID: 29453256 PMCID: PMC5881061 DOI: 10.1128/aem.02695-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/26/2018] [Indexed: 02/04/2023] Open
Abstract
A hot desert hypolith metagenomic DNA sequence data set was screened in silico for genes annotated as acetyl xylan esterases (AcXEs). One of the genes identified encoded an ∼36-kDa protein (Axe1NaM1). The synthesized gene was cloned and expressed, and the resulting protein was purified. NaM1 was optimally active at pH 8.5 and 30°C and functionally stable at salt concentrations of up to 5 M. The specific activity and catalytic efficiency were 488.9 U mg-1 and 3.26 × 106 M-1 s-1, respectively. The crystal structure of wild-type NaM1 was solved at a resolution of 2.03 Å, and a comparison with the structures and models of more thermostable carbohydrate esterase 7 (CE7) family enzymes and variants of NaM1 from a directed evolution experiment suggests that reduced side-chain volume of protein core residues is relevant to the thermal stability of NaM1. Surprisingly, a single point mutation (N96S) not only resulted in a simultaneous improvement in thermal stability and catalytic efficiency but also increased the acyl moiety substrate range of NaM1.IMPORTANCE AcXEs belong to nine carbohydrate esterase families (CE1 to CE7, CE12, and CE16), of which CE7 enzymes possess a unique and narrow specificity for acetylated substrates. All structurally characterized members of this family are moderately to highly thermostable. The crystal structure of a novel, mesophilic CE7 AcXE (Axe1NaM1), from a soil metagenome, provides a basis for comparisons with thermostable CE7 enzymes. Using error-prone PCR and site-directed mutagenesis, we enhanced both the stability and activity of the mesophilic AcXE. With comparative structural analyses, we have also identified possible thermal stability determinants. These are valuable for understanding the thermal stability of enzymes within this family and as a guide for future protein engineering of CE7 and other α/β hydrolase enzymes.
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Affiliation(s)
- Fiyinfoluwa A Adesioye
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Bryan T Sewell
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
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23
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Musdal Y, Govindarajan S, Mannervik B. Exploring sequence-function space of a poplar glutathione transferase using designed information-rich gene variants. Protein Eng Des Sel 2017; 30:543-549. [PMID: 28967959 PMCID: PMC5914380 DOI: 10.1093/protein/gzx045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 08/15/2017] [Indexed: 01/19/2023] Open
Abstract
Exploring the vicinity around a locus of a protein in sequence space may identify homologs with enhanced properties, which could become valuable in biotechnical and other applications. A rational approach to this pursuit is the use of ‘infologs’, i.e. synthetic sequences with specific substitutions capturing maximal sequence information derived from the evolutionary history of the protein family. Ninety-five such infolog genes of poplar glutathione transferase were synthesized and expressed in Escherichia coli, and the catalytic activities of the proteins determined with alternative substrates. Sequence–activity relationships derived from the infologs were used to design a second set of 47 infologs in which 90% of the members exceeded wild-type properties. Two mutants, C2 (V55I/E95D/D108E/A160V) and G5 (F13L/C70A/G122E), were further functionally characterized. The activities of the infologs with the alternative substrates 1-chloro-2,4-dinitrobenzene and phenethyl isothiocyanate, subject to different chemistries, were positively correlated, indicating that the examined mutations were affecting the overall catalytic competence without major shift in substrate discrimination. By contrast, the enhanced protein expressivity observed in many of the mutants were not similarly correlated with the activities. In conclusion, small libraries of well-defined infologs can be used to systematically explore sequence space to optimize proteins in multidimensional functional space.
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Affiliation(s)
- Yaman Musdal
- Department of Neurochemistry, Arrhenius Laboratories, Stockholm University, Svante Arrhenius väg 16B, SE-10691 Stockholm, Sweden
| | | | - Bengt Mannervik
- Department of Neurochemistry, Arrhenius Laboratories, Stockholm University, Svante Arrhenius väg 16B, SE-10691 Stockholm, Sweden
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24
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Cárcamo E, Roldán-Salgado A, Osuna J, Bello-Sanmartin I, Yáñez JA, Saab-Rincón G, Viadiu H, Gaytán P. Spiked Genes: A Method to Introduce Random Point Nucleotide Mutations Evenly throughout an Entire Gene Using a Complete Set of Spiked Oligonucleotides for the Assembly. ACS OMEGA 2017; 2:3183-3191. [PMID: 30023688 PMCID: PMC6044943 DOI: 10.1021/acsomega.7b00508] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/21/2017] [Indexed: 06/08/2023]
Abstract
In vitro mutagenesis methods have revolutionized biological research and the biotechnology industry. In this study, we describe a mutagenesis method based on synthesizing a gene using a complete set of forward and reverse spiked oligonucleotides that have been modified to introduce a low ratio of mutant nucleotides at each position. This novel mutagenesis scheme named "Spiked Genes" yields a library of clones with an enhanced mutation distribution due to its unbiased nucleotide incorporation. Using the far-red fluorescent protein emKate as a model, we demonstrated that Spiked Genes yields richer libraries than those obtained via enzymatic methods. We obtained a library without bias toward any nucleotide or base pair and with even mutations, transitions, and transversion frequencies. Compared with enzymatic methods, the proposed synthetic approach for the creation of gene libraries represents an improved strategy for screening protein variants and does not require a starting template.
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Affiliation(s)
- Edson Cárcamo
- Instituto
de Biotecnología, Universidad Nacional
Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Abigail Roldán-Salgado
- Instituto
de Biotecnología, Universidad Nacional
Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Joel Osuna
- Instituto
de Biotecnología, Universidad Nacional
Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Iván Bello-Sanmartin
- Instituto
de Biotecnología, Universidad Nacional
Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Jorge A. Yáñez
- Instituto
de Biotecnología, Universidad Nacional
Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Gloria Saab-Rincón
- Instituto
de Biotecnología, Universidad Nacional
Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Héctor Viadiu
- Instituto
de Química, Universidad Nacional
Autónoma de México, Circuito Exterior, Ciudad Universitaria, Ciudad
de Mexico 04510, México
| | - Paul Gaytán
- Instituto
de Biotecnología, Universidad Nacional
Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
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25
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Kell DB. Evolutionary algorithms and synthetic biology for directed evolution: commentary on "on the mapping of genotype to phenotype in evolutionary algorithms" by Peter A. Whigham, Grant Dick, and James Maclaurin. GENETIC PROGRAMMING AND EVOLVABLE MACHINES 2017; 18:373-378. [PMID: 29033669 PMCID: PMC5618731 DOI: 10.1007/s10710-017-9292-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
I rehearse two issues around the commentary of Whigham and colleagues. (1) There really are many more reasons than those given as to why natural evolution cannot reasonably find or select the 'optimal' individual. (2) A series of experimental molecular biology programmes, known generically as directed evolution, can use operators and selection schemes that natural evolution cannot. When developed further using the methods of synthetic biology, there are no operators or schemes for in silico evolution that cannot be applied precisely to directed evolution. The issues raised apply only to natural evolution but not to directed evolution.
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Affiliation(s)
- Douglas B. Kell
- School of Chemistry, The University of Manchester, 131, Princess St, Manchester, Lancs, M1 7DN UK
- The Manchester Institute of Biotechnology, The University of Manchester, 131, Princess St, Manchester, Lancs, M1 7DN UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals, The University of Manchester, 131, Princess St, Manchester, Lancs, M1 7DN UK
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26
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Modification of fatty acid selectivity of Candida antarctica lipase A by error-prone PCR. Biotechnol Lett 2017; 39:767-773. [PMID: 28281023 PMCID: PMC5409807 DOI: 10.1007/s10529-017-2299-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/02/2017] [Indexed: 11/30/2022]
Abstract
Objective To generate Candida antarctica lipase A (CAL-A) mutants with modified fatty acid selectivities and improved lipolytic activities using error-prone PCR (epPCR). Results A Candida antarctica lipase A mutant was obtained in three rounds of epPCR. This mutant showed a 14 times higher ability to hydrolyze triacylglycerols containing conjugated linoleic acids, and was 12 and 14 times more selective towards cis-9, trans-11 and trans-10, cis-12 isomers respectively, compared to native lipase. Lipolytic activities towards fatty acid esters were markedly improved, in particular towards butyric, lauric, stearic and palmitic esters. Conclusion Directed molecular evolution is an efficient method to generate lipases with desirable selectivity towards CLA isomers and improved lipolytic activities towards esters of fatty acids. Electronic supplementary material The online version of this article (doi:10.1007/s10529-017-2299-0) contains supplementary material, which is available to authorized users.
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27
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Owen JG, Calcott MJ, Robins KJ, Ackerley DF. Generating Functional Recombinant NRPS Enzymes in the Laboratory Setting via Peptidyl Carrier Protein Engineering. Cell Chem Biol 2016; 23:1395-1406. [PMID: 27984027 DOI: 10.1016/j.chembiol.2016.09.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/08/2016] [Accepted: 10/07/2016] [Indexed: 01/29/2023]
Abstract
Non-ribosomal peptide synthetases (NRPSs) are modular enzymatic assembly lines where substrates and intermediates undergo rounds of transformation catalyzed by adenylation (A), condensation (C), and thioesterase (TE) domains. Central to the NRPS biosynthesis are peptidyl carrier protein (PCP) domains, small, catalytically inactive domains that shuttle substrates and intermediates between the catalytic modules and govern product release from TE domains. There is strong interest in recombination of NRPS systems to generate new chemical entities. However, the intrinsic complexity of these systems has been a major challenge. Here, we employ domain substitution and random mutagenesis to recapitulate NRPS evolution, focusing on PCP domains. Using NRPS model systems that produce two different pigmented molecules, pyoverdine and indigoidine, we found that only evolutionarily specialized recombinant PCP domains could interact effectively with the native TE domain for product release. Overall, we highlight that substituted PCP domains require very minor changes to result in functional NRPSs, and infer that positive selection pressure may improve recombinant NRPS outcomes.
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Affiliation(s)
- Jeremy G Owen
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand; Centre for Biodiscovery, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Mark J Calcott
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Katherine J Robins
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand; Centre for Biodiscovery, Victoria University of Wellington, Wellington 6140, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Auckland 1023, New Zealand.
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28
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Massively parallel single-nucleotide mutagenesis using reversibly terminated inosine. Nat Methods 2016; 13:923-924. [PMID: 27694911 DOI: 10.1038/nmeth.4015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 08/30/2016] [Indexed: 12/27/2022]
Abstract
Large-scale mutagenesis of target DNA sequences allows researchers to comprehensively assess the effects of single-nucleotide changes. Here we demonstrate the construction of a systematic allelic series (SAS) using massively parallel single-nucleotide mutagenesis with reversibly terminated deoxyinosine triphosphates (rtITP). We created a mutational library containing every possible single-nucleotide mutation surrounding the active site of the TEM-1 β-lactamase gene. When combined with high-throughput functional assays, SAS mutational libraries can expedite the functional assessment of genetic variation.
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29
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Paritala H, Palde PB, Carroll KS. Functional Site Discovery in a Sulfur Metabolism Enzyme by Using Directed Evolution. Chembiochem 2016; 17:1873-1878. [PMID: 27411165 DOI: 10.1002/cbic.201600264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Indexed: 11/07/2022]
Abstract
In human pathogens, the sulfate assimilation pathway provides reduced sulfur for biosynthesis of essential metabolites, including cysteine and low-molecular-weight thiol compounds. Sulfonucleotide reductases (SRs) catalyze the first committed step of sulfate reduction. In this reaction, activated sulfate in the form of adenosine-5'-phosphosulfate (APS) or 3'-phosphoadenosine 5'-phosphosulfate (PAPS) is reduced to sulfite. Gene knockout, transcriptomic and proteomic data have established the importance of SRs in oxidative stress-inducible antimicrobial resistance mechanisms. In previous work, we focused on rational and high-throughput design of small-molecule inhibitors that target the active site of SRs. However, another critical goal is to discover functionally important regions in SRs beyond the traditional active site. As an alternative to conservation analysis, we used directed evolution to rapidly identify functional sites in PAPS reductase (PAPR). Four new regions were discovered that are essential to PAPR function and lie outside the substrate binding pocket. Our results highlight the use of directed evolution as a tool to rapidly discover functionally important sites in proteins.
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Affiliation(s)
- Hanumantharao Paritala
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, 2B2, Jupiter, FL, 33458, USA
| | - Prakash B Palde
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, 2B2, Jupiter, FL, 33458, USA
| | - Kate S Carroll
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, 2B2, Jupiter, FL, 33458, USA.
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30
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Engineering of Harobin for enhanced fibrinolytic activity obtained by random and site-directed mutagenesis. Protein Expr Purif 2015; 129:162-172. [PMID: 26363113 DOI: 10.1016/j.pep.2015.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/06/2015] [Accepted: 09/08/2015] [Indexed: 11/21/2022]
Abstract
We have previously published a report on the cloning and characterization of Harobin, a fibrinolytic serine protease. However, the broad application of this fibrinolytic enzyme is limited by its low expression level that was achieved in Pichia pastoris. To counteract this shortcoming, random and site-directed mutagenesis have been combined in order to improve functional expression and activity of Harobin. By screening 400 clones from random mutant libraries for enhanced fibrinolytic activity, two mutants were obtained: N111R, R230G. By performing site-directed mutagenesis, a Harobin double mutant, N111R/R230G, was constructed and can be functionally expressed at higher level than the wild type enzyme. In addition, it possessed much higher fibrinolytic and amidolytic activity than the wild type enzyme and other single mutants. The N111R/R230G expressed in basal salts medium was purified by a three step purification procedure. At pH of 6.0-9.0, and the temperature range of 40-90 °C, N111R/R230G was more active and more heat resistant. The fibrinolytic activities of Harobin mutants were completely inhibited by PMSF and SBTI, but not by EDTA, EGTA, DTT, indicating that Harobin is a serine protease. N111R/R230G showed much better anti-thrombosis effect than wild type Harobin and single mutants, and could significantly increase bleeding and clotting time. Intravenous injection of N111R/R230G in spontaneous hypertensive rats (SHR) led to a significant reduction in systolic blood pressure (SBP), diastolic blood pressure (DBP) and mean arterial pressure (MAP) (p < 0.01), while heart rate (HR) was not affected. The in vitro and in vivo results of the present study revealed that Harobin double mutant N111R/R230G is an appropriate candidate for biotechnological applications due to its high expression level and high activity in area of thrombosis and hypertension.
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31
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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