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Zhang S, Ma Z, Li W, Shen Y, Xu Y, Liu G, Chang J, Li Z, Qin H, Tian B, Gong H, Liu D, Thuronyi B, Voigt C. EvoAI enables extreme compression and reconstruction of the protein sequence space. RESEARCH SQUARE 2024:rs.3.rs-3930833. [PMID: 38464127 PMCID: PMC10925456 DOI: 10.21203/rs.3.rs-3930833/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Designing proteins with improved functions requires a deep understanding of how sequence and function are related, a vast space that is hard to explore. The ability to efficiently compress this space by identifying functionally important features is extremely valuable. Here, we first establish a method called EvoScan to comprehensively segment and scan the high-fitness sequence space to obtain anchor points that capture its essential features, especially in high dimensions. Our approach is compatible with any biomolecular function that can be coupled to a transcriptional output. We then develop deep learning and large language models to accurately reconstruct the space from these anchors, allowing computational prediction of novel, highly fit sequences without prior homology-derived or structural information. We apply this hybrid experimental-computational method, which we call EvoAI, to a repressor protein and find that only 82 anchors are sufficient to compress the high-fitness sequence space with a compression ratio of 1048. The extreme compressibility of the space informs both applied biomolecular design and understanding of natural evolution.
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2
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Dziubańska-Kusibab PJ, Nevedomskaya E, Haendler B. Preclinical Anticipation of On- and Off-Target Resistance Mechanisms to Anti-Cancer Drugs: A Systematic Review. Int J Mol Sci 2024; 25:705. [PMID: 38255778 PMCID: PMC10815614 DOI: 10.3390/ijms25020705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
The advent of targeted therapies has led to tremendous improvements in treatment options and their outcomes in the field of oncology. Yet, many cancers outsmart precision drugs by developing on-target or off-target resistance mechanisms. Gaining the ability to resist treatment is the rule rather than the exception in tumors, and it remains a major healthcare challenge to achieve long-lasting remission in most cancer patients. Here, we discuss emerging strategies that take advantage of innovative high-throughput screening technologies to anticipate on- and off-target resistance mechanisms before they occur in treated cancer patients. We divide the methods into non-systematic approaches, such as random mutagenesis or long-term drug treatment, and systematic approaches, relying on the clustered regularly interspaced short palindromic repeats (CRISPR) system, saturated mutagenesis, or computational methods. All these new developments, especially genome-wide CRISPR-based screening platforms, have significantly accelerated the processes for identification of the mechanisms responsible for cancer drug resistance and opened up new avenues for future treatments.
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Affiliation(s)
| | | | - Bernard Haendler
- Research and Early Development Oncology, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany; (P.J.D.-K.); (E.N.)
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3
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Wei H, Li X. Deep mutational scanning: A versatile tool in systematically mapping genotypes to phenotypes. Front Genet 2023; 14:1087267. [PMID: 36713072 PMCID: PMC9878224 DOI: 10.3389/fgene.2023.1087267] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
Unveiling how genetic variations lead to phenotypic variations is one of the key questions in evolutionary biology, genetics, and biomedical research. Deep mutational scanning (DMS) technology has allowed the mapping of tens of thousands of genetic variations to phenotypic variations efficiently and economically. Since its first systematic introduction about a decade ago, we have witnessed the use of deep mutational scanning in many research areas leading to scientific breakthroughs. Also, the methods in each step of deep mutational scanning have become much more versatile thanks to the oligo-synthesizing technology, high-throughput phenotyping methods and deep sequencing technology. However, each specific possible step of deep mutational scanning has its pros and cons, and some limitations still await further technological development. Here, we discuss recent scientific accomplishments achieved through the deep mutational scanning and describe widely used methods in each step of deep mutational scanning. We also compare these different methods and analyze their advantages and disadvantages, providing insight into how to design a deep mutational scanning study that best suits the aims of the readers' projects.
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Affiliation(s)
- Huijin Wei
- Zhejiang University—University of Edinburgh Institute, Zhejiang University, Haining, Zhejiang, China
| | - Xianghua Li
- Zhejiang University—University of Edinburgh Institute, Zhejiang University, Haining, Zhejiang, China,Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom,The Second Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China,Biomedical and Health Translational Centre of Zhejiang Province, Haining, Zhejiang, China,*Correspondence: Xianghua Li,
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4
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Hao W, Cui W, Suo F, Han L, Cheng Z, Zhou Z. Construction and application of an efficient dual-base editing platform for Bacillus subtilis evolution employing programmable base conversion. Chem Sci 2022; 13:14395-14409. [PMID: 36545152 PMCID: PMC9749471 DOI: 10.1039/d2sc05824c] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/20/2022] [Indexed: 12/03/2022] Open
Abstract
The functionally evolved bacterial chassis is of great importance to manufacture a group of assorted high value-added chemicals, from small molecules to biologically active macromolecules. However, the current evolution frameworks are less efficienct in generating in vivo genomic diversification because of insufficient tunability, rendering limited evolution spacing for chassis. Here, an engineered genomic diversification platform (CRISPR-ABE8e-CDA-nCas9) leveraging a programmable dual-deaminases base editor was fabricated for rapidly evolving bacterial chassis. The dual-base editor was constructed by reprogramming the CRISPR array, nCas9, and cytidine and adenosine deaminase, enabling single or multiple base conversion at the genomic scale by simultaneous C-to-T and A-to-G conversion in vivo. Employing titration of the Cas-deaminase fusion protein, the platform enabled editing any pre-defined genomic loci with tunable conversion efficiency and editable window, generating a repertoire of mutants with highly diversified genomic sequences. Leveraging the genomic diversification platform, we successfully evolved the nisin-resistant capability of Bacillus subtilis through directed evolution of the subunit of lantibiotic ATP-binding cassette. Therefore, our work provides a portable and programmable genomic diversification platform, which is promising to expedite the fabrication of high-performance and robust bacterial chassis used in the development of biomanufacturing and biopharmaceuticals.
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Affiliation(s)
- Wenliang Hao
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University1800 Lihu AvenueWuxi 214122JiangsuChina
| | - Wenjing Cui
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University1800 Lihu AvenueWuxi 214122JiangsuChina
| | - Feiya Suo
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University1800 Lihu AvenueWuxi 214122JiangsuChina
| | - Laichuang Han
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University1800 Lihu AvenueWuxi 214122JiangsuChina
| | - Zhongyi Cheng
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University1800 Lihu AvenueWuxi 214122JiangsuChina
| | - Zhemin Zhou
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University1800 Lihu AvenueWuxi 214122JiangsuChina
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5
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Lee SO, Xie Q, Fried SD. Optimized Loopable Translation as a Platform for the Synthesis of Repetitive Proteins. ACS CENTRAL SCIENCE 2021; 7:1736-1750. [PMID: 34729417 PMCID: PMC8554844 DOI: 10.1021/acscentsci.1c00574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Indexed: 06/13/2023]
Abstract
The expression of long proteins with repetitive amino acid sequences often presents a challenge in recombinant systems. To overcome this obstacle, we report a genetic construct that circularizes mRNA in vivo by rearranging the topology of a group I self-splicing intron from T4 bacteriophage, thereby enabling "loopable" translation. Using a fluorescence-based assay to probe the translational efficiency of circularized mRNAs, we identify several conditions that optimize protein expression from this system. Our data suggested that translation of circularized mRNAs could be limited primarily by the rate of ribosomal initiation; therefore, using a modified error-prone PCR method, we generated a library that concentrated mutations into the initiation region of circularized mRNA and discovered mutants that generated markedly higher expression levels. Combining our rational improvements with those discovered through directed evolution, we report a loopable translator that achieves protein expression levels within 1.5-fold of the levels of standard vectorial translation. In summary, our work demonstrates loopable translation as a promising platform for the creation of large peptide chains, with potential utility in the development of novel protein materials.
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6
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Wang Y, Xue P, Cao M, Yu T, Lane ST, Zhao H. Directed Evolution: Methodologies and Applications. Chem Rev 2021; 121:12384-12444. [PMID: 34297541 DOI: 10.1021/acs.chemrev.1c00260] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Directed evolution aims to expedite the natural evolution process of biological molecules and systems in a test tube through iterative rounds of gene diversifications and library screening/selection. It has become one of the most powerful and widespread tools for engineering improved or novel functions in proteins, metabolic pathways, and even whole genomes. This review describes the commonly used gene diversification strategies, screening/selection methods, and recently developed continuous evolution strategies for directed evolution. Moreover, we highlight some representative applications of directed evolution in engineering nucleic acids, proteins, pathways, genetic circuits, viruses, and whole cells. Finally, we discuss the challenges and future perspectives in directed evolution.
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Affiliation(s)
- Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mingfeng Cao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tianhao Yu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stephan T Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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7
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Lee SO, Fried SD. An error prone PCR method for small amplicons. Anal Biochem 2021; 628:114266. [PMID: 34081928 DOI: 10.1016/j.ab.2021.114266] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022]
Abstract
Error-prone PCR (epPCR) is a commonly employed approach in molecular biology, especially in directed evolution, to generate libraries of DNA molecules with broad mutational spectrums. Though commonly applied to mutagenize protein coding sequences of several hundreds or thousands of basepairs, we found that commonly used protocols were not suitable for small (<100 bp) amplicons. Here we report a modified error-prone PCR protocol utilizing a Touchdown approach and employing only commercially available components, that should be broadly useful for the researcher interested in concentrating mutations into a small region of plasmid DNA. It will also be useful for achieving very high mutational loads on a standard-sized amplicon.
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Affiliation(s)
- Sea On Lee
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
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8
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Burton TD, Eyre NS. Applications of Deep Mutational Scanning in Virology. Viruses 2021; 13:1020. [PMID: 34071591 PMCID: PMC8227372 DOI: 10.3390/v13061020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
Several recently developed high-throughput techniques have changed the field of molecular virology. For example, proteomics studies reveal complete interactomes of a viral protein, genome-wide CRISPR knockout and activation screens probe the importance of every single human gene in aiding or fighting a virus, and ChIP-seq experiments reveal genome-wide epigenetic changes in response to infection. Deep mutational scanning is a relatively novel form of protein science which allows the in-depth functional analysis of every nucleotide within a viral gene or genome, revealing regions of importance, flexibility, and mutational potential. In this review, we discuss the application of this technique to RNA viruses including members of the Flaviviridae family, Influenza A Virus and Severe Acute Respiratory Syndrome Coronavirus 2. We also briefly discuss the reverse genetics systems which allow for analysis of viral replication cycles, next-generation sequencing technologies and the bioinformatics tools that facilitate this research.
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Affiliation(s)
| | - Nicholas S. Eyre
- College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia;
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9
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Zrimec J, Börlin CS, Buric F, Muhammad AS, Chen R, Siewers V, Verendel V, Nielsen J, Töpel M, Zelezniak A. Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure. Nat Commun 2020; 11:6141. [PMID: 33262328 PMCID: PMC7708451 DOI: 10.1038/s41467-020-19921-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 11/02/2020] [Indexed: 12/31/2022] Open
Abstract
Understanding the genetic regulatory code governing gene expression is an important challenge in molecular biology. However, how individual coding and non-coding regions of the gene regulatory structure interact and contribute to mRNA expression levels remains unclear. Here we apply deep learning on over 20,000 mRNA datasets to examine the genetic regulatory code controlling mRNA abundance in 7 model organisms ranging from bacteria to Human. In all organisms, we can predict mRNA abundance directly from DNA sequence, with up to 82% of the variation of transcript levels encoded in the gene regulatory structure. By searching for DNA regulatory motifs across the gene regulatory structure, we discover that motif interactions could explain the whole dynamic range of mRNA levels. Co-evolution across coding and non-coding regions suggests that it is not single motifs or regions, but the entire gene regulatory structure and specific combination of regulatory elements that define gene expression levels.
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Affiliation(s)
- Jan Zrimec
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Christoph S Börlin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Filip Buric
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Azam Sheikh Muhammad
- Computer Science and Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Rhongzen Chen
- Computer Science and Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Vilhelm Verendel
- Computer Science and Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Mats Töpel
- Department of Marine Sciences, University of Gothenburg, Box 461, SE-405 30, Gothenburg, Sweden
- Gothenburg Global Biodiversity Center (GGBC), Box 461, 40530, Gothenburg, Sweden
| | - Aleksej Zelezniak
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23a, SE-171 65, Stockholm, Sweden.
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10
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He W, Zhang J, Sachsenhauser V, Wang L, Bardwell JCA, Quan S. Increased surface charge in the protein chaperone Spy enhances its anti-aggregation activity. J Biol Chem 2020; 295:14488-14500. [PMID: 32817055 PMCID: PMC7573262 DOI: 10.1074/jbc.ra119.012300] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 07/31/2020] [Indexed: 12/21/2022] Open
Abstract
Chaperones are essential components of the protein homeostasis network. There is a growing interest in optimizing chaperone function, but exactly how to achieve this aim is unclear. Here, using a model chaperone, the bacterial protein Spy, we demonstrate that substitutions that alter the electrostatic potential of Spy's concave, client-binding surface enhance Spy's anti-aggregation activity. We show that this strategy is more efficient than one that enhances the hydrophobicity of Spy's surface. Our findings thus challenge the traditional notion that hydrophobic interactions are the major driving forces that guide chaperone-substrate binding. Kinetic data revealed that both charge- and hydrophobicity-enhanced Spy variants release clients more slowly, resulting in a greater "holdase" activity. However, increasing short-range hydrophobic interactions deleteriously affected Spy's ability to capture substrates, thus reducing its in vitro chaperone activity toward fast-aggregating substrates. Our strategy in chaperone surface engineering therefore sought to fine-tune the different molecular forces involved in chaperone-substrate interactions rather than focusing on enhancing hydrophobic interactions. These results improve our understanding of the mechanistic basis of chaperone-client interactions and illustrate how protein surface-based mutational strategies can facilitate the rational improvement of molecular chaperones.
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Affiliation(s)
- Wei He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China
| | - Jiayin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China
| | - Veronika Sachsenhauser
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lili Wang
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - James C A Bardwell
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China
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11
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12
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Bozovičar K, Bratkovič T. Evolving a Peptide: Library Platforms and Diversification Strategies. Int J Mol Sci 2019; 21:E215. [PMID: 31892275 PMCID: PMC6981544 DOI: 10.3390/ijms21010215] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/22/2019] [Accepted: 12/25/2019] [Indexed: 12/22/2022] Open
Abstract
Peptides are widely used in pharmaceutical industry as active pharmaceutical ingredients, versatile tools in drug discovery, and for drug delivery. They find themselves at the crossroads of small molecules and proteins, possessing favorable tissue penetration and the capability to engage into specific and high-affinity interactions with endogenous receptors. One of the commonly employed approaches in peptide discovery and design is to screen combinatorial libraries, comprising a myriad of peptide variants of either chemical or biological origin. In this review, we focus mainly on recombinant peptide libraries, discussing different platforms for their display or expression, and various diversification strategies for library design. We take a look at well-established technologies as well as new developments and future directions.
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Affiliation(s)
| | - Tomaž Bratkovič
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, SI-1000 Ljubljana, Slovenia;
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13
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Zinkus-Boltz J, DeValk C, Dickinson BC. A Phage-Assisted Continuous Selection Approach for Deep Mutational Scanning of Protein-Protein Interactions. ACS Chem Biol 2019; 14:2757-2767. [PMID: 31808666 DOI: 10.1021/acschembio.9b00669] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein-protein interactions (PPIs) are critical for organizing molecules in a cell and mediating signaling pathways. Dysregulation of PPIs is often a key driver of disease. To better understand the biophysical basis of such disease processes-and to potentially target them-it is critical to understand the molecular determinants of PPIs. Deep mutational scanning (DMS) facilitates the acquisition of large amounts of biochemical data by coupling selection with high throughput sequencing (HTS). The challenging and labor-intensive design and optimization of a relevant selection platform for DMS, however, limits the use of powerful directed evolution and selection approaches. To address this limitation, we designed a versatile new phage-assisted continuous selection (PACS) system using our previously reported proximity-dependent split RNA polymerase (RNAP) biosensors, with the aim of greatly simplifying and streamlining the design of a new selection platform for PPIs. After characterization and validation using the model KRAS/RAF PPI, we generated a library of RAF variants and subjected them to PACS and DMS. Our HTS data revealed positions along the binding interface that are both tolerant and intolerant to mutations, as well as which substitutions are tolerated at each position. Critically, the "functional scores" obtained from enrichment data through continuous selection for individual variants correlated with KD values measured in vitro, indicating that biochemical data can be extrapolated from sequencing using our new system. Due to the plug and play nature of RNAP biosensors, this method can likely be extended to a variety of other PPIs. More broadly, this, and other methods under development support the continued development of evolutionary and high-throughput approaches to address biochemical problems, moving toward a more comprehensive understanding of sequence-function relationships in proteins.
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Affiliation(s)
- Julia Zinkus-Boltz
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Craig DeValk
- The Center for Physics of Evolving Systems, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Bryan C. Dickinson
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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14
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Parola C, Neumeier D, Friedensohn S, Csepregi L, Di Tacchio M, Mason DM, Reddy ST. Antibody discovery and engineering by enhanced CRISPR-Cas9 integration of variable gene cassette libraries in mammalian cells. MAbs 2019; 11:1367-1380. [PMID: 31478465 PMCID: PMC6816377 DOI: 10.1080/19420862.2019.1662691] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Antibody engineering in mammalian cells offers the important advantage of expression and screening of libraries in their native conformation, increasing the likelihood of generating candidates with more favorable molecular properties. Major advances in cellular engineering enabled by CRISPR-Cas9 genome editing have made it possible to expand the use of mammalian cells in biotechnological applications. Here, we describe an antibody engineering and screening approach where complete variable light (VL) and heavy (VH) chain cassette libraries are stably integrated into the genome of hybridoma cells by enhanced Cas9-driven homology-directed repair (HDR), resulting in their surface display and secretion. By developing an improved HDR donor format that utilizes in situ linearization, we are able to achieve >15-fold improvement of genomic integration, resulting in a screening workflow that only requires a simple plasmid electroporation. This proved suitable for different applications in antibody discovery and engineering. By integrating and screening an immune library obtained from the variable gene repertoire of an immunized mouse, we could isolate a diverse panel of >40 unique antigen-binding variants. Additionally, we successfully performed affinity maturation by directed evolution screening of an antibody library based on random mutagenesis, leading to the isolation of several clones with affinities in the picomolar range.
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Affiliation(s)
- Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Simon Friedensohn
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Lucia Csepregi
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | | | - Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
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15
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Seo JH, Min WK, Lee SG, Yun H, Kim BG. To the Final Goal: Can We Predict and Suggest Mutations for Protein to Develop Desired Phenotype? BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-018-0064-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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16
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Bratulic S, Badran AH. Modern methods for laboratory diversification of biomolecules. Curr Opin Chem Biol 2017; 41:50-60. [PMID: 29096324 PMCID: PMC6062405 DOI: 10.1016/j.cbpa.2017.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/03/2017] [Accepted: 10/08/2017] [Indexed: 11/29/2022]
Abstract
Genetic variation fuels Darwinian evolution, yet spontaneous mutation rates are maintained at low levels to ensure cellular viability. Low mutation rates preclude the exhaustive exploration of sequence space for protein evolution and genome engineering applications, prompting scientists to develop methods for efficient and targeted diversification of nucleic acid sequences. Directed evolution of biomolecules relies upon the generation of unbiased genetic diversity to discover variants with desirable properties, whereas genome-engineering applications require selective modifications on a genomic scale with minimal off-targets. Here, we review the current toolkit of mutagenesis strategies employed in directed evolution and genome engineering. These state-of-the-art methods enable facile modifications and improvements of single genes, multicomponent pathways, and whole genomes for basic and applied research, while simultaneously paving the way for genome editing therapeutic interventions.
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Affiliation(s)
- Sinisa Bratulic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ahmed H Badran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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17
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Library Generation and Auxotrophic Selection Assays in Escherichia coli and Thermus thermophilus. Methods Mol Biol 2017. [PMID: 29086319 DOI: 10.1007/978-1-4939-7366-8_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The selection of optimized enzymes from gene libraries is important, both for basic and applied research. Here, we first describe the generation of plasmid-borne libraries using error-prone PCR and highly competent Escherichia coli cells. We then provide protocols for the use of these libraries for auxotrophic selection assays with E. coli and the extremely thermophilic bacterium Thermus thermophilus as hosts.
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18
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Laboratory Evolution of Bacillus circulans Xylanase Inserted into Pyrococcus furiosus Maltodextrin-Binding Protein for Increased Xylanase Activity and Thermal Stability Toward Alkaline pH. Appl Biochem Biotechnol 2017; 184:1232-1246. [DOI: 10.1007/s12010-017-2619-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/27/2017] [Indexed: 12/26/2022]
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19
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Groot-Kormelink PJ, Ferrand S, Kelley N, Bill A, Freuler F, Imbert PE, Marelli A, Gerwin N, Sivilotti LG, Miraglia L, Orth AP, Oakeley EJ, Schopfer U, Siehler S. High Throughput Random Mutagenesis and Single Molecule Real Time Sequencing of the Muscle Nicotinic Acetylcholine Receptor. PLoS One 2016; 11:e0163129. [PMID: 27649498 PMCID: PMC5029940 DOI: 10.1371/journal.pone.0163129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/03/2016] [Indexed: 12/15/2022] Open
Abstract
High throughput random mutagenesis is a powerful tool to identify which residues are important for the function of a protein, and gain insight into its structure-function relation. The human muscle nicotinic acetylcholine receptor was used to test whether this technique previously used for monomeric receptors can be applied to a pentameric ligand-gated ion channel. A mutant library for the α1 subunit of the channel was generated by error-prone PCR, and full length sequences of all 2816 mutants were retrieved using single molecule real time sequencing. Each α1 mutant was co-transfected with wildtype β1, δ, and ε subunits, and the channel function characterized by an ion flux assay. To test whether the strategy could map the structure-function relation of this receptor, we attempted to identify mutations that conferred resistance to competitive antagonists. Mutant hits were defined as receptors that responded to the nicotinic agonist epibatidine, but were not inhibited by either α-bungarotoxin or tubocurarine. Eight α1 subunit mutant hits were identified, six of which contained mutations at position Y233 or V275 in the transmembrane domain. Three single point mutations (Y233N, Y233H, and V275M) were studied further, and found to enhance the potencies of five channel agonists tested. This suggests that the mutations made the channel resistant to the antagonists, not by impairing antagonist binding, but rather by producing a gain-of-function phenotype, e.g. increased agonist sensitivity. Our data show that random high throughput mutagenesis is applicable to multimeric proteins to discover novel functional mutants, and outlines the benefits of using single molecule real time sequencing with regards to quality control of the mutant library as well as downstream mutant data interpretation.
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Affiliation(s)
- Paul J. Groot-Kormelink
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Sandrine Ferrand
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Nicholas Kelley
- Analytical Sciences and Imaging, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Anke Bill
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Felix Freuler
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Pierre-Eloi Imbert
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Anthony Marelli
- Genomics Institute of the Novartis Research Foundation, Novartis Institutes for BioMedical Research, San Diego, California, United States of America
| | - Nicole Gerwin
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Lucia G. Sivilotti
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
| | - Loren Miraglia
- Genomics Institute of the Novartis Research Foundation, Novartis Institutes for BioMedical Research, San Diego, California, United States of America
| | - Anthony P. Orth
- Genomics Institute of the Novartis Research Foundation, Novartis Institutes for BioMedical Research, San Diego, California, United States of America
| | - Edward J. Oakeley
- Analytical Sciences and Imaging, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Ulrich Schopfer
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Sandra Siehler
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
- * E-mail:
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20
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Abstract
Directed evolution has proved to be an effective strategy for improving or altering the activity of biomolecules for industrial, research and therapeutic applications. The evolution of proteins in the laboratory requires methods for generating genetic diversity and for identifying protein variants with desired properties. This Review describes some of the tools used to diversify genes, as well as informative examples of screening and selection methods that identify or isolate evolved proteins. We highlight recent cases in which directed evolution generated enzymatic activities and substrate specificities not known to exist in nature.
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Affiliation(s)
- Michael S Packer
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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21
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Doolan KM, Colby DW. Conformation-dependent epitopes recognized by prion protein antibodies probed using mutational scanning and deep sequencing. J Mol Biol 2014; 427:328-40. [PMID: 25451031 DOI: 10.1016/j.jmb.2014.10.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 10/23/2014] [Accepted: 10/24/2014] [Indexed: 11/24/2022]
Abstract
Prion diseases are caused by a structural rearrangement of the cellular prion protein, PrP(C), into a disease-associated conformation, PrP(Sc), which may be distinguished from one another using conformation-specific antibodies. We used mutational scanning by cell-surface display to screen 1341 PrP single point mutants for attenuated interaction with four anti-PrP antibodies, including several with conformational specificity. Single-molecule real-time gene sequencing was used to quantify enrichment of mutants, returning 26,000 high-quality full-length reads for each screened population on average. Relative enrichment of mutants correlated to the magnitude of the change in binding affinity. Mutations that diminished binding of the antibody ICSM18 represented the core of contact residues in the published crystal structure of its complex. A similarly located binding site was identified for D18, comprising discontinuous residues in helix 1 of PrP, brought into close proximity to one another only when the alpha helix is intact. The specificity of these antibodies for the normal form of PrP likely arises from loss of this conformational feature after conversion to the disease-associated form. Intriguingly, 6H4 binding was found to depend on interaction with the same residues, among others, suggesting that its ability to recognize both forms of PrP depends on a structural rearrangement of the antigen. The application of mutational scanning and deep sequencing provides residue-level resolution of positions in the protein-protein interaction interface that are critical for binding, as well as a quantitative measure of the impact of mutations on binding affinity.
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Affiliation(s)
- Kyle M Doolan
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - David W Colby
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
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22
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Zhao J, Kardashliev T, Joëlle Ruff A, Bocola M, Schwaneberg U. Lessons from diversity of directed evolution experiments by an analysis of 3,000 mutations. Biotechnol Bioeng 2014; 111:2380-9. [DOI: 10.1002/bit.25302] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/14/2014] [Accepted: 05/27/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Jing Zhao
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
| | - Tsvetan Kardashliev
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
| | - Marco Bocola
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
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23
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Bill A, Rosethorne EM, Kent TC, Fawcett L, Burchell L, van Diepen MT, Marelli A, Batalov S, Miraglia L, Orth AP, Renaud NA, Charlton SJ, Gosling M, Gaither LA, Groot-Kormelink PJ. High throughput mutagenesis for identification of residues regulating human prostacyclin (hIP) receptor expression and function. PLoS One 2014; 9:e97973. [PMID: 24886841 PMCID: PMC4041722 DOI: 10.1371/journal.pone.0097973] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 04/25/2014] [Indexed: 12/12/2022] Open
Abstract
The human prostacyclin receptor (hIP receptor) is a seven-transmembrane G protein-coupled receptor (GPCR) that plays a critical role in vascular smooth muscle relaxation and platelet aggregation. hIP receptor dysfunction has been implicated in numerous cardiovascular abnormalities, including myocardial infarction, hypertension, thrombosis and atherosclerosis. Genomic sequencing has discovered several genetic variations in the PTGIR gene coding for hIP receptor, however, its structure-function relationship has not been sufficiently explored. Here we set out to investigate the applicability of high throughput random mutagenesis to study the structure-function relationship of hIP receptor. While chemical mutagenesis was not suitable to generate a mutagenesis library with sufficient coverage, our data demonstrate error-prone PCR (epPCR) mediated mutagenesis as a valuable method for the unbiased screening of residues regulating hIP receptor function and expression. Here we describe the generation and functional characterization of an epPCR derived mutagenesis library compromising >4000 mutants of the hIP receptor. We introduce next generation sequencing as a useful tool to validate the quality of mutagenesis libraries by providing information about the coverage, mutation rate and mutational bias. We identified 18 mutants of the hIP receptor that were expressed at the cell surface, but demonstrated impaired receptor function. A total of 38 non-synonymous mutations were identified within the coding region of the hIP receptor, mapping to 36 distinct residues, including several mutations previously reported to affect the signaling of the hIP receptor. Thus, our data demonstrates epPCR mediated random mutagenesis as a valuable and practical method to study the structure-function relationship of GPCRs.
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Affiliation(s)
- Anke Bill
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Elizabeth M. Rosethorne
- Respiratory Disease Area, Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - Toby C. Kent
- Respiratory Disease Area, Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - Lindsay Fawcett
- Respiratory Disease Area, Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - Lynn Burchell
- Respiratory Disease Area, Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - Michiel T. van Diepen
- Respiratory Disease Area, Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - Anthony Marelli
- Infectious Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Sergey Batalov
- Infectious Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Loren Miraglia
- Infectious Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Anthony P. Orth
- Infectious Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Nicole A. Renaud
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Steven J. Charlton
- Respiratory Disease Area, Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - Martin Gosling
- Respiratory Disease Area, Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - L. Alex Gaither
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Paul J. Groot-Kormelink
- Respiratory Disease Area, Novartis Institutes for Biomedical Research, Horsham, United Kingdom
- Musculoskeletal Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland
- * E-mail:
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24
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Probabilistic methods in directed evolution: library size, mutation rate, and diversity. Methods Mol Biol 2014; 1179:261-78. [PMID: 25055784 DOI: 10.1007/978-1-4939-1053-3_18] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Directed evolution has emerged as an important tool for engineering proteins with improved or novel properties. Because of their inherent reliance on randomness, directed evolution protocols are amenable to probabilistic modeling and analysis. This chapter summarizes and reviews in a nonmathematical way some of the probabilistic works related to directed evolution, with particular focus on three of the most widely used methods: saturation mutagenesis, error-prone PCR, and in vitro recombination. The ultimate aim is to provide the reader with practical information to guide the planning and design of directed evolution studies. Importantly, the applications and locations of freely available computational resources to assist with this process are described in detail.
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25
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Directed evolution of G-protein-coupled receptors for high functional expression and detergent stability. Methods Enzymol 2013; 520:67-97. [PMID: 23332696 DOI: 10.1016/b978-0-12-391861-1.00004-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
G-protein-coupled receptors (GPCRs) are cell-surface receptors exhibiting a key role in cellular signal transduction processes, thus making them pharmacologically highly relevant target proteins. However, the molecular mechanisms driving receptor activation by ligand binding and signal transduction are poorly understood, since as integral membrane proteins, most GPCRs are very challenging for functional and structural studies. The biophysical properties of natural GPCRs, usually required by the cell in only low amounts, support their functionality in the lipid bilayer but are insufficient for high-level recombinant overexpression and stability in detergent solution. Current structural information about GPCRs is thus limited to a subset of GPCRs with either intrinsically favorable or properly improved biophysical behavior. Recently, directed protein evolution techniques for functional expression and detergent stability have been developed to increase the accessibility of GPCRs for functional and structural studies. Directed evolution does not rely on any preconceived notion of what might be limiting biophysical properties. By random mutagenesis combined with a high-throughput screening and selection system, directed protein evolution has the power to efficiently isolate rare phenotypes and thus contribute to the elucidation of the stability-determining factors, in addition to solving the practical problem of creating stable GPCRs. In the current chapter, protocols for generation of genetic diversity within GPCRs and selection are provided and discussed.
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26
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Ruff AJ, Marienhagen J, Verma R, Roccatano D, Genieser HG, Niemann P, Shivange AV, Schwaneberg U. dRTP and dPTP a complementary nucleotide couple for the Sequence Saturation Mutagenesis (SeSaM) method. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2012.04.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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27
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Verma R, Schwaneberg U, Roccatano D. MAP(2.0)3D: a sequence/structure based server for protein engineering. ACS Synth Biol 2012; 1:139-50. [PMID: 23651115 DOI: 10.1021/sb200019x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The Mutagenesis Assistant Program (MAP) is a web-based tool to provide statistical analyses of the mutational biases of directed evolution experiments on amino acid substitution patterns. MAP analysis assists protein engineers in the benchmarking of random mutagenesis methods that generate single nucleotide mutations in a codon. Herein, we describe a completely renewed and improved version of the MAP server, the MAP(2.0)3D server, which correlates the generated amino acid substitution patterns to the structural information of the target protein. This correlation aids in the selection of a more suitable random mutagenesis method with specific biases on amino acid substitution patterns. In particular, the new server represents MAP indicators on secondary and tertiary structure and correlates them to specific structural components such as hydrogen bonds, hydrophobic contacts, salt bridges, solvent accessibility, and crystallographic B-factors. Three model proteins (D-amino oxidase, phytase, and N-acetylneuraminic acid aldolase) are used to illustrate the novel capability of the server. MAP(2.0)3D server is available publicly at http://map.jacobs-university.de/map3d.html.
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Affiliation(s)
- Rajni Verma
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen,
Germany
- Department of Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen,
Germany
| | - Ulrich Schwaneberg
- Department of Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen,
Germany
| | - Danilo Roccatano
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen,
Germany
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28
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A new method for random mutagenesis by error-prone polymerase chain reaction using heavy water. J Biotechnol 2012; 157:71-4. [DOI: 10.1016/j.jbiotec.2011.09.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 08/19/2011] [Accepted: 09/07/2011] [Indexed: 11/19/2022]
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30
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Strohmeier GA, Pichler H, May O, Gruber-Khadjawi M. Application of Designed Enzymes in Organic Synthesis. Chem Rev 2011; 111:4141-64. [DOI: 10.1021/cr100386u] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Gernot A. Strohmeier
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, A-8010 Graz, Austria
| | - Oliver May
- DSM—Innovative Synthesis BV, Geleen, P.O. Box 18, 6160 MD Geleen, The Netherlands
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31
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Vanhercke T, Shrestha P, Green AG, Singh SP. Mechanistic and structural insights into the regioselectivity of an acyl-CoA fatty acid desaturase via directed molecular evolution. J Biol Chem 2011; 286:12860-9. [PMID: 21300802 PMCID: PMC3075633 DOI: 10.1074/jbc.m110.191098] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2010] [Revised: 02/03/2011] [Indexed: 11/06/2022] Open
Abstract
Membrane-bound fatty acid desaturases and related enzymes play a pivotal role in the biosynthesis of unsaturated and various unusual fatty acids. Structural insights into the remarkable catalytic diversity and wide range of substrate specificities of this class of enzymes remain limited due to the lack of a crystal structure. To investigate the structural basis of the double bond positioning (regioselectivity) of the desaturation reaction in more detail, we relied on a combination of directed evolution in vitro and a powerful yeast complementation assay to screen for Δx regioselectivity. After two selection rounds, variants of the bifunctional Δ12/Δ9-desaturase from the house cricket (Acheta domesticus) exhibited increased Δ9-desaturation activity on shorter chain fatty acids. This change in specificity was the result of as few as three mutations, some of them near the putative active site. Subsequent analysis of individual substitutions revealed an important role of residue Phe-52 in facilitating Δ9-desaturation of shorter chain acyl substrates and allowed for the redesign of the cricket Δ12/Δ9-desaturase into a 16:0-specific Δ9-desaturase. Our results demonstrate that a minimal number of mutations can have a profound impact on the regioselectivity of acyl-CoA fatty acid desaturases and include the first biochemical data supporting the acyl-CoA acyl carrier specificity of a desaturase able to carry out Δ12-desaturation.
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Affiliation(s)
- Thomas Vanhercke
- From the Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Canberra, Australian Capital Territory 2601, Australia
| | - Pushkar Shrestha
- From the Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Canberra, Australian Capital Territory 2601, Australia
| | - Allan G. Green
- From the Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Canberra, Australian Capital Territory 2601, Australia
| | - Surinder P. Singh
- From the Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Canberra, Australian Capital Territory 2601, Australia
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32
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Abstract
In Escherichia coli, the aerotaxis receptor Aer is an atypical receptor because it senses intracellular redox potential. The Aer sensor is a cytoplasmic, N-terminal PAS domain that is tethered to the membrane by a 47-residue F1 linker. Here we investigated the function, topology, and orientation of F1 by employing random mutagenesis, cysteine scanning, and disulfide cross-linking. No native residue was obligatory for function, most deleterious substitutions had radically different side chain properties, and all F1 mutants but one were functionally rescued by the chemoreceptor Tar. Cross-linking studies were consistent with the predicted α-helical structure in the N-terminal F1 region and demonstrated trigonal interactions among the F1 linkers from three Aer monomers, presumably within trimer-of-dimer units, as well as binary interactions between subunits. Using heterodimer analyses, we also demonstrated the importance of arginine residues near the membrane interface, which may properly anchor the Aer protein in the membrane. By incorporating these data into a homology model of Aer, we developed a model for the orientation of the Aer F1 and PAS regions in an Aer lattice that is compatible with the known dimensions of the chemoreceptor lattice. We propose that the F1 region facilitates the orientation of PAS and HAMP domains during folding and thereby promotes the stability of the PAS and HAMP domains in Aer.
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33
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Reetz MT. Gerichtete Evolution stereoselektiver Enzyme: Eine ergiebige Katalysator‐Quelle für asymmetrische Reaktionen. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000826] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Manfred T. Reetz
- Max‐Planck‐Institut für Kohlenforschung, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Deutschland), Fax: (+49) 208‐306‐2985 http://www.mpi‐muelheim.mpg.de/mpikofo_home.html
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34
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Reetz MT. Laboratory Evolution of Stereoselective Enzymes: A Prolific Source of Catalysts for Asymmetric Reactions. Angew Chem Int Ed Engl 2010; 50:138-74. [DOI: 10.1002/anie.201000826] [Citation(s) in RCA: 441] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Manfred T. Reetz
- Max‐Planck‐Institut für Kohlenforschung, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Germany), Fax: (+49) 208‐306‐2985 http://www.mpi‐muelheim.mpg.de/mpikofo_home.html
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35
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Campbell AJ, Watts KJ, Johnson MS, Taylor BL. Gain-of-function mutations cluster in distinct regions associated with the signalling pathway in the PAS domain of the aerotaxis receptor, Aer. Mol Microbiol 2010; 77:575-86. [PMID: 20545849 DOI: 10.1111/j.1365-2958.2010.07231.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The Aer receptor monitors internal energy (redox) levels in Escherichia coli with an FAD-containing PAS domain. Here, we randomly mutagenized the region encoding residues 14-119 of the PAS domain and found 72 aerotaxis-defective mutants, 24 of which were gain-of-function, signal-on mutants. The mutations were mapped onto an Aer homology model based on the structure of the PAS-FAD domain in NifL from Azotobacter vinlandii. Signal-on lesions clustered in the FAD binding pocket, the beta-scaffolding and in the N-cap loop. We suggest that the signal-on lesions mimic the 'signal-on' state of the PAS domain, and therefore may be markers for the signal-in and signal-out regions of this domain. We propose that the reduction of FAD rearranges the FAD binding pocket in a way that repositions the beta-scaffolding and the N-cap loop. The resulting conformational changes are likely to be conveyed directly to the HAMP domain, and on to the kinase control module. In support of this hypothesis, we demonstrated disulphide band formation between cysteines substituted at residues N98C or I114C in the PAS beta-scaffold and residue Q248C in the HAMP AS-2 helix.
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Affiliation(s)
- Asharie J Campbell
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, CA 92350, USA
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36
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Enzyme engineering for enantioselectivity: from trial-and-error to rational design? Trends Biotechnol 2009; 28:46-54. [PMID: 19913316 DOI: 10.1016/j.tibtech.2009.10.001] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 10/02/2009] [Accepted: 10/05/2009] [Indexed: 11/23/2022]
Abstract
The availability of tailored enzymes is crucial for the implementation of biocatalysis in organic chemistry. Enantioselectivity is one key parameter defining the usefulness of an enzyme and, therefore, the competitiveness of the corresponding industrial process. Hence, identification of enzymes with high enantioselectivity in the desired transformation is important. Currently, this is achieved by screening collections and libraries comprising natural or man-made diversity for the desired trait. Recently, a variety of improved methods have been developed to generate and screen this diversity more efficiently. Here, we present and discuss the most important advances in both library generation and screening. We also evaluate future trends, such as moving from random evolution to more rational.
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37
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Critical evaluation of random mutagenesis by error-prone polymerase chain reaction protocols, Escherichia coli mutator strain, and hydroxylamine treatment. Anal Biochem 2009; 388:71-80. [PMID: 19454214 DOI: 10.1016/j.ab.2009.02.008] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 02/05/2009] [Accepted: 02/05/2009] [Indexed: 11/21/2022]
Abstract
Random mutagenesis methods constitute a valuable protein modification toolbox with applications ranging from protein engineering to directed protein evolution studies. Although a variety of techniques are currently available, the field is lacking studies that would directly compare the performance parameters and operational range of different methods. In this study, we have scrutinized several of the most commonly used random mutagenesis techniques by critically evaluating popular error-prone polymerase chain reaction (PCR) protocols as well as hydroxylamine and a mutator Escherichia coli strain mutagenesis methods. Relative mutation frequencies were analyzed using a reporter plasmid that allowed direct comparison of the methods. Error-prone PCR methods yielded the highest mutation rates and the widest operational ranges, whereas the chemical and biological methods generated a low level of mutations and exhibited a narrow range of operation. The repertoire of transitions versus transversions varied among the methods, suggesting the use of a combination of methods for high-diversity full-scale mutagenesis. Using the parameters defined in this study, the evaluated mutagenesis methods can be used for controlled mutagenesis, where the intended average frequency of induced mutations can be adjusted to a desirable level.
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Rohrbach AS, Dickerson TJ. Predicting protein evolution in vitro by phage escape technology. MOLECULAR BIOSYSTEMS 2009; 5:128-33. [PMID: 19156257 DOI: 10.1039/b814768j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The relationship between host and pathogen is inherently dynamic at the genetic level. A plethora of host defensive systems have evolved to counteract and/or eliminate invading pathogens. These strategies exert selection pressure upon the pathogen, leading to the emergence of mechanisms to combat the host including immune evasion and resistance. Consequently, effective control of rapidly evolving diseases is contingent on the ability to predict pathogen evolution prior to the emergence of resistant phenotypes. Highlighted in this article is a bacteriophage-based technology capable of screening hundreds of millions of binding events simultaneously at single molecule resolution, thus providing an in vitro mimetic of protein evolution. This technology, termed phage escape, can be utilized to model the evolution of proteins in the presence of antibodies or other selective pressure, providing a predictive solution to the coevolution of antigens and the immune system. Foresight into the evolutionary path of an antigen and subsequent neutralization strategies can facilitate more efficacious vaccination formulation and have important implications in the treatment of a range of evolving diseases, including viral infections and cancer.
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Affiliation(s)
- Amanda S Rohrbach
- Department of Chemistry and Worm Institute for Research and Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
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Emond S, Mondon P, Pizzut-Serin S, Douchy L, Crozet F, Bouayadi K, Kharrat H, Potocki-Véronèse G, Monsan P, Remaud-Simeon M. A novel random mutagenesis approach using human mutagenic DNA polymerases to generate enzyme variant libraries. Protein Eng Des Sel 2008; 21:267-74. [DOI: 10.1093/protein/gzn004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Stevenson BJ, Liu JW, Ollis DL. Directed Evolution of Yeast Pyruvate Decarboxylase 1 for Attenuated Regulation and Increased Stability. Biochemistry 2008; 47:3013-25. [DOI: 10.1021/bi701858u] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bradley J. Stevenson
- Research School of Chemistry, Australian National University, Canberra 0200, Australia
| | - Jian-Wei Liu
- Research School of Chemistry, Australian National University, Canberra 0200, Australia
| | - David L. Ollis
- Research School of Chemistry, Australian National University, Canberra 0200, Australia
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41
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Developments in Directed Evolution for Improving Enzyme Functions. Appl Biochem Biotechnol 2007; 143:212-23. [DOI: 10.1007/s12010-007-8003-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 10/22/2022]
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Bordes F, Fudalej F, Dossat V, Nicaud JM, Marty A. A new recombinant protein expression system for high-throughput screening in the yeast Yarrowia lipolytica. J Microbiol Methods 2007; 70:493-502. [PMID: 17669530 DOI: 10.1016/j.mimet.2007.06.008] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 06/05/2007] [Accepted: 06/08/2007] [Indexed: 10/23/2022]
Abstract
Development of a high-throughput eukaryotic screening procedure is important to increase success in obtaining improved enzymes through directed enzyme evolution. This procedure was developed for the yeast Yarrowia lipolytica which becomes the second eukaryotic host for this purpose. The extracellular lipase Lip2 was used as expressed enzyme but this system will be easily adjusted for other enzymes. We adapted and optimized the protocol for protein expression by Y. lipolytica in 96-well microplates. Yeast transformation efficiency and expression cassette insertion were increased by constructing a strain containing a zeta docking platform for targeted integration into the genome. The coefficient of variance of the full process was reduced from 36.3% to 18.9%. The main part of the variability (11.7%) arises from the specific lipase enzyme assay whereas the coefficient of variance concerning transformation, growth and expression steps represents only 7.2%. The rate of clone with no activity was reduced from 5.8% to 0.2%. Both transformation efficiency and variability are then compatible with high-throughput screening in the yeast Y. lipolytica.
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Affiliation(s)
- Florence Bordes
- UMR5504, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, CNRS, INRA, INSA, 135 Rangueil av., F-31400 Toulouse, France
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43
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Smith BD, Raines RT. Genetic selection for critical residues in ribonucleases. J Mol Biol 2006; 362:459-78. [PMID: 16920150 DOI: 10.1016/j.jmb.2006.07.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Revised: 07/03/2006] [Accepted: 07/11/2006] [Indexed: 11/24/2022]
Abstract
Homologous mammalian proteins were subjected to an exhaustive search for residues that are critical to their structure/function. Error-prone polymerase chain reactions were used to generate random mutations in the genes of bovine pancreatic ribonuclease (RNase A) and human angiogenin, and a genetic selection based on the intrinsic cytotoxicity of ribonucleolytic activity was used to isolate inactive variants. Twenty-three of the 124 residues in RNase A were found to be intolerant to substitution with at least one particular amino acid. Twenty-nine of the 123 residues in angiogenin were likewise intolerant. In both RNase A and angiogenin, only six residues appeared to be wholly intolerant to substitution: two histidine residues involved in general acid/base catalysis and four cysteine residues that form two disulfide bonds. With few exceptions, the remaining critical residues were buried in the hydrophobic core of the proteins. Most of these residues were found to tolerate only conservative substitutions. The importance of a particular residue as revealed by this genetic selection correlated with its sequence conservation, though several non-conserved residues were found to be critical for protein structure/function. Despite voluminous research on RNase A, the importance of many residues identified herein was unknown, and those can now serve as targets for future work. Moreover, a comparison of the critical residues in RNase A and human angiogenin, which share only 35% amino acid sequence identity, provides a unique perspective on the molecular evolution of the RNase A superfamily, as well as an impetus for applying this methodology to other ribonucleases.
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Affiliation(s)
- Bryan D Smith
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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Patrick WM, Firth AE. Strategies and computational tools for improving randomized protein libraries. ACTA ACUST UNITED AC 2005; 22:105-12. [PMID: 16095966 DOI: 10.1016/j.bioeng.2005.06.001] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2005] [Revised: 06/20/2005] [Accepted: 06/21/2005] [Indexed: 11/15/2022]
Abstract
In the last decade, directed evolution has become a routine approach for engineering proteins with novel or altered properties. Concurrently, a trend away from purely 'blind' randomization strategies and towards more 'semi-rational' approaches has also become apparent. In this review, we discuss ways in which structural information and predictive computational tools are playing an increasingly important role in guiding the design of randomized libraries: web servers such as ConSurf-HSSP and SCHEMA allow the prediction of sites to target for producing functional variants, while algorithms such as GLUE, PEDEL and DRIVeR are useful for estimating library completeness and diversity. In addition, we review recent methodological developments that facilitate the construction of unbiased libraries, which are inherently more diverse than biased libraries and therefore more likely to yield improved variants.
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Affiliation(s)
- Wayne M Patrick
- Center for Fundamental and Applied Molecular Evolution, Emory University, 1510 Clifton Road, Atlanta GA 30322, USA.
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Volles MJ, Lansbury PT. A computer program for the estimation of protein and nucleic acid sequence diversity in random point mutagenesis libraries. Nucleic Acids Res 2005; 33:3667-77. [PMID: 15990391 PMCID: PMC1166583 DOI: 10.1093/nar/gki669] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A computer program for the generation and analysis of in silico random point mutagenesis libraries is described. The program operates by mutagenizing an input nucleic acid sequence according to mutation parameters specified by the user for each sequence position and type of point mutation. The program can mimic almost any type of random mutagenesis library, including those produced via error-prone PCR (ep-PCR), mutator Escherichia coli strains, chemical mutagenesis, and doped or random oligonucleotide synthesis. The program analyzes the generated nucleic acid sequences and/or the associated protein library to produce several estimates of library diversity (number of unique sequences, point mutations, and single point mutants) and the rate of saturation of these diversities during experimental screening or selection of clones. This information allows one to select the optimal screen size for a given mutagenesis library, necessary to efficiently obtain a certain coverage of the sequence-space. The program also reports the abundance of each specific protein mutation at each sequence position, which is useful as a measure of the level and type of mutation bias in the library. Alternatively, one can use the program to evaluate the relative merits of preexisting libraries, or to examine various hypothetical mutation schemes to determine the optimal method for creating a library that serves the screen/selection of interest. Simulated libraries of at least 109 sequences are accessible by the numerical algorithm with currently available personal computers; an analytical algorithm is also available which can rapidly calculate a subset of the numerical statistics in libraries of arbitrarily large size. A multi-type double-strand stochastic model of ep-PCR is developed in an appendix to demonstrate the applicability of the algorithm to amplifying mutagenesis procedures. Estimators of DNA polymerase mutation-type-specific error rates are derived using the model. Analyses of an alpha-synuclein ep-PCR library and NNS synthetic oligonucleotide libraries are given as examples.
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Affiliation(s)
- Michael J Volles
- Center for Neurologic Diseases, Brigham and Women's Hospital and Department of Neurology, Harvard Medical School 65 Landsdowne Street, Cambridge, MA 02139, USA.
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