51
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Li G, Huang D, Sui X, Li S, Huang B, Zhang X, Wu H, Deng Y. Advances in microbial production of medium-chain dicarboxylic acids for nylon materials. REACT CHEM ENG 2020. [DOI: 10.1039/c9re00338j] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Medium-chain dicarboxylic acids (MDCAs) are widely used in the production of nylon materials, and among which, succinic, glutaric, adipic, pimelic, suberic, azelaic and sebacic acids are particularly important for that purpose.
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Affiliation(s)
- Guohui Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
| | - Dixuan Huang
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
| | - Xue Sui
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
| | - Shiyun Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
| | - Bing Huang
- State Key Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology
| | - Xiaojuan Zhang
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
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52
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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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53
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Thuronyi BW, Koblan LW, Levy JM, Yeh WH, Zheng C, Newby GA, Wilson C, Bhaumik M, Shubina-Oleinik O, Holt JR, Liu DR. Continuous evolution of base editors with expanded target compatibility and improved activity. Nat Biotechnol 2019; 37:1070-1079. [PMID: 31332326 PMCID: PMC6728210 DOI: 10.1038/s41587-019-0193-0] [Citation(s) in RCA: 188] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 06/14/2019] [Indexed: 12/15/2022]
Abstract
Base editors use DNA-modifying enzymes targeted with a catalytically impaired CRISPR protein to precisely install point mutations. Here, we develop phage-assisted continuous evolution of base editors (BE-PACE) to improve their editing efficiency and target sequence compatibility. We used BE-PACE to evolve cytosine base editors (CBEs) that overcome target sequence context constraints of canonical CBEs. One evolved CBE, evoAPOBEC1-BE4max, is up to 26-fold more efficient at editing cytosine in the GC context, a disfavored context for wild-type APOBEC1 deaminase, while maintaining efficient editing in all other sequence contexts tested. Another evolved deaminase, evoFERNY, is 29% smaller than APOBEC1 and edits efficiently in all tested sequence contexts. We also evolved a CBE based on CDA1 deaminase with much higher editing efficiency at difficult target sites. Finally, we used data from evolved CBEs to illuminate the relationship between deaminase activity, base editing efficiency, editing window width and byproduct formation. These findings establish a system for rapid evolution of base editors and inform their use and improvement.
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Affiliation(s)
- B W Thuronyi
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Chemistry, Williams College, Williamstown, MA, USA
| | - Luke W Koblan
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jonathan M Levy
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Wei-Hsi Yeh
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA, USA
| | - Christine Zheng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Christopher Wilson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Mantu Bhaumik
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Olga Shubina-Oleinik
- Departments of Otolaryngology and Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jeffrey R Holt
- Departments of Otolaryngology and Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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54
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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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55
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English JG, Olsen RHJ, Lansu K, Patel M, White K, Cockrell AS, Singh D, Strachan RT, Wacker D, Roth BL. VEGAS as a Platform for Facile Directed Evolution in Mammalian Cells. Cell 2019; 178:748-761.e17. [PMID: 31280962 DOI: 10.1016/j.cell.2019.05.051] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/06/2019] [Accepted: 05/23/2019] [Indexed: 02/08/2023]
Abstract
Directed evolution, artificial selection toward designed objectives, is routinely used to develop new molecular tools and therapeutics. Successful directed molecular evolution campaigns repeatedly test diverse sequences with a designed selective pressure. Unicellular organisms and their viral pathogens are exceptional for this purpose and have been used for decades. However, many desirable targets of directed evolution perform poorly or unnaturally in unicellular backgrounds. Here, we present a system for facile directed evolution in mammalian cells. Using the RNA alphavirus Sindbis as a vector for heredity and diversity, we achieved 24-h selection cycles surpassing 10-3 mutations per base. Selection is achieved through genetically actuated sequences internal to the host cell, thus the system's name: viral evolution of genetically actuating sequences, or "VEGAS." Using VEGAS, we evolve transcription factors, GPCRs, and allosteric nanobodies toward functional signaling endpoints each in less than 1 weeks' time.
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Affiliation(s)
- Justin G English
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA.
| | - Reid H J Olsen
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Katherine Lansu
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Michael Patel
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Karoline White
- Department of Biology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Adam S Cockrell
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Darshan Singh
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Ryan T Strachan
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Daniel Wacker
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA.
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56
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Abstract
The combination of modern biotechnologies such as DNA synthesis, λ red recombineering, CRISPR-based editing and next-generation high-throughput sequencing increasingly enables precise manipulation of genes and genomes. Beyond rational design, these technologies also enable the targeted, and potentially continuous, introduction of multiple mutations. While this might seem to be merely a return to natural selection, the ability to target evolution greatly reduces fitness burdens and focuses mutation and selection on those genes and traits that best contribute to a desired phenotype, ultimately throwing evolution into fast forward.
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57
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Heins ZJ, Mancuso CP, Kiriakov S, Wong BG, Bashor CJ, Khalil AS. Designing Automated, High-throughput, Continuous Cell Growth Experiments Using eVOLVER. J Vis Exp 2019. [PMID: 31157778 DOI: 10.3791/59652] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Continuous culture methods enable cells to be grown under quantitatively controlled environmental conditions, and are thus broadly useful for measuring fitness phenotypes and improving our understanding of how genotypes are shaped by selection. Extensive recent efforts to develop and apply niche continuous culture devices have revealed the benefits of conducting new forms of cell culture control. This includes defining custom selection pressures and increasing throughput for studies ranging from long-term experimental evolution to genome-wide library selections and synthetic gene circuit characterization. The eVOLVER platform was recently developed to meet this growing demand: a continuous culture platform with a high degree of scalability, flexibility, and automation. eVOLVER provides a single standardizing platform that can be (re)-configured and scaled with minimal effort to perform many different types of high-throughput or multi-dimensional growth selection experiments. Here, a protocol is presented to provide users of the eVOLVER framework a description for configuring the system to conduct a custom, large-scale continuous growth experiment. Specifically, the protocol guides users on how to program the system to multiplex two selection pressures - temperature and osmolarity - across many eVOLVER vials in order to quantify fitness landscapes of Saccharomyces cerevisiae mutants at fine resolution. We show how the device can be configured both programmatically, through its open-source web-based software, and physically, by arranging fluidic and hardware layouts. The process of physically setting up the device, programming the culture routine, monitoring and interacting with the experiment in real-time over the internet, sampling vials for subsequent offline analysis, and post experiment data analysis are detailed. This should serve as a starting point for researchers across diverse disciplines to apply eVOLVER in the design of their own complex and high-throughput cell growth experiments to study and manipulate biological systems.
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Affiliation(s)
- Zachary J Heins
- Biological Design Center, Boston University; Department of Biomedical Engineering, Boston University
| | - Christopher P Mancuso
- Biological Design Center, Boston University; Department of Biomedical Engineering, Boston University
| | - Szilvia Kiriakov
- Biological Design Center, Boston University; Program in Molecular Biology, Cell Biology and Biochemistry, Boston University
| | - Brandon G Wong
- Biological Design Center, Boston University; Department of Biomedical Engineering, Boston University
| | | | - Ahmad S Khalil
- Biological Design Center, Boston University; Department of Biomedical Engineering, Boston University; Wyss Institute for Biologically Inspired Engineering, Harvard University;
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58
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Roth TB, Woolston BM, Stephanopoulos G, Liu DR. Phage-Assisted Evolution of Bacillus methanolicus Methanol Dehydrogenase 2. ACS Synth Biol 2019; 8:796-806. [PMID: 30856338 PMCID: PMC6479731 DOI: 10.1021/acssynbio.8b00481] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Synthetic methylotrophy, the modification of organisms such as E. coli to grow on methanol, is a longstanding goal of metabolic engineering and synthetic biology. The poor kinetic properties of NAD-dependent methanol dehydrogenase, the first enzyme in most methanol assimilation pathways, limit pathway flux and present a formidable challenge to synthetic methylotrophy. To address this bottleneck, we used a formaldehyde biosensor to develop a phage-assisted noncontinuous evolution (PANCE) selection for variants of Bacillus methanolicus methanol dehydrogenase 2 (Bm Mdh2). Using this selection, we evolved Mdh2 variants with up to 3.5-fold improved Vmax. The mutations responsible for enhanced activity map to the predicted active site region homologous to that of type III iron-dependent alcohol dehydrogenases, suggesting a new critical region for future methanol dehydrogenase engineering strategies. Evolved Mdh2 variants enable twice as much 13C-methanol assimilation into central metabolites than previously reported state-of-the-art methanol dehydrogenases. This work provides improved Mdh2 variants and establishes a laboratory evolution approach for metabolic pathways in bacterial cells.
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Affiliation(s)
- Timothy B. Roth
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Benjamin M. Woolston
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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59
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Tran DT. Engineering Proteases for Mass Spectrometry‐Based Post Translational Modification Analyses. Proteomics 2018; 19:e1700471. [DOI: 10.1002/pmic.201700471] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 10/23/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Duc T. Tran
- School of BiotechnologyInternational University—Vietnam National University in HCMC Ho Chi Minh City 720351 Vietnam
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60
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Berman CM, Papa LJ, Hendel SJ, Moore CL, Suen PH, Weickhardt AF, Doan ND, Kumar CM, Uil TG, Butty VL, Hoeben RC, Shoulders MD. An Adaptable Platform for Directed Evolution in Human Cells. J Am Chem Soc 2018; 140:18093-18103. [PMID: 30427676 DOI: 10.1021/jacs.8b10937] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The discovery and optimization of biomolecules that reliably function in metazoan cells is imperative for both the study of basic biology and the treatment of disease. We describe the development, characterization, and proof-of-concept application of a platform for directed evolution of diverse biomolecules of interest (BOIs) directly in human cells. The platform relies on a custom-designed adenovirus variant lacking multiple genes, including the essential DNA polymerase and protease genes, features that allow us to evolve BOIs encoded by genes as large as 7 kb while attaining the mutation rates and enforcing the selection pressure required for successful directed evolution. High mutagenesis rates are continuously attained by trans-complementation of a newly engineered, highly error-prone form of the adenoviral polymerase. Selection pressure that couples desired BOI functions to adenoviral propagation is achieved by linking the functionality of the encoded BOI to the production of adenoviral protease activity by the human cell. The dynamic range for directed evolution can be enhanced to several orders of magnitude via application of a small-molecule adenoviral protease inhibitor to modulate selection pressure during directed evolution experiments. This platform makes it possible, in principle, to evolve any biomolecule activity that can be coupled to adenoviral protease expression or activation by simply serially passaging adenoviral populations carrying the BOI. As proof-of-concept, we use the platform to evolve, directly in the human cell environment, several transcription factor variants that maintain high levels of function while gaining resistance to a small-molecule inhibitor. We anticipate that this platform will substantially expand the repertoire of biomolecules that can be reliably and robustly engineered for both research and therapeutic applications in metazoan systems.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Taco G Uil
- Department of Cell and Chemical Biology , Leiden University Medical Center , 2300 RC Leiden , The Netherlands
| | | | - Robert C Hoeben
- Department of Cell and Chemical Biology , Leiden University Medical Center , 2300 RC Leiden , The Netherlands
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61
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Wang T, Badran AH, Huang TP, Liu DR. Continuous directed evolution of proteins with improved soluble expression. Nat Chem Biol 2018; 14:972-980. [PMID: 30127387 PMCID: PMC6143403 DOI: 10.1038/s41589-018-0121-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/17/2018] [Indexed: 01/20/2023]
Abstract
We report the development of soluble expression phage-assisted continuous evolution (SE-PACE), a system for rapidly evolving proteins with increased soluble expression. Through use of a PACE-compatible AND gate that uses a split-intein pIII, SE-PACE enables two simultaneous positive selections to evolve proteins with improved expression while maintaining their desired activities. In as little as three days, SE-PACE evolved several antibody fragments with >5-fold improvement in expression yield while retaining binding activity. We also developed an activity-independent form of SE-PACE to correct folding-defective variants of maltose-binding protein (MBP) and to evolve variants of the eukaryotic cytidine deaminase APOBEC1 with improved expression properties. These evolved APOBEC1 variants were found to improve the expression and apparent activity of Cas9-derived base editors when used in place of the wild-type cytidine deaminase. Together, these results suggest that SE-PACE can be applied to a wide variety of proteins to rapidly improve their soluble expression.
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Affiliation(s)
- Tina Wang
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Ahmed H Badran
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Tony P Huang
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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62
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Abstract
Bacteriophage research has been instrumental to advancing many fields of biology, such as genetics, molecular biology, and synthetic biology. Many phage-derived technologies have been adapted for building gene circuits to program biological systems. Phages also exhibit significant medical potential as antibacterial agents and bacterial diagnostics due to their extreme specificity for their host, and our growing ability to engineer them further enhances this potential. Phages have also been used as scaffolds for genetically programmable biomaterials that have highly tunable properties. Furthermore, phages are central to powerful directed evolution platforms, which are being leveraged to enhance existing biological functions and even produce new ones. In this review, we discuss recent examples of how phage research is influencing these next-generation biotechnologies.
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Affiliation(s)
- Sebastien Lemire
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Kevin M Yehl
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Timothy K Lu
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; .,Synthetic Biology Group, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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63
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64
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Tang W, Liu DR. Rewritable multi-event analog recording in bacterial and mammalian cells. Science 2018; 360:eaap8992. [PMID: 29449507 PMCID: PMC5898985 DOI: 10.1126/science.aap8992] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/22/2017] [Accepted: 02/08/2018] [Indexed: 12/26/2022]
Abstract
We present two CRISPR-mediated analog multi-event recording apparatus (CAMERA) systems that use base editors and Cas9 nucleases to record cellular events in bacteria and mammalian cells. The devices record signal amplitude or duration as changes in the ratio of mutually exclusive DNA sequences (CAMERA 1) or as single-base modifications (CAMERA 2). We achieved recording of multiple stimuli in bacteria or mammalian cells, including exposure to antibiotics, nutrients, viruses, light, and changes in Wnt signaling. When recording to multicopy plasmids, reliable readout requires as few as 10 to 100 cells. The order of stimuli can be recorded through an overlapping guide RNA design, and memories can be erased and re-recorded over multiple cycles. CAMERA systems serve as "cell data recorders" that write a history of endogenous or exogenous signaling events into permanent DNA sequence modifications in living cells.
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Affiliation(s)
- Weixin Tang
- Merkin Institute for Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, and Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - David R Liu
- Merkin Institute for Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, and Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
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65
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Cheng F, Tang XL, Kardashliev T. Transcription Factor-Based Biosensors in High-Throughput Screening: Advances and Applications. Biotechnol J 2018; 13:e1700648. [DOI: 10.1002/biot.201700648] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/17/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Feng Cheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology; Hangzhou 310014 P. R. China
| | - Xiao-Ling Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology; Hangzhou 310014 P. R. China
| | - Tsvetan Kardashliev
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich; Mattenstrasse 26 4058 Basel Switzerland
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66
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Renteln M. Conditional replication of oncolytic viruses based on detection of oncogenic mRNA. Gene Ther 2018; 25:1-3. [PMID: 29350682 DOI: 10.1038/gt.2017.99] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 09/19/2017] [Accepted: 10/26/2017] [Indexed: 12/22/2022]
Abstract
Recently, split intein-based detection sensors for RNA have been developed that can target custom sequences in a modular fashion. If multi-region, multi-sample sequencing were to be applied to a patient's cancer, truncal (that is, earliest-occurring) mutations could be identified and could serve as targets for these sense-and-respond modules. The next step would be to utilize an effective vector for treatment. A hyper-virulent herpes simplex virus could possibly serve as this vector, with concurrent immunosuppression to allow for unhindered infection of the tumor regions. Given that, the oncogenic mutations could serve as molecular 'kindling', with exogenous small molecule-mediated enhancement of replication after initial seeding of tumors and metastases. Then, a toxin may be induced to destroy the cancer entirely, ideally with a bystander effect.
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Affiliation(s)
- M Renteln
- Integrative Molecular Genetics and Biochemistry, University of Southern California, Baylor College of Medicine, Altadena, CA, USA
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67
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Liu SD, Wu YN, Wang TM, Zhang C, Xing XH. Maltose Utilization as a Novel Selection Strategy for Continuous Evolution of Microbes with Enhanced Metabolite Production. ACS Synth Biol 2017; 6:2326-2338. [PMID: 28841296 DOI: 10.1021/acssynbio.7b00247] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have developed a novel selection circuit based on carbon source utilization that establishes and sustains growth-production coupling over several generations in a medium with maltose as the sole carbon source. In contrast to traditional antibiotic resistance-based circuits, we first proved that coupling of cell fitness to metabolite production by our circuit was more robust with a much lower escape risk even after many rounds of selection. We then applied the selection circuit to the optimization of L-tryptophan (l-Trp) production. We demonstrated that it enriched for specific mutants with increased l-Trp productivity regardless of whether it was applied to a small and defined mutational library or a relatively large and undefined one. From the latter, we identified four novel mutations with enhanced l-Trp output. Finally, we used it to select for several high l-Trp producers with randomly generated genome-wide mutations and obtained strains with up to 65% increased l-Trp production. This selection circuit provides new perspectives for the optimization of microbial cell factories for diverse metabolite production and the discovery of novel genotype-phenotype associations at the single-gene and whole-genome levels.
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Affiliation(s)
- Shu-De Liu
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
| | - Yi-Nan Wu
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
| | - Tian-Min Wang
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
| | - Xin-Hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
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68
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Bryson DI, Fan C, Guo LT, Miller C, Söll D, Liu DR. Continuous directed evolution of aminoacyl-tRNA synthetases. Nat Chem Biol 2017; 13:1253-1260. [PMID: 29035361 PMCID: PMC5724969 DOI: 10.1038/nchembio.2474] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/08/2017] [Indexed: 12/19/2022]
Abstract
Directed evolution of orthogonal aminoacyl-tRNA synthetases (AARSs) enables site-specific installation of noncanonical amino acids (ncAAs) into proteins. Traditional evolution techniques typically produce AARSs with greatly reduced activity and selectivity compared to their wild-type counterparts. We designed phage-assisted continuous evolution (PACE) selections to rapidly produce highly active and selective orthogonal AARSs through hundreds of generations of evolution. PACE of a chimeric Methanosarcina spp. pyrrolysyl-tRNA synthetase (PylRS) improved its enzymatic efficiency (kcat/KMtRNA) 45-fold compared to the parent enzyme. Transplantation of the evolved mutations into other PylRS-derived synthetases improved yields of proteins containing noncanonical residues up to 9.7-fold. Simultaneous positive and negative selection PACE over 48 h greatly improved the selectivity of a promiscuous Methanocaldococcus jannaschii tyrosyl-tRNA synthetase variant for site-specific incorporation of p-iodo-L-phenylalanine. These findings offer new AARSs that increase the utility of orthogonal translation systems and establish the capability of PACE to efficiently evolve orthogonal AARSs with high activity and amino acid specificity.
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Affiliation(s)
- David I. Bryson
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701
| | - Li-Tao Guo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520
| | - Corwin Miller
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520
- Department of Chemistry, Yale University, New Haven, CT, 06520
| | - David R. Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142
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69
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Brödel AK, Isalan M, Jaramillo A. Engineering of biomolecules by bacteriophage directed evolution. Curr Opin Biotechnol 2017; 51:32-38. [PMID: 29175708 DOI: 10.1016/j.copbio.2017.11.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/10/2017] [Accepted: 11/09/2017] [Indexed: 01/21/2023]
Abstract
Conventional in vivo directed evolution methods have primarily linked the biomolecule's activity to bacterial cell growth. Recent developments instead rely on the conditional growth of bacteriophages (phages), viruses that infect and replicate within bacteria. Here we review recent phage-based selection systems for in vivo directed evolution. These approaches have been applied to evolve a wide range of proteins including transcription factors, polymerases, proteases, DNA-binding proteins, and protein-protein interactions. Advances in this field expand the possible applications of protein and RNA engineering. This will ultimately result in new biomolecules with tailor-made properties, as well as giving us a better understanding of basic evolutionary processes.
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Affiliation(s)
- Andreas K Brödel
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; CNRS-UMR8030, Laboratoire iSSB, Évry 91000, France; Université Paris-Saclay, Évry 91000, France; Université d'Évry, Évry 91000, France; CEA, DRF, IG, Genoscope, Évry 91000, France; Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, 46980 Paterna, Spain.
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70
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Baumschlager A, Aoki SK, Khammash M. Dynamic Blue Light-Inducible T7 RNA Polymerases (Opto-T7RNAPs) for Precise Spatiotemporal Gene Expression Control. ACS Synth Biol 2017; 6:2157-2167. [PMID: 29045151 DOI: 10.1021/acssynbio.7b00169] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Light has emerged as a control input for biological systems due to its precise spatiotemporal resolution. The limited toolset for light control in bacteria motivated us to develop a light-inducible transcription system that is independent from cellular regulation through the use of an orthogonal RNA polymerase. Here, we present our engineered blue light-responsive T7 RNA polymerases (Opto-T7RNAPs) that show properties such as low leakiness of gene expression in the dark state, high expression strength when induced with blue light, and an inducible range of more than 300-fold. Following optimization of the system to reduce expression variability, we created a variant that returns to the inactive dark state within minutes once the blue light is turned off. This allows for precise dynamic control of gene expression, which is a key aspect for most applications using optogenetic regulation. The regulators, which only require blue light from ordinary light-emitting diodes for induction, were developed and tested in the bacterium Escherichia coli, which is a crucial cell factory for biotechnology due to its fast and inexpensive cultivation and well understood physiology and genetics. Opto-T7RNAP, with minor alterations, should be extendable to other bacterial species as well as eukaryotes such as mammalian cells and yeast in which the T7 RNA polymerase and the light-inducible Vivid regulator have been shown to be functional. We anticipate that our approach will expand the applicability of using light as an inducer for gene expression independent from cellular regulation and allow for a more reliable dynamic control of synthetic and natural gene networks.
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Affiliation(s)
- Armin Baumschlager
- Department of Biosystems
Science and Engineering (D-BSSE), ETH−Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Stephanie K. Aoki
- Department of Biosystems
Science and Engineering (D-BSSE), ETH−Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems
Science and Engineering (D-BSSE), ETH−Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
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71
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Song L, Zeng AP. Engineering 'cell robots' for parallel and highly sensitive screening of biomolecules under in vivo conditions. Sci Rep 2017; 7:15145. [PMID: 29123248 PMCID: PMC5680304 DOI: 10.1038/s41598-017-15621-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 10/31/2017] [Indexed: 02/03/2023] Open
Abstract
Cells are capable of rapid replication and performing tasks adaptively and ultra-sensitively and can be considered as cheap "biological-robots". Here we propose to engineer cells for screening biomolecules in parallel and with high sensitivity. Specifically, we place the biomolecule variants (library) on the bacterial phage M13. We then design cells to screen the library based on cell-phage interactions mediated by a specific intracellular signal change caused by the biomolecule of interest. For proof of concept, we used intracellular lysine concentration in E. coli as a signal to successfully screen variants of functional aspartate kinase III (AK-III) under in vivo conditions, a key enzyme in L-lysine biosynthesis which is strictly inhibited by L-lysine. Comparative studies with flow cytometry method failed to distinguish the wild-type from lysine resistance variants of AK-III, confirming a higher sensitivity of the method. It opens up a new and effective way of in vivo high-throughput screening for functional molecules and can be easily implemented at low costs.
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Affiliation(s)
- Lifu Song
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestrasse 15, D-21073, Hamburg, Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestrasse 15, D-21073, Hamburg, Germany.
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72
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Woolston BM, Roth T, Kohale I, Liu DR, Stephanopoulos G. Development of a formaldehyde biosensor with application to synthetic methylotrophy. Biotechnol Bioeng 2017; 115:206-215. [PMID: 28921510 DOI: 10.1002/bit.26455] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/01/2017] [Accepted: 09/14/2017] [Indexed: 02/03/2023]
Abstract
Formaldehyde is a prevalent environmental toxin and a key intermediate in single carbon metabolism. The ability to monitor formaldehyde concentration is, therefore, of interest for both environmental monitoring and for metabolic engineering of native and synthetic methylotrophs, but current methods suffer from low sensitivity, complex workflows, or require expensive analytical equipment. Here we develop a formaldehyde biosensor based on the FrmR repressor protein and cognate promoter of Escherichia coli. Optimization of the native repressor binding site and regulatory architecture enabled detection at levels as low as 1 µM. We then used the sensor to benchmark the in vivo activity of several NAD-dependent methanol dehydrogenase (Mdh) variants, the rate-limiting enzyme that catalyzes the first step of methanol assimilation. In order to use this biosensor to distinguish individuals in a mixed population of Mdh variants, we developed a strategy to prevent cross-talk by using glutathione as a formaldehyde sink to minimize intercellular formaldehyde diffusion. Finally, we applied this biosensor to balance expression of mdh and the formaldehyde assimilation enzymes hps and phi in an engineered E. coli strain to minimize formaldehyde build-up while also reducing the burden of heterologous expression. This biosensor offers a quick and simple method for sensitively detecting formaldehyde, and has the potential to be used as the basis for directed evolution of Mdh and dynamic formaldehyde control strategies for establishing synthetic methylotrophy.
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Affiliation(s)
| | - Timothy Roth
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Ishwar Kohale
- Department of Biological Engineering, MIT, Cambridge 02139, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
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73
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Higgins SA, Savage DF. Protein Science by DNA Sequencing: How Advances in Molecular Biology Are Accelerating Biochemistry. Biochemistry 2017; 57:38-46. [DOI: 10.1021/acs.biochem.7b00886] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sean A. Higgins
- Department
of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
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74
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Goldsmith M, Tawfik DS. Enzyme engineering: reaching the maximal catalytic efficiency peak. Curr Opin Struct Biol 2017; 47:140-150. [PMID: 29035814 DOI: 10.1016/j.sbi.2017.09.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/04/2017] [Accepted: 09/20/2017] [Indexed: 01/01/2023]
Abstract
The practical need for highly efficient enzymes presents new challenges in enzyme engineering, in particular, the need to improve catalytic turnover (kcat) or efficiency (kcat/KM) by several orders of magnitude. However, optimizing catalysis demands navigation through complex and rugged fitness landscapes, with optimization trajectories often leading to strong diminishing returns and dead-ends. When no further improvements are observed in library screens or selections, it remains unclear whether the maximal catalytic efficiency of the enzyme (the catalytic 'fitness peak') has been reached; or perhaps, an alternative combination of mutations exists that could yield additional improvements. Here, we discuss fundamental aspects of the process of catalytic optimization, and offer practical solutions with respect to overcoming optimization plateaus.
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Affiliation(s)
- Moshe Goldsmith
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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75
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Suzuki T, Miller C, Guo LT, Ho JML, Bryson DI, Wang YS, Liu DR, Söll D. Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase. Nat Chem Biol 2017; 13:1261-1266. [PMID: 29035363 PMCID: PMC5698177 DOI: 10.1038/nchembio.2497] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/13/2017] [Indexed: 11/16/2022]
Abstract
Pyrrolysyl-tRNA synthetase (PylRS) is a major tool in genetic code expansion with non-canonical amino acids, yet understanding of its structure and activity is incomplete. Here we describe the crystal structure of the previously uncharacterized essential N-terminal domain of this unique enzyme in complex with tRNAPyl. This structure explains why PylRS remains orthogonal in a broad range of organisms, from bacteria to humans. The structure also illustrates why tRNAPyl recognition by PylRS is anticodon-independent; the anticodon does not contact the enzyme. Using standard microbiological culture equipment, we then established a new method for laboratory evolution – a non-continuous counterpart of the previously developed phage-assisted continuous evolution. With this method, we evolved novel PylRS variants with enhanced activity and amino acid specificity. We finally employed an evolved PylRS variant to determine its N-terminal domain structure and show how its mutations improve PylRS activity in the genetic encoding of a non-canonical amino acid.
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Affiliation(s)
- Tateki Suzuki
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Corwin Miller
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Li-Tao Guo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Joanne M L Ho
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - David I Bryson
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Yane-Shih Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.,Department of Chemistry, Yale University, New Haven, Connecticut, USA
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76
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Packer MS, Rees HA, Liu DR. Phage-assisted continuous evolution of proteases with altered substrate specificity. Nat Commun 2017; 8:956. [PMID: 29038472 PMCID: PMC5643515 DOI: 10.1038/s41467-017-01055-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/14/2017] [Indexed: 01/15/2023] Open
Abstract
Here we perform phage-assisted continuous evolution (PACE) of TEV protease, which canonically cleaves ENLYFQS, to cleave a very different target sequence, HPLVGHM, that is present in human IL-23. A protease emerging from ∼2500 generations of PACE contains 20 non-silent mutations, cleaves human IL-23 at the target peptide bond, and when pre-mixed with IL-23 in primary cultures of murine splenocytes inhibits IL-23-mediated immune signaling. We characterize the substrate specificity of this evolved enzyme, revealing shifted and broadened specificity changes at the six positions in which the target amino acid sequence differed. Mutational dissection and additional protease specificity profiling reveal the molecular basis of some of these changes. This work establishes the capability of changing the substrate specificity of a protease at many positions in a practical time scale and provides a foundation for the development of custom proteases that catalytically alter or destroy target proteins for biotechnological and therapeutic applications.Proteases are promising therapeutics to treat diseases such as hemophilia which are due to endogenous protease deficiency. Here the authors use phage-assisted continuous evolution to evolve a variant TEV protease with altered target peptide sequence specificities.
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Affiliation(s)
- Michael S Packer
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA.,Graduate Program in Biophysics Program, Harvard University, 240 Longwood Avenue, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Holly A Rees
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA.,Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA, 02142, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA. .,Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA, 02142, USA. .,Howard Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA.
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77
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Pu J, Dewey JA, Hadji A, LaBelle JL, Dickinson BC. RNA Polymerase Tags To Monitor Multidimensional Protein-Protein Interactions Reveal Pharmacological Engagement of Bcl-2 Proteins. J Am Chem Soc 2017; 139:11964-11972. [PMID: 28767232 PMCID: PMC5828006 DOI: 10.1021/jacs.7b06152] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We report the development of a new technology for monitoring multidimensional protein-protein interactions (PPIs) inside live mammalian cells using split RNA polymerase (RNAP) tags. In this new system, a protein-of-interest is tagged with an N-terminal split RNAP (RNAPN), and multiple potential binding partners are each fused to orthogonal C-terminal RNAPs (RNAPC). Assembly of RNAPN with each RNAPC is highly dependent on interactions between the tagged proteins. Each PPI-mediated RNAPN-RNAPC assembly transcribes from a separate promoter on a supplied DNA substrate, thereby generating a unique RNA output signal for each PPI. We develop and validate this new approach in the context of the Bcl-2 family of proteins. These key regulators of apoptosis are important cancer mediators, but are challenging to therapeutically target due to imperfect selectivity that leads to either off-target toxicity or tumor resistance. We demonstrate binary (1 × 1) and ternary (1 × 2) Bcl-2 PPI analyses by imaging fluorescent protein translation from mRNA outputs. Next, we perform a 1 × 4 PPI network analysis by direct measurement of four unique RNA signals via RT-qPCR. Finally, we use these new tools to monitor pharmacological engagement of Bcl-2 protein inhibitors, and uncover inhibitor-dependent competitive PPIs. The split RNAP tags improve upon other protein fragment complementation (PFC) approaches by offering both multidimensionality and sensitive detection using nucleic acid amplification and analysis techniques. Furthermore, this technology opens new opportunities for synthetic biology applications due to the versatility of RNA outputs for cellular engineering applications.
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Affiliation(s)
- Jinyue Pu
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Jeffrey A. Dewey
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Abbas Hadji
- Section of Hematology, Oncology, Stem Cell Transplantation, Department of Pediatrics, The University of Chicago, Comer Children’s Hospital, Chicago, IL, 60637
| | - James L. LaBelle
- Section of Hematology, Oncology, Stem Cell Transplantation, Department of Pediatrics, The University of Chicago, Comer Children’s Hospital, Chicago, IL, 60637
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78
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Yin K, Gao C, Qiu JL. Progress and prospects in plant genome editing. NATURE PLANTS 2017; 3:17107. [PMID: 28758991 DOI: 10.1038/nplants.2017.107] [Citation(s) in RCA: 223] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 06/16/2017] [Indexed: 05/18/2023]
Abstract
The emergence of sequence-specific nucleases that enable genome editing is revolutionizing basic and applied biology. Since the introduction of CRISPR-Cas9, genome editing has become widely used in transformable plants for characterizing gene function and improving traits, mainly by inducing mutations through non-homologous end joining of double-stranded breaks generated by CRISPR-Cas9. However, it would be highly desirable to perform precision gene editing in plants, especially in transformation-recalcitrant species. Recently developed Cas9 variants, novel RNA-guided nucleases and base-editing systems, and DNA-free CRISPR-Cas9 delivery methods now provide great opportunities for plant genome engineering. In this Review Article, we describe the current status of plant genome editing, focusing on newly developed genome editing tools and methods and their potential applications in plants. We also discuss the specific challenges facing plant genome editing, and future prospects.
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Affiliation(s)
- Kangquan Yin
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jin-Long Qiu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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79
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Castro-Fernandez V, Herrera-Morande A, Zamora R, Merino F, Gonzalez-Ordenes F, Padilla-Salinas F, Pereira HM, Brandão-Neto J, Garratt RC, Guixe V. Reconstructed ancestral enzymes reveal that negative selection drove the evolution of substrate specificity in ADP-dependent kinases. J Biol Chem 2017; 292:15598-15610. [PMID: 28726643 DOI: 10.1074/jbc.m117.790865] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/05/2017] [Indexed: 11/06/2022] Open
Abstract
One central goal in molecular evolution is to pinpoint the mechanisms and evolutionary forces that cause an enzyme to change its substrate specificity; however, these processes remain largely unexplored. Using the glycolytic ADP-dependent kinases of archaea, including the orders Thermococcales, Methanosarcinales, and Methanococcales, as a model and employing an approach involving paleoenzymology, evolutionary statistics, and protein structural analysis, we could track changes in substrate specificity during ADP-dependent kinase evolution along with the structural determinants of these changes. To do so, we studied five key resurrected ancestral enzymes as well as their extant counterparts. We found that a major shift in function from a bifunctional ancestor that could phosphorylate either glucose or fructose 6-phosphate (fructose-6-P) as a substrate to a fructose 6-P-specific enzyme was started by a single amino acid substitution resulting in negative selection with a ground-state mode against glucose and a subsequent 1,600-fold change in specificity of the ancestral protein. This change rendered the residual phosphorylation of glucose a promiscuous and physiologically irrelevant activity, highlighting how promiscuity may be an evolutionary vestige of ancestral enzyme activities, which have been eliminated over time. We also could reconstruct the evolutionary history of substrate utilization by using an evolutionary model of discrete binary characters, indicating that substrate uses can be discretely lost or acquired during enzyme evolution. These findings exemplify how negative selection and subtle enzyme changes can lead to major evolutionary shifts in function, which can subsequently generate important adaptive advantages, for example, in improving glycolytic efficiency in Thermococcales.
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Affiliation(s)
- Víctor Castro-Fernandez
- From the Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 800003, Chile,
| | - Alejandra Herrera-Morande
- From the Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 800003, Chile
| | - Ricardo Zamora
- From the Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 800003, Chile
| | - Felipe Merino
- From the Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 800003, Chile
| | - Felipe Gonzalez-Ordenes
- From the Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 800003, Chile
| | - Felipe Padilla-Salinas
- From the Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 800003, Chile
| | - Humberto M Pereira
- the São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo 13563-120, Brazil, and
| | - Jose Brandão-Neto
- the Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DF, United Kingdom
| | - Richard C Garratt
- the São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo 13563-120, Brazil, and
| | - Victoria Guixe
- From the Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 800003, Chile,
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80
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de Jong H, Geiselmann J, Ropers D. Resource Reallocation in Bacteria by Reengineering the Gene Expression Machinery. Trends Microbiol 2017; 25:480-493. [DOI: 10.1016/j.tim.2016.12.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/03/2016] [Accepted: 12/15/2016] [Indexed: 11/27/2022]
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81
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Chen J, Alcaine SD, Jackson AA, Rotello VM, Nugen SR. Development of Engineered Bacteriophages for Escherichia coli Detection and High-Throughput Antibiotic Resistance Determination. ACS Sens 2017; 2:484-489. [PMID: 28723178 DOI: 10.1021/acssensors.7b00021] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
T7 bacteriophages (phages) have been genetically engineered to carry the lacZ operon, enabling the overexpression of beta-galactosidase (β-gal) during phage infection and allowing for the enhanced colorimetric detection of Escherichia coli (E. coli). Following the phage infection of E. coli, the enzymatic activity of the released β-gal was monitored using a colorimetric substrate. Compared with a control T7 phage, our T7lacZ phage generated significantly higher levels of β-gal expression following phage infection, enabling a lower limit of detection for E. coli cells. Using this engineered T7lacZ phage, we were able to detect E. coli cells at 10 CFU·mL-1 within 7 h. Furthermore, we demonstrated the potential for phage-based sensing of bacteria antibiotic resistance profiling using our T7lacZ phage, and subsequent β-gal expression to detect antibiotic resistant profile of E. coli strains.
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Affiliation(s)
- Juhong Chen
- Department
of Food Science, Cornell University, Stocking Hall, Ithaca, New
York 14853, United States
- Department
of Food Science, University of Massachusetts, 102 Holdsworth Way, Amherst, Massachusetts 01003, United States
| | - Samuel D. Alcaine
- Department
of Food Science, Cornell University, Stocking Hall, Ithaca, New
York 14853, United States
- Department
of Food Science, University of Massachusetts, 102 Holdsworth Way, Amherst, Massachusetts 01003, United States
| | - Angelyca A. Jackson
- Department
of Food Science, Cornell University, Stocking Hall, Ithaca, New
York 14853, United States
| | - Vincent M. Rotello
- Department
of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Sam R. Nugen
- Department
of Food Science, Cornell University, Stocking Hall, Ithaca, New
York 14853, United States
- Department
of Food Science, University of Massachusetts, 102 Holdsworth Way, Amherst, Massachusetts 01003, United States
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82
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Evolution of a split RNA polymerase as a versatile biosensor platform. Nat Chem Biol 2017; 13:432-438. [PMID: 28192413 DOI: 10.1038/nchembio.2299] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 12/05/2016] [Indexed: 12/21/2022]
Abstract
Biosensors that transduce target chemical and biochemical inputs into genetic outputs are essential for bioengineering and synthetic biology. Current biosensor design strategies are often limited by a low signal-to-noise ratio, the extensive optimization required for each new input, and poor performance in mammalian cells. Here we report the development of a proximity-dependent split RNA polymerase (RNAP) as a general platform for biosensor engineering. After discovering that interactions between fused proteins modulate the assembly of a split T7 RNAP, we optimized the split RNAP components for protein-protein interaction detection by phage-assisted continuous evolution (PACE). We then applied the resulting activity-responsive RNAP (AR) system to create biosensors that can be activated by light and small molecules, demonstrating the 'plug-and-play' nature of the platform. Finally, we validated that ARs can interrogate multidimensional protein-protein interactions and trigger RNA nanostructure production, protein synthesis, and gene knockdown in mammalian systems, illustrating the versatility of ARs in synthetic biology applications.
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83
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Frappier V, Chartier M, Najmanovich R. Applications of Normal Mode Analysis Methods in Computational Protein Design. Methods Mol Biol 2017; 1529:203-214. [PMID: 27914052 DOI: 10.1007/978-1-4939-6637-0_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Recent advances in coarse-grained normal mode analysis methods make possible the large-scale prediction of the effect of mutations on protein stability and dynamics as well as the generation of biologically relevant conformational ensembles. Given the interplay between flexibility and enzymatic activity, the combined analysis of stability and dynamics using the Elastic Network Contact Model (ENCoM) method has ample applications in protein engineering in industrial and medical applications such as in computational antibody design. Here, we present a detailed tutorial on how to perform such calculations using ENCoM.
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Affiliation(s)
- Vincent Frappier
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts avenue, Cambridge, MA, 02139, USA
- Faculty of Medicine and Health Sciences, Department of Biochemistry, University of Sherbrooke, 3001, 12 Av., NordSherbrooke, QCJ1H 5N4, Canada
| | - Matthieu Chartier
- Faculty of Medicine and Health Sciences, Department of Biochemistry, University of Sherbrooke, 3001, 12 Av., NordSherbrooke, QCJ1H 5N4, Canada
| | - Rafael Najmanovich
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montreal, Montreal, H3C 3J7, QC, Canada.
- Faculty of Medicine and Health Sciences, Department of Biochemistry, University of Sherbrooke, 3001, 12 Av., NordSherbrooke, QCJ1H 5N4, Canada.
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84
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Brödel AK, Jaramillo A, Isalan M. Engineering orthogonal dual transcription factors for multi-input synthetic promoters. Nat Commun 2016; 7:13858. [PMID: 27982027 PMCID: PMC5171851 DOI: 10.1038/ncomms13858] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/04/2016] [Indexed: 11/30/2022] Open
Abstract
Synthetic biology has seen an explosive growth in the capability of engineering artificial gene circuits from transcription factors (TFs), particularly in bacteria. However, most artificial networks still employ the same core set of TFs (for example LacI, TetR and cI). The TFs mostly function via repression and it is difficult to integrate multiple inputs in promoter logic. Here we present to our knowledge the first set of dual activator-repressor switches for orthogonal logic gates, based on bacteriophage λ cI variants and multi-input promoter architectures. Our toolkit contains 12 TFs, flexibly operating as activators, repressors, dual activator–repressors or dual repressor–repressors, on up to 270 synthetic promoters. To engineer non cross-reacting cI variants, we design a new M13 phagemid-based system for the directed evolution of biomolecules. Because cI is used in so many synthetic biology projects, the new set of variants will easily slot into the existing projects of other groups, greatly expanding current engineering capacities.
Genetic circuits usually employ the same set of transcription factors which can act via repression or activation of the target promoter. Here the authors present dual activator-repressor switches, designed via directed evolution, for orthogonal logic gates and multi-input circuit architectures.
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Affiliation(s)
- Andreas K Brödel
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Alfonso Jaramillo
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.,Institute of Systems and Synthetic Biology, Genopole, CNRS, Université d'Évry, 91030 Évry, France
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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85
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Crook N, Abatemarco J, Sun J, Wagner JM, Schmitz A, Alper HS. In vivo continuous evolution of genes and pathways in yeast. Nat Commun 2016; 7:13051. [PMID: 27748457 PMCID: PMC5071640 DOI: 10.1038/ncomms13051] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/30/2016] [Indexed: 11/17/2022] Open
Abstract
Directed evolution remains a powerful, highly generalizable approach for improving the performance of biological systems. However, implementations in eukaryotes rely either on in vitro diversity generation or limited mutational capacities. Here we synthetically optimize the retrotransposon Ty1 to enable in vivo generation of mutant libraries up to 1.6 × 107 l−1 per round, which is the highest of any in vivo mutational generation approach in yeast. We demonstrate this approach by using in vivo-generated libraries to evolve single enzymes, global transcriptional regulators and multi-gene pathways. When coupled to growth selection, this approach enables in vivo continuous evolution (ICE) of genes and pathways. Through a head-to-head comparison, we find that ICE libraries yield higher-performing variants faster than error-prone PCR-derived libraries. Finally, we demonstrate transferability of ICE to divergent yeasts, including Kluyveromyces lactis and alternative S. cerevisiae strains. Collectively, this work establishes a generic platform for rapid eukaryotic-directed evolution across an array of target cargo. Directed evolution is a powerful technique for generating improved biological systems through repeated rounds of mutagenesis and selection. Here the authors engineer the yeast retrotransposon Ty1 to enable the creation of large mutant libraries in vivo and use this system to generate improved variants of single enzymes and multigene pathways.
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Affiliation(s)
- Nathan Crook
- Department of Chemical Engineering, The University of Texas at Austin, 200 East Dean Keeton Street, Stop C0400, Austin, Texas 78712, USA
| | - Joseph Abatemarco
- Department of Chemical Engineering, The University of Texas at Austin, 200 East Dean Keeton Street, Stop C0400, Austin, Texas 78712, USA
| | - Jie Sun
- Department of Chemical Engineering, The University of Texas at Austin, 200 East Dean Keeton Street, Stop C0400, Austin, Texas 78712, USA
| | - James M Wagner
- Department of Chemical Engineering, The University of Texas at Austin, 200 East Dean Keeton Street, Stop C0400, Austin, Texas 78712, USA
| | - Alexander Schmitz
- Department of Chemical Engineering, The University of Texas at Austin, 200 East Dean Keeton Street, Stop C0400, Austin, Texas 78712, USA
| | - Hal S Alper
- Department of Chemical Engineering, The University of Texas at Austin, 200 East Dean Keeton Street, Stop C0400, Austin, Texas 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, Texas 78712, USA
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86
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Bassalo MC, Liu R, Gill RT. Directed evolution and synthetic biology applications to microbial systems. Curr Opin Biotechnol 2016; 39:126-133. [DOI: 10.1016/j.copbio.2016.03.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 03/12/2016] [Accepted: 03/20/2016] [Indexed: 10/22/2022]
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87
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Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance. Nature 2016; 533:58-63. [PMID: 27120167 PMCID: PMC4865400 DOI: 10.1038/nature17938] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 03/23/2016] [Indexed: 12/17/2022]
Abstract
The Bacillus thuringiensis δ-endotoxins (Bt toxins) are widely used insecticidal proteins in engineered crops that provide agricultural, economic, and environmental benefits. The development of insect resistance to Bt toxins endangers their long-term effectiveness. Here we have developed a phage-assisted continuous evolution selection that rapidly evolves high-affinity protein-protein interactions, and applied this system to evolve variants of the Bt toxin Cry1Ac that bind a cadherin-like receptor from the insect pest Trichoplusia ni (TnCAD) that is not natively bound by wild-type Cry1Ac. The resulting evolved Cry1Ac variants bind TnCAD with high affinity (dissociation constant Kd = 11-41 nM), kill TnCAD-expressing insect cells that are not susceptible to wild-type Cry1Ac, and kill Cry1Ac-resistant T. ni insects up to 335-fold more potently than wild-type Cry1Ac. Our findings establish that the evolution of Bt toxins with novel insect cell receptor affinity can overcome insect Bt toxin resistance and confer lethality approaching that of the wild-type Bt toxin against non-resistant insects.
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88
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Glasscock C, Lucks J, DeLisa M. Engineered Protein Machines: Emergent Tools for Synthetic Biology. Cell Chem Biol 2016; 23:45-56. [DOI: 10.1016/j.chembiol.2015.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/01/2015] [Accepted: 12/01/2015] [Indexed: 11/25/2022]
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89
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Sagona AP, Grigonyte AM, MacDonald PR, Jaramillo A. Genetically modified bacteriophages. Integr Biol (Camb) 2016; 8:465-74. [DOI: 10.1039/c5ib00267b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Applications of genetically modified bacteriophages.
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Affiliation(s)
- Antonia P. Sagona
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences
- University of Warwick
- Coventry
- UK
| | - Aurelija M. Grigonyte
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences
- University of Warwick
- Coventry
- UK
- Synthetic Biology Centre for Doctoral Training
| | - Paul R. MacDonald
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences
- University of Warwick
- Coventry
- UK
- MOAC DTC
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences
- University of Warwick
- Coventry
- UK
- iSSB
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90
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Pu J, Chronis I, Ahn D, Dickinson BC. A Panel of Protease-Responsive RNA Polymerases Respond to Biochemical Signals by Production of Defined RNA Outputs in Live Cells. J Am Chem Soc 2015; 137:15996-9. [PMID: 26652972 DOI: 10.1021/jacs.5b10290] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA is an attractive biomolecule for biosensing and engineering applications due to its information storage capacity and ability to drive gene expression or knockdown. However, methods to link chemical signals to the production of specific RNAs are lacking. Here, we develop protease-responsive RNA polymerases (PRs) as a strategy to encode multiple specific proteolytic events in defined sequences of RNA in live mammalian cells. This work demonstrates that RNAP-based molecular recording devices can be deployed for multimodal analyses of biochemical activities or to trigger gene circuits using measured signaling events.
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Affiliation(s)
- Jinyue Pu
- Department of Chemistry, The University of Chicago , 5801 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Ian Chronis
- Department of Chemistry, The University of Chicago , 5801 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Daniel Ahn
- Department of Chemistry, The University of Chicago , 5801 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago , 5801 South Ellis Avenue, Chicago, Illinois 60637, United States
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91
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Development of potent in vivo mutagenesis plasmids with broad mutational spectra. Nat Commun 2015; 6:8425. [PMID: 26443021 PMCID: PMC4633624 DOI: 10.1038/ncomms9425] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 08/21/2015] [Indexed: 02/07/2023] Open
Abstract
Methods to enhance random mutagenesis in cells offer advantages over in vitro mutagenesis, but current in vivo methods suffer from a lack of control, genomic instability, low efficiency and narrow mutational spectra. Using a mechanism-driven approach, we created a potent, inducible, broad-spectrum and vector-based mutagenesis system in E. coli that enhances mutation 322,000-fold over basal levels, surpassing the mutational efficiency and spectra of widely used in vivo and in vitro methods. We demonstrate that this system can be used to evolve antibiotic resistance in wild-type E. coli in <24 h, outperforming chemical mutagens, ultraviolet light and the mutator strain XL1-Red under similar conditions. This system also enables the continuous evolution of T7 RNA polymerase variants capable of initiating transcription using the T3 promoter in <10 h. Our findings enable broad-spectrum mutagenesis of chromosomes, episomes and viruses in vivo, and are applicable to both bacterial and bacteriophage-mediated laboratory evolution platforms. Random DNA mutagenesis provides genetic diversity both in nature and the laboratory. Here, Badran and Liu present a potent, inducible, broad-spectrum and vector-based mutagenesis system in E. coli that surpasses the mutational efficiency and spectra of the most widely used in vivo and in vitro mutagenesis methods.
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92
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Library construction, selection and modification strategies to generate therapeutic peptide-based modulators of protein-protein interactions. Future Med Chem 2015; 6:2073-92. [PMID: 25531969 DOI: 10.4155/fmc.14.134] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In the modern age of proteomics, vast numbers of protein-protein interactions (PPIs) are being identified as causative agents in pathogenesis, and are thus attractive therapeutic targets for intervention. Although traditionally regarded unfavorably as druggable agents relative to small molecules, peptides in recent years have gained considerable attention. Their previous dismissal had been largely due to the susceptibility of unmodified peptides to the barriers and pressures exerted by the circulation, immune system, proteases, membranes and other stresses. However, recent advances in high-throughput peptide isolation techniques, as well as a huge variety of direct modification options and approaches to allow targeted delivery, mean that peptides and their mimetics can now be designed to circumvent many of these traditional barriers. As a result, an increasing number of peptide-based drugs are reaching clinical trials and patients beyond.
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93
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Abstract
Next-generation DNA sequencing has revealed the complete genome sequences of numerous organisms, establishing a fundamental and growing understanding of genetic variation and phenotypic diversity. Engineering at the gene, network and whole-genome scale aims to introduce targeted genetic changes both to explore emergent phenotypes and to introduce new functionalities. Expansion of these approaches into massively parallel platforms establishes the ability to generate targeted genome modifications, elucidating causal links between genotype and phenotype, as well as the ability to design and reprogramme organisms. In this Review, we explore techniques and applications in genome engineering, outlining key advances and defining challenges.
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94
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Hubbard BP, Badran AH, Zuris JA, Guilinger JP, Davis KM, Chen L, Tsai SQ, Sander JD, Joung JK, Liu DR. Continuous directed evolution of DNA-binding proteins to improve TALEN specificity. Nat Methods 2015; 12:939-42. [PMID: 26258293 PMCID: PMC4589463 DOI: 10.1038/nmeth.3515] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 06/26/2015] [Indexed: 11/09/2022]
Abstract
Nucleases containing programmable DNA-binding domains can alter the genomes of model organisms and have the potential to become human therapeutics. Here we present DNA-binding phage-assisted continuous evolution (DB-PACE) as a general approach for the laboratory evolution of DNA-binding activity and specificity. We used this system to generate transcription activator-like effectors nucleases (TALENs) with broadly improved DNA cleavage specificity, establishing DB-PACE as a versatile approach for improving the accuracy of genome-editing agents.
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Affiliation(s)
- Basil P Hubbard
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Ahmed H Badran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - John A Zuris
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - John P Guilinger
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Kevin M Davis
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Liwei Chen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Shengdar Q Tsai
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffry D Sander
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
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95
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Henry KA, Arbabi-Ghahroudi M, Scott JK. Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold. Front Microbiol 2015; 6:755. [PMID: 26300850 PMCID: PMC4523942 DOI: 10.3389/fmicb.2015.00755] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 07/10/2015] [Indexed: 12/23/2022] Open
Abstract
For the past 25 years, phage display technology has been an invaluable tool for studies of protein-protein interactions. However, the inherent biological, biochemical, and biophysical properties of filamentous bacteriophage, as well as the ease of its genetic manipulation, also make it an attractive platform outside the traditional phage display canon. This review will focus on the unique properties of the filamentous bacteriophage and highlight its diverse applications in current research. Particular emphases are placed on: (i) the advantages of the phage as a vaccine carrier, including its high immunogenicity, relative antigenic simplicity and ability to activate a range of immune responses, (ii) the phage's potential as a prophylactic and therapeutic agent for infectious and chronic diseases, (iii) the regularity of the virion major coat protein lattice, which enables a variety of bioconjugation and surface chemistry applications, particularly in nanomaterials, and (iv) the phage's large population sizes and fast generation times, which make it an excellent model system for directed protein evolution. Despite their ubiquity in the biosphere, metagenomics work is just beginning to explore the ecology of filamentous and non-filamentous phage, and their role in the evolution of bacterial populations. Thus, the filamentous phage represents a robust, inexpensive, and versatile microorganism whose bioengineering applications continue to expand in new directions, although its limitations in some spheres impose obstacles to its widespread adoption and use.
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Affiliation(s)
- Kevin A. Henry
- Human Health Therapeutics Portfolio, National Research Council Canada, OttawaON, Canada
| | - Mehdi Arbabi-Ghahroudi
- Human Health Therapeutics Portfolio, National Research Council Canada, OttawaON, Canada
- School of Environmental Sciences, University of Guelph, GuelphON, Canada
- Department of Biology, Carleton University, OttawaON, Canada
| | - Jamie K. Scott
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BCCanada
- Faculty of Health Sciences, Simon Fraser University, BurnabyBC, Canada
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96
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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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97
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Del Vecchio D. Modularity, context-dependence, and insulation in engineered biological circuits. Trends Biotechnol 2015; 33:111-9. [DOI: 10.1016/j.tibtech.2014.11.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 11/06/2014] [Accepted: 11/19/2014] [Indexed: 01/21/2023]
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98
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Abstract
Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA(Pyl) have emerged as ideal translation components for genetic code innovation. Variants of the enzyme facilitate the incorporation >100 noncanonical amino acids (ncAAs) into proteins. PylRS variants were previously selected to acylate N(ε)-acetyl-Lys (AcK) onto tRNA(Pyl). Here, we examine an N(ε)-acetyl-lysyl-tRNA synthetase (AcKRS), which is polyspecific (i.e., active with a broad range of ncAAs) and 30-fold more efficient with Phe derivatives than it is with AcK. Structural and biochemical data reveal the molecular basis of polyspecificity in AcKRS and in a PylRS variant [iodo-phenylalanyl-tRNA synthetase (IFRS)] that displays both enhanced activity and substrate promiscuity over a chemical library of 313 ncAAs. IFRS, a product of directed evolution, has distinct binding modes for different ncAAs. These data indicate that in vivo selections do not produce optimally specific tRNA synthetases and suggest that translation fidelity will become an increasingly dominant factor in expanding the genetic code far beyond 20 amino acids.
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99
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Badran AH, Liu DR. In vivo continuous directed evolution. Curr Opin Chem Biol 2014; 24:1-10. [PMID: 25461718 DOI: 10.1016/j.cbpa.2014.09.040] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 09/12/2014] [Indexed: 01/22/2023]
Abstract
The development and application of methods for the laboratory evolution of biomolecules has rapidly progressed over the last few decades. Advancements in continuous microbe culturing and selection design have facilitated the development of new technologies that enable the continuous directed evolution of proteins and nucleic acids. These technologies have the potential to support the extremely rapid evolution of biomolecules with tailor-made functional properties. Continuous evolution methods must support all of the key steps of laboratory evolution - translation of genes into gene products, selection or screening, replication of genes encoding the most fit gene products, and mutation of surviving genes - in a self-sustaining manner that requires little or no researcher intervention. Continuous laboratory evolution has been historically used to study problems including antibiotic resistance, organismal adaptation, phylogenetic reconstruction, and host-pathogen interactions, with more recent applications focusing on the rapid generation of proteins and nucleic acids with useful, tailor-made properties. The advent of increasingly general methods for continuous directed evolution should enable researchers to address increasingly complex questions and to access biomolecules with more novel or even unprecedented properties.
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Affiliation(s)
- Ahmed H Badran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, United States
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, United States.
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100
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Dickinson BC, Packer MS, Badran AH, Liu DR. A system for the continuous directed evolution of proteases rapidly reveals drug-resistance mutations. Nat Commun 2014; 5:5352. [PMID: 25355134 PMCID: PMC4215169 DOI: 10.1038/ncomms6352] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 09/19/2014] [Indexed: 12/11/2022] Open
Abstract
The laboratory evolution of protease enzymes has the potential to generate proteases with therapeutically relevant specificities, and to assess the vulnerability of protease inhibitor drug candidates to the evolution of drug resistance. Here we describe a system for the continuous directed evolution of proteases using phage-assisted continuous evolution (PACE) that links the proteolysis of a target peptide to phage propagation through a protease-activated RNA polymerase (PA-RNAP). We use protease PACE in the presence of danoprevir or asunaprevir, two hepatitis C virus (HCV) protease inhibitor drug candidates in clinical trials, to continuously evolve HCV protease variants that exhibit up to 30-fold drug resistance in only 1 to 3 days of PACE. The predominant mutations evolved during PACE are mutations observed to arise in human patients treated with danoprevir or asunaprevir, demonstrating that protease PACE can rapidly identify the vulnerabilities of drug candidates to the evolution of clinically relevant drug resistance.
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Affiliation(s)
- Bryan C Dickinson
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, USA
| | - Michael S Packer
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, USA
| | - Ahmed H Badran
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, USA
| | - David R Liu
- 1] Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, USA [2] Howard Hughes Medical Institute, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, USA
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