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Zhang X, Mille-Fragoso LS, Kaseniit KE, Call CC, Zhang M, Hu Y, Xie Y, Gao XJ. Post-Transcriptional Modular Synthetic Receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592453. [PMID: 38746461 PMCID: PMC11092781 DOI: 10.1101/2024.05.03.592453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Inspired by the power of transcriptional synthetic receptors and hoping to complement them to expand the toolbox for cell engineering, we establish LIDAR (Ligand-Induced Dimerization Activating RNA editing), a modular post-transcriptional synthetic receptor platform that harnesses RNA editing by ADAR. LIDAR is compatible with various receptor architectures in different cellular contexts, and enables the sensing of diverse ligands and the production of functional outputs. Furthermore, LIDAR can sense orthogonal signals in the same cell and produce synthetic spatial patterns, potentially enabling the programming of complex multicellular behaviors. Finally, LIDAR is compatible with compact encoding and can be delivered by synthetic mRNA. Thus, LIDAR expands the family of synthetic receptors, holding the promise to empower basic research and therapeutic applications.
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Chen Y, Hu R, Li K, Zhang Y, Fu L, Zhang J, Si T. Deep Mutational Scanning of an Oxygen-Independent Fluorescent Protein CreiLOV for Comprehensive Profiling of Mutational and Epistatic Effects. ACS Synth Biol 2023; 12:1461-1473. [PMID: 37066862 PMCID: PMC10204710 DOI: 10.1021/acssynbio.2c00662] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Indexed: 04/18/2023]
Abstract
Oxygen-independent, flavin mononucleotide-based fluorescent proteins (FbFPs) are promising alternatives to green fluorescent protein in anaerobic contexts. Deep mutational scanning performs systematic profiling of protein sequence-function relationships but has not been applied to FbFPs. Focusing on CreiLOV from Chlamydomonas reinhardtii, we created and analyzed two comprehensive mutant collections: (1) single-residue, site-saturation mutagenesis libraries covering all 118 residues; and (2) a full combinatorial metagenesis library among 20 mutations at 15 residues, where mutation and residue selection was based on single-site mutagenesis results. Notably, the second type of library is indispensable to study higher-order epistasis but underrepresented in the literature. Using optimized FACS-seq assays, 2,185 (>92.5%) out of 2,360 possible single-site mutants and 165,428 (>89.7%) out of 184,320 possible combinatorial mutants were reliably assigned with fitness values. We constructed statistical and machine-learning models to analyze the CreiLOV data set, enabling accurate fitness prediction of higher-order mutants using lower-order mutagenesis data. In addition, we successfully isolated CreiLOV variants with improved fluorescence quantum yield and thermostability. This work provides new empirical data and design rules to engineer combinatorial protein variants.
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Affiliation(s)
- Yongcan Chen
- CAS
Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ruyun Hu
- CAS
Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Keyi Li
- CAS
Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yating Zhang
- CAS
Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lihao Fu
- CAS
Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianzhi Zhang
- CAS
Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tong Si
- CAS
Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- BGI-Shenzhen, Shenzhen 518083, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
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Formation of synthetic RNA protein granules using engineered phage-coat-protein -RNA complexes. Nat Commun 2022; 13:6811. [PMID: 36357399 PMCID: PMC9649756 DOI: 10.1038/s41467-022-34644-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 11/02/2022] [Indexed: 11/12/2022] Open
Abstract
Liquid-solid transition, also known as gelation, is a specific form of phase separation in which molecules cross-link to form a highly interconnected compartment with solid - like dynamical properties. Here, we utilize RNA hairpin coat-protein binding sites to form synthetic RNA based gel-like granules via liquid-solid phase transition. We show both in-vitro and in-vivo that hairpin containing synthetic long non-coding RNA (slncRNA) molecules granulate into bright localized puncta. We further demonstrate that upon introduction of the coat-proteins, less-condensed gel-like granules form with the RNA creating an outer shell with the proteins mostly present inside the granule. Moreover, by tracking puncta fluorescence signals over time, we detected addition or shedding events of slncRNA-CP nucleoprotein complexes. Consequently, our granules constitute a genetically encoded storage compartment for protein and RNA with a programmable controlled release profile that is determined by the number of hairpins encoded into the RNA. Our findings have important implications for the potential regulatory role of naturally occurring granules and for the broader biotechnology field.
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Guo Y, Lee RE. Long-term imaging of individual mRNA molecules in living cells. CELL REPORTS METHODS 2022; 2:100226. [PMID: 35784652 PMCID: PMC9243547 DOI: 10.1016/j.crmeth.2022.100226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/10/2022] [Accepted: 05/04/2022] [Indexed: 12/04/2022]
Abstract
Single-cell imaging of individual mRNAs has revealed core mechanisms of the central dogma. However, most approaches require cell fixation or have limited sensitivity for live-cell applications. Here, we describe SunRISER (SunTag-based reporter for imaging signal-enriched mRNA), a computationally and experimentally optimized approach for unambiguous detection of single mRNA molecules in living cells. When viewed by epifluorescence microscopy, SunRISER-labeled mRNAs show strong signal to background and resistance to photobleaching, which together enable long-term mRNA imaging studies. SunRISER variants, using 8× and 10× stem-loop arrays, demonstrate effective mRNA detection while significantly reducing alterations to target mRNA sequences. We characterize SunRISER to observe mRNA inheritance during mitosis and find that stressors enhance diversity among post-mitotic sister cells. Taken together, SunRISER enables a glimpse into living cells to observe aspects of the central dogma and the role of mRNAs in rare and dynamical trafficking events.
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Affiliation(s)
- Yue Guo
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Robin E.C. Lee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Systems Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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Vaknin I, Amit R. Molecular and experimental tools to design synthetic enhancers. Curr Opin Biotechnol 2022; 76:102728. [PMID: 35525178 DOI: 10.1016/j.copbio.2022.102728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 03/16/2022] [Accepted: 04/03/2022] [Indexed: 11/03/2022]
Abstract
Understanding the grammar of enhancers and how they regulate gene expression is key for both basic research and for the pharma and biotech industries. The design and characterization of synthetic enhancers can expand the known regulatory space. This is achieved by the utilization of DNA Oligo Libraries (OLs), which facilitates screening of as many as millions of synthetic enhancer variants simultaneously. This review includes the latest commercial DNA OL synthesis technology and its capabilities, and a general 'know-how' guide for the design, construction, and analysis of OL-based synthetic enhancer characterization experiments. Specifically, we focus on synthetic-enhancer-based massively parallel reporter assay, Sort-seq methodologies (e.g. flow cytometry, deep sequencing), and a brief description of machine learning-based attempts for OL-analysis and follow-up validation experiments.
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Affiliation(s)
- Inbal Vaknin
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 3200000, Israel
| | - Roee Amit
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 3200000, Israel; The Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa 3200000, Israel.
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Intelligent host engineering for metabolic flux optimisation in biotechnology. Biochem J 2021; 478:3685-3721. [PMID: 34673920 PMCID: PMC8589332 DOI: 10.1042/bcj20210535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Optimising the function of a protein of length N amino acids by directed evolution involves navigating a 'search space' of possible sequences of some 20N. Optimising the expression levels of P proteins that materially affect host performance, each of which might also take 20 (logarithmically spaced) values, implies a similar search space of 20P. In this combinatorial sense, then, the problems of directed protein evolution and of host engineering are broadly equivalent. In practice, however, they have different means for avoiding the inevitable difficulties of implementation. The spare capacity exhibited in metabolic networks implies that host engineering may admit substantial increases in flux to targets of interest. Thus, we rehearse the relevant issues for those wishing to understand and exploit those modern genome-wide host engineering tools and thinking that have been designed and developed to optimise fluxes towards desirable products in biotechnological processes, with a focus on microbial systems. The aim throughput is 'making such biology predictable'. Strategies have been aimed at both transcription and translation, especially for regulatory processes that can affect multiple targets. However, because there is a limit on how much protein a cell can produce, increasing kcat in selected targets may be a better strategy than increasing protein expression levels for optimal host engineering.
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Kaufmann B, Willinger O, Kikuchi N, Navon N, Kermas L, Goldberg S, Amit R. An Oligo-Library-Based Approach for Mapping DNA-DNA Triplex Interactions In Vitro. ACS Synth Biol 2021; 10:1808-1820. [PMID: 34374529 DOI: 10.1021/acssynbio.1c00122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We present Triplex-seq, a deep-sequencing method that systematically maps the interaction space between an oligo library of ssDNA triplex-forming oligos (TFOs) and a particular dsDNA triplex target site (TTS). We demonstrate the method using a randomized oligo library comprising 67 million variants, with five TTSs that differ in guanine (G) content, at two different buffer conditions, denoted pH 5 and pH 7. Our results show that G-rich triplexes form at both pH 5 and pH 7, with the pH 5 set being more stable, indicating that there is a subset of TFOs that form triplexes only at pH 5. In addition, using information analysis, we identify triplex-forming motifs (TFMs), which correspond to minimal functional TFO sequences. We demonstrate, in single-variant verification experiments, that TFOs with these TFMs indeed form a triplex with G-rich TTSs, and that a single mutation in the TFM motif can alleviate binding. Our results show that deep-sequencing platforms can substantially expand our understanding of triplex binding rules and aid in refining the DNA triplex code.
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Affiliation(s)
- Beate Kaufmann
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Or Willinger
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Nanami Kikuchi
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Noa Navon
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Lisa Kermas
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Sarah Goldberg
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Roee Amit
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
- Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa 32000, Israel
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