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Radford F, Rinehart J, Isaacs FJ. Mapping the in vivo fitness landscape of a tethered ribosome. Sci Adv 2023; 9:eade8934. [PMID: 37115918 PMCID: PMC10146877 DOI: 10.1126/sciadv.ade8934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Fitness landscapes are models of the sequence space of a genetic element that map how each sequence corresponds to its activity and can be used to guide laboratory evolution. The ribosome is a macromolecular machine that is essential for protein synthesis in all organisms. Because of the prevalence of dominant lethal mutations, a comprehensive fitness landscape of the ribosomal peptidyl transfer center (PTC) has not yet been attained. Here, we develop a method to functionally map an orthogonal tethered ribosome (oRiboT), which permits complete mutagenesis of nucleotides located in the PTC and the resulting epistatic interactions. We found that most nucleotides studied showed flexibility to mutation, and identified epistatic interactions between them, which compensate for deleterious mutations. This work provides a basis for a deeper understanding of ribosome function and malleability and could be used to inform design of engineered ribosomes with applications to synthesize next-generation biomaterials and therapeutics.
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Affiliation(s)
- Felix Radford
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jesse Rinehart
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Farren J. Isaacs
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Corresponding author.
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Radford F, Elliott SD, Schepartz A, Isaacs FJ. Targeted editing and evolution of engineered ribosomes in vivo by filtered editing. Nat Commun 2022; 13:180. [PMID: 35013328 PMCID: PMC8748908 DOI: 10.1038/s41467-021-27836-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/13/2021] [Indexed: 12/26/2022] Open
Abstract
Genome editing technologies introduce targeted chromosomal modifications in organisms yet are constrained by the inability to selectively modify repetitive genetic elements. Here we describe filtered editing, a genome editing method that embeds group 1 self-splicing introns into repetitive genetic elements to construct unique genetic addresses that can be selectively modified. We introduce intron-containing ribosomes into the E. coli genome and perform targeted modifications of these ribosomes using CRISPR/Cas9 and multiplex automated genome engineering. Self-splicing of introns post-transcription yields scarless RNA molecules, generating a complex library of targeted combinatorial variants. We use filtered editing to co-evolve the 16S rRNA to tune the ribosome's translational efficiency and the 23S rRNA to isolate antibiotic-resistant ribosome variants without interfering with native translation. This work sets the stage to engineer mutant ribosomes that polymerize abiological monomers with diverse chemistries and expands the scope of genome engineering for precise editing and evolution of repetitive DNA sequences.
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MESH Headings
- Anti-Bacterial Agents/pharmacology
- CRISPR-Cas Systems
- Escherichia coli/drug effects
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Exons
- Gene Editing/methods
- Genetic Engineering
- Genome, Bacterial
- Introns
- Mutagenesis, Site-Directed/methods
- Polymers/chemistry
- Protein Biosynthesis
- RNA Splicing
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Repetitive Sequences, Nucleic Acid
- Ribosomes/genetics
- Ribosomes/metabolism
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Affiliation(s)
- Felix Radford
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Shane D Elliott
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Farren J Isaacs
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA.
- Systems Biology Institute, Yale University, West Haven, CT, 06516, USA.
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA.
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Arrigucci R, Bushkin Y, Radford F, Lakehal K, Vir P, Pine R, Martin D, Sugarman J, Zhao Y, Yap GS, Lardizabal AA, Tyagi S, Gennaro ML. FISH-Flow, a protocol for the concurrent detection of mRNA and protein in single cells using fluorescence in situ hybridization and flow cytometry. Nat Protoc 2017; 12:1245-1260. [PMID: 28518171 DOI: 10.1038/nprot.2017.039] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We describe a flow-cytometry-based protocol for intracellular mRNA measurements in nonadherent mammalian cells using fluorescence in situ hybridization (FISH) probes. The method, which we call FISH-Flow, allows for high-throughput multiparametric measurements of gene expression, a task that was not feasible with earlier, microscopy-based approaches. The FISH-Flow protocol involves cell fixation, permeabilization and hybridization with a set of fluorescently labeled oligonucleotide probes. In this protocol, surface and intracellular protein markers can also be stained with fluorescently labeled antibodies for simultaneous protein and mRNA measurement. Moreover, a semiautomated, single-tube version of the protocol can be performed with a commercially available cell-wash device that reduces cell loss, operator time and interoperator variability. It takes ∼30 h to perform this protocol. An example of FISH-Flow measurements of cytokine mRNA induction by ex vivo stimulation of primed T cells with specific antigens is described.
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Affiliation(s)
- Riccardo Arrigucci
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Yuri Bushkin
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Felix Radford
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Karim Lakehal
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Pooja Vir
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Richard Pine
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | | | | | - Yanlin Zhao
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - George S Yap
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Alfred A Lardizabal
- Global Tuberculosis Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Maria Laura Gennaro
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
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Radford F, Tyagi S, Gennaro ML, Pine R, Bushkin Y. Flow Cytometric Characterization of Antigen-Specific T Cells Based on RNA and Its Advantages in Detecting Infections and Immunological Disorders. Crit Rev Immunol 2016; 36:359-378. [PMID: 28605344 PMCID: PMC5548664 DOI: 10.1615/critrevimmunol.2017018316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Fluorescence in situ hybridization coupled with flow cytometry (FISH-Flow) is a highly quantitative, high-throughput platform allowing precise quantification of total mRNA transcripts in single cells. In undiagnosed infections posing a significant health burden worldwide, such as latent tuberculosis or asymptomatic recurrent malaria, an important challenge is to develop accurate diagnostic tools. Antigen-specific T cells create a persistent memory to pathogens, making them useful for diagnosis of infection. Stimulation of memory response initiates T-cell transitions between functional states. Numerous studies have shown that changes in protein levels lag real-time T-cell transitions. However, analysis at the single-cell transcriptional level can determine the differences. FISH-Flow is a powerful tool with which to study the functional states of T-cell subsets and to identify the gene expression profiles of antigen-specific T cells during disease progression. Advances in instrumentation, fluorophores, and FISH methodologies will broaden and deepen the use of FISH-Flow, changing the immunological field by allowing determination of functional immune signatures at the mRNA level and the development of new diagnostic tools.
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Affiliation(s)
- Felix Radford
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Maria Laura Gennaro
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Richard Pine
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Yuri Bushkin
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
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Bushkin Y, Radford F, Pine R, Lardizabal A, Mangura BT, Gennaro ML, Tyagi S. Profiling T cell activation using single-molecule fluorescence in situ hybridization and flow cytometry. J Immunol 2014; 194:836-41. [PMID: 25505292 DOI: 10.4049/jimmunol.1401515] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Flow cytometric characterization of Ag-specific T cells typically relies on detection of protein analytes. Shifting the analysis to detection of RNA would provide several significant advantages, which we illustrate by developing a new host immunity-based platform for detection of infections. Cytokine mRNAs synthesized in response to ex vivo stimulation with pathogen-specific Ags are detected in T cells with single-molecule fluorescence in situ hybridization followed by flow cytometry. Background from pre-existing in vivo analytes is lower for RNAs than for proteins, allowing greater sensitivity for detection of low-frequency cells. Moreover, mRNA analysis reveals kinetic differences in cytokine expression that are not apparent at the protein level but provide novel insights into gene expression programs expected to define different T cell subsets. The utility of probing immunological memory of infections is demonstrated by detecting T cells that recognize mycobacterial and viral Ags in donors exposed to the respective pathogens.
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Affiliation(s)
- Yuri Bushkin
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103; and
| | - Felix Radford
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103; and
| | - Richard Pine
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103; and
| | - Alfred Lardizabal
- Global Tuberculosis Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Bonita T Mangura
- Global Tuberculosis Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Maria Laura Gennaro
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103; and
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103; and
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Radford F, Zinser G. Inside HFMA: membership benefits. Hosp Financ Manage 1979; 33:56-7. [PMID: 10239812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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