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d’Aquino AE, Azim T, Aleksashin NA, Hockenberry AJ, Krüger A, Jewett MC. Mutational characterization and mapping of the 70S ribosome active site. Nucleic Acids Res 2020; 48:2777-2789. [PMID: 32009164 PMCID: PMC7049736 DOI: 10.1093/nar/gkaa001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 12/06/2019] [Accepted: 01/03/2020] [Indexed: 12/20/2022] Open
Abstract
The synthetic capability of the Escherichia coli ribosome has attracted efforts to repurpose it for novel functions, such as the synthesis of polymers containing non-natural building blocks. However, efforts to repurpose ribosomes are limited by the lack of complete peptidyl transferase center (PTC) active site mutational analyses to inform design. To address this limitation, we leverage an in vitro ribosome synthesis platform to build and test every possible single nucleotide mutation within the PTC-ring, A-loop and P-loop, 180 total point mutations. These mutant ribosomes were characterized by assessing bulk protein synthesis kinetics, readthrough, assembly, and structure mapping. Despite the highly-conserved nature of the PTC, we found that >85% of the PTC nucleotides possess mutational flexibility. Our work represents a comprehensive single-point mutant characterization and mapping of the 70S ribosome's active site. We anticipate that it will facilitate structure-function relationships within the ribosome and make possible new synthetic biology applications.
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Affiliation(s)
- Anne E d’Aquino
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Tasfia Azim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Nikolay A Aleksashin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Adam J Hockenberry
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Antje Krüger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Michael C Jewett
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA
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Caschera F, Karim AS, Gazzola G, d’Aquino AE, Packard NH, Jewett MC. High-Throughput Optimization Cycle of a Cell-Free Ribosome Assembly and Protein Synthesis System. ACS Synth Biol 2018; 7:2841-2853. [PMID: 30354075 DOI: 10.1021/acssynbio.8b00276] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Building variant ribosomes offers opportunities to reveal fundamental principles underlying ribosome biogenesis and to make ribosomes with altered properties. However, cell viability limits mutations that can be made to the ribosome. To address this limitation, the in vitro integrated synthesis, assembly and translation (iSAT) method for ribosome construction from the bottom up was recently developed. Unfortunately, iSAT is complex, costly, and laborious to researchers, partially due to the high cost of reaction buffer containing over 20 components. In this study, we develop iSAT in Escherichia coli BL21Rosetta2 cell lysates, a commonly used bacterial strain, with a cost-effective poly sugar and nucleotide monophosphate-based metabolic scheme. We achieved a 10-fold increase in protein yield over our base case with an evolutionary design of experiments approach, screening 490 reaction conditions to optimize the reaction buffer. The computationally guided, cell-free, high-throughput technology presented here augments the way we approach multicomponent synthetic biology projects and efforts to repurpose ribosomes.
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Affiliation(s)
| | | | - Gianluca Gazzola
- Rutgers Center for Operations Research, Rutgers Business School, 100 Rockafeller Road, Piscataway, New Jersey 08854, United States
| | | | - Norman H. Packard
- ProtoLife, Inc., 57 Post Street Suite 908, San Francisco, California 94104, United States
| | - Michael C. Jewett
- Rutgers Center for Operations Research, Rutgers Business School, 100 Rockafeller Road, Piscataway, New Jersey 08854, United States
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d'Aquino AE, Kim DS, Jewett MC. Engineered Ribosomes for Basic Science and Synthetic Biology. Annu Rev Chem Biomol Eng 2018; 9:311-340. [DOI: 10.1146/annurev-chembioeng-060817-084129] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ribosome is the cell's factory for protein synthesis. With protein synthesis rates of up to 20 amino acids per second and at an accuracy of 99.99%, the extraordinary catalytic capacity of the bacterial translation machinery has attracted extensive efforts to engineer, reconstruct, and repurpose it for biochemical studies and novel functions. Despite these efforts, the potential for harnessing the translation apparatus to manufacture bio-based products beyond natural limits remains underexploited, and fundamental constraints on the chemistry that the ribosome's RNA-based active site can carry out are unknown. This review aims to cover the past and present advances in ribosome design and engineering to understand the fundamental biology of the ribosome to facilitate the construction of synthetic manufacturing machines. The prospects for the development of engineered, or designer, ribosomes for novel polymer synthesis are reviewed, future challenges are considered, and promising advances in a variety of applications are discussed.
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Affiliation(s)
- Anne E. d'Aquino
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA
| | - Do Soon Kim
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Michael C. Jewett
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
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Liu Y, Fritz BR, Anderson MJ, Schoborg JA, Jewett MC. Characterizing and alleviating substrate limitations for improved in vitro ribosome construction. ACS Synth Biol 2015; 4:454-62. [PMID: 25079899 DOI: 10.1021/sb5002467] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Complete cell-free synthesis of ribosomes could make possible minimal cell projects and the construction of variant ribosomes with new functions. Recently, we reported the development of an integrated synthesis, assembly, and translation (iSAT) method for in vitro construction of Escherichia coli ribosomes. iSAT allows simultaneous rRNA synthesis, ribosome assembly, and reporter protein expression as a measure of ribosome activity. Here, we explore causes of iSAT reaction termination to improve efficiency and yields. We discovered that phosphoenolpyruvate (PEP), the secondary energy substrate, and nucleoside triphosphates (NTPs) were rapidly degraded during iSAT reactions. In turn, we observed a significant drop in the adenylate energy charge and termination of protein synthesis. Furthermore, we identified that the accumulation of inorganic phosphate is inhibitory to iSAT. Fed-batch replenishment of PEP and magnesium glutamate (to offset the inhibitory effects of accumulating phosphate by repeated additions of PEP) prior to energy depletion prolonged the reaction duration 2-fold and increased superfolder green fluorescent protein (sfGFP) yield by ~75%. By adopting a semi-continuous method, where passive diffusion enables substrate replenishment and byproduct removal, we prolonged iSAT reaction duration 5-fold and increased sfGFP yield 7-fold to 7.5 ± 0.7 μmol L(-1). This protein yield is the highest ever reported for iSAT reactions. Our results underscore the critical role energy substrates play in iSAT and highlight the importance of understanding metabolic processes that influence substrate depletion for cell-free synthetic biology.
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Affiliation(s)
- Yi Liu
- Interdepartmental Biological Sciences Graduate
Program, ‡Chemistry of Life
Processes Institute, §Department of Chemical and Biological Engineering, ∥Member, Robert H. Lurie Comprehensive
Cancer Center, ⊥Affiliate Member, Institute for Bionanotechnology in Medicine, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Brian R. Fritz
- Interdepartmental Biological Sciences Graduate
Program, ‡Chemistry of Life
Processes Institute, §Department of Chemical and Biological Engineering, ∥Member, Robert H. Lurie Comprehensive
Cancer Center, ⊥Affiliate Member, Institute for Bionanotechnology in Medicine, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Mark J. Anderson
- Interdepartmental Biological Sciences Graduate
Program, ‡Chemistry of Life
Processes Institute, §Department of Chemical and Biological Engineering, ∥Member, Robert H. Lurie Comprehensive
Cancer Center, ⊥Affiliate Member, Institute for Bionanotechnology in Medicine, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Jennifer A. Schoborg
- Interdepartmental Biological Sciences Graduate
Program, ‡Chemistry of Life
Processes Institute, §Department of Chemical and Biological Engineering, ∥Member, Robert H. Lurie Comprehensive
Cancer Center, ⊥Affiliate Member, Institute for Bionanotechnology in Medicine, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Interdepartmental Biological Sciences Graduate
Program, ‡Chemistry of Life
Processes Institute, §Department of Chemical and Biological Engineering, ∥Member, Robert H. Lurie Comprehensive
Cancer Center, ⊥Affiliate Member, Institute for Bionanotechnology in Medicine, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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Jewett MC, Fritz BR, Timmerman LE, Church GM. In vitro integration of ribosomal RNA synthesis, ribosome assembly, and translation. Mol Syst Biol 2013; 9:678. [PMID: 23799452 PMCID: PMC3964315 DOI: 10.1038/msb.2013.31] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Accepted: 05/12/2013] [Indexed: 01/22/2023] Open
Abstract
This report describes an integrated method for in vitro construction of Escherichia coli ribosomes under near-physiological conditions. This method enables coupling of ribosome synthesis and assembly in a single, integrated system. ![]()
An integrated synthesis, assembly, and translation technology (termed iSAT) was developed to construct ribosomes in vitro. iSAT mimics co-transcription of rRNA and ribosome assembly as it occurs in vivo. iSAT makes possible the in vitro construction of modified ribosomes. iSAT is expected to aid studies of ribosome assembly and open new avenues for making ribosomes with altered capabilities.
Purely in vitro ribosome synthesis could provide a critical step towards unraveling the systems biology of ribosome biogenesis, constructing minimal cells from defined components, and engineering ribosomes with new functions. Here, as an initial step towards this goal, we report a method for constructing Escherichia coli ribosomes in crude S150 E. coli extracts. While conventional methods for E. coli ribosome reconstitution are non-physiological, our approach attempts to mimic chemical conditions in the cytoplasm, thus permitting several biological processes to occur simultaneously. Specifically, our integrated synthesis, assembly, and translation (iSAT) technology enables one-step co-activation of rRNA transcription, assembly of transcribed rRNA with native ribosomal proteins into functional ribosomes, and synthesis of active protein by these ribosomes in the same compartment. We show that iSAT makes possible the in vitro construction of modified ribosomes by introducing a 23S rRNA mutation that mediates resistance against clindamycin. We anticipate that iSAT will aid studies of ribosome assembly and open new avenues for making ribosomes with altered properties.
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Affiliation(s)
- Michael C Jewett
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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