1
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Ishida S, Ngo PHT, Gundlach A, Ellington A. Engineering Ribosomal Machinery for Noncanonical Amino Acid Incorporation. Chem Rev 2024; 124:7712-7730. [PMID: 38829723 DOI: 10.1021/acs.chemrev.3c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
The introduction of noncanonical amino acids into proteins has enabled researchers to modify fundamental physicochemical and functional properties of proteins. While the alteration of the genetic code, via the introduction of orthogonal aminoacyl-tRNA synthetase:tRNA pairs, has driven many of these efforts, the various components involved in the process of translation are important for the development of new genetic codes. In this review, we will focus on recent advances in engineering ribosomal machinery for noncanonical amino acid incorporation and genetic code modification. The engineering of the ribosome itself will be considered, as well as the many factors that interact closely with the ribosome, including both tRNAs and accessory factors, such as the all-important EF-Tu. Given the success of genome re-engineering efforts, future paths for radical alterations of the genetic code will require more expansive alterations in the translation machinery.
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Affiliation(s)
- Satoshi Ishida
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Phuoc H T Ngo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Arno Gundlach
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
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2
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Cruz-Navarrete FA, Griffin WC, Chan YC, Martin MI, Alejo JL, Brady RA, Natchiar SK, Knudson IJ, Altman RB, Schepartz A, Miller SJ, Blanchard SC. β-Amino Acids Reduce Ternary Complex Stability and Alter the Translation Elongation Mechanism. ACS CENTRAL SCIENCE 2024; 10:1262-1275. [PMID: 38947208 PMCID: PMC11212133 DOI: 10.1021/acscentsci.4c00314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024]
Abstract
Templated synthesis of proteins containing non-natural amino acids (nnAAs) promises to expand the chemical space available to biological therapeutics and materials, but existing technologies are still limiting. Addressing these limitations requires a deeper understanding of the mechanism of protein synthesis and how it is perturbed by nnAAs. Here we examine the impact of nnAAs on the formation and ribosome utilization of the central elongation substrate: the ternary complex of native, aminoacylated tRNA, thermally unstable elongation factor, and GTP. By performing ensemble and single-molecule fluorescence resonance energy transfer measurements, we reveal that both the (R)- and (S)-β2 isomers of phenylalanine (Phe) disrupt ternary complex formation to levels below in vitro detection limits, while (R)- and (S)-β3-Phe reduce ternary complex stability by 1 order of magnitude. Consistent with these findings, (R)- and (S)-β2-Phe-charged tRNAs were not utilized by the ribosome, while (R)- and (S)-β3-Phe stereoisomers were utilized inefficiently. (R)-β3-Phe but not (S)-β3-Phe also exhibited order of magnitude defects in the rate of translocation after mRNA decoding. We conclude from these findings that non-natural amino acids can negatively impact the translation mechanism on multiple fronts and that the bottlenecks for improvement must include the consideration of the efficiency and stability of ternary complex formation.
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Affiliation(s)
- F. Aaron Cruz-Navarrete
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Wezley C. Griffin
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Yuk-Cheung Chan
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Maxwell I. Martin
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Jose L. Alejo
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Ryan A. Brady
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - S. Kundhavai Natchiar
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Isaac J. Knudson
- College
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Roger B. Altman
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Alanna Schepartz
- College
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Molecular
and Cell Biology, University of California,
Berkeley, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California 94720, United States
- Chan
Zuckerberg Biohub, San Francisco, California 94158, United States
- Innovation
Investigator, ARC Institute, Palo Alto, California 94304, United States
| | - Scott J. Miller
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Scott C. Blanchard
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
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3
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Weiss JL, Decker JC, Bolano A, Krahn N. Tuning tRNAs for improved translation. Front Genet 2024; 15:1436860. [PMID: 38983271 PMCID: PMC11231383 DOI: 10.3389/fgene.2024.1436860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 07/11/2024] Open
Abstract
Transfer RNAs have been extensively explored as the molecules that translate the genetic code into proteins. At this interface of genetics and biochemistry, tRNAs direct the efficiency of every major step of translation by interacting with a multitude of binding partners. However, due to the variability of tRNA sequences and the abundance of diverse post-transcriptional modifications, a guidebook linking tRNA sequences to specific translational outcomes has yet to be elucidated. Here, we review substantial efforts that have collectively uncovered tRNA engineering principles that can be used as a guide for the tuning of translation fidelity. These principles have allowed for the development of basic research, expansion of the genetic code with non-canonical amino acids, and tRNA therapeutics.
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Affiliation(s)
- Joshua L Weiss
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - J C Decker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Ariadna Bolano
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Natalie Krahn
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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4
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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5
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Hamlish NX, Abramyan AM, Shah B, Zhang Z, Schepartz A. Incorporation of Multiple β 2-Hydroxy Acids into a Protein In Vivo Using an Orthogonal Aminoacyl-tRNA Synthetase. ACS CENTRAL SCIENCE 2024; 10:1044-1053. [PMID: 38799653 PMCID: PMC11117724 DOI: 10.1021/acscentsci.3c01366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/22/2024] [Accepted: 04/03/2024] [Indexed: 05/29/2024]
Abstract
The programmed synthesis of sequence-defined biomaterials whose monomer backbones diverge from those of canonical α-amino acids represents the next frontier in protein and biomaterial evolution. Such next-generation molecules provide otherwise nonexistent opportunities to develop improved biologic therapies, bioremediation tools, and biodegradable plastic-like materials. One monomer family of particular interest for biomaterials includes β-hydroxy acids. Many natural products contain isolated β-hydroxy acid monomers, and polymers of β-hydroxy acids (β-esters) are found in polyhydroxyalkanoate (PHA) polyesters under development as bioplastics and drug encapsulation/delivery systems. Here we report that β2-hydroxy acids possessing both (R) and (S) absolute configuration are substrates for pyrrolysyl-tRNA synthetase (PylRS) enzymes in vitro and that (S)-β2-hydroxy acids are substrates in cellulo. Using the orthogonal MaPylRS/MatRNAPyl synthetase/tRNA pair, in conjunction with wild-type E. coli ribosomes and EF-Tu, we report the cellular synthesis of model proteins containing two (S)-β2-hydroxy acid residues at internal positions. Metadynamics simulations provide a rationale for the observed preference for the (S)-β2-hydroxy acid and provide mechanistic insights that inform future engineering efforts. As far as we know, this finding represents the first example of an orthogonal synthetase that acylates tRNA with a β2-hydroxy acid substrate and the first example of a protein hetero-oligomer containing multiple expanded-backbone monomers produced in cellulo.
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Affiliation(s)
- Noah X. Hamlish
- Department
of Molecular and Cellular Biology, University
of California, Berkeley, California 94720, United States
| | - Ara M. Abramyan
- Schrödinger,
Inc., San Diego, California 92121, United States
| | - Bhavana Shah
- Process
Development, Attribute Sciences, Amgen Inc., Thousand Oaks, California 91320, United
States
| | - Zhongqi Zhang
- Process
Development, Attribute Sciences, Amgen Inc., Thousand Oaks, California 91320, United
States
| | - Alanna Schepartz
- Department
of Molecular and Cellular Biology, University
of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, Calfornia 94720, United States
- California
Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
- ARC
Institute, Palo Alto, California 94304, United States
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6
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Cruz-Navarrete FA, Griffin WC, Chan YC, Martin MI, Alejo JL, Natchiar SK, Knudson IJ, Altman RB, Schepartz A, Miller SJ, Blanchard SC. β-amino acids reduce ternary complex stability and alter the translation elongation mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.24.581891. [PMID: 38464221 PMCID: PMC10925103 DOI: 10.1101/2024.02.24.581891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Templated synthesis of proteins containing non-natural amino acids (nnAAs) promises to vastly expand the chemical space available to biological therapeutics and materials. Existing technologies limit the identity and number of nnAAs than can be incorporated into a given protein. Addressing these bottlenecks requires deeper understanding of the mechanism of messenger RNA (mRNA) templated protein synthesis and how this mechanism is perturbed by nnAAs. Here we examine the impact of both monomer backbone and side chain on formation and ribosome-utilization of the central protein synthesis substate: the ternary complex of native, aminoacylated transfer RNA (aa-tRNA), thermally unstable elongation factor (EF-Tu), and GTP. By performing ensemble and single-molecule fluorescence resonance energy transfer (FRET) measurements, we reveal the dramatic effect of monomer backbone on ternary complex formation and protein synthesis. Both the (R) and (S)-β2 isomers of Phe disrupt ternary complex formation to levels below in vitro detection limits, while (R)- and (S)-β3-Phe reduce ternary complex stability by approximately one order of magnitude. Consistent with these findings, (R)- and (S)-β2-Phe-charged tRNAs were not utilized by the ribosome, while (R)- and (S)-β3-Phe stereoisomers were utilized inefficiently. The reduced affinities of both species for EF-Tu ostensibly bypassed the proofreading stage of mRNA decoding. (R)-β3-Phe but not (S)-β3-Phe also exhibited order of magnitude defects in the rate of substrate translocation after mRNA decoding, in line with defects in peptide bond formation that have been observed for D-α-Phe. We conclude from these findings that non-natural amino acids can negatively impact the translation mechanism on multiple fronts and that the bottlenecks for improvement must include consideration of the efficiency and stability of ternary complex formation.
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Affiliation(s)
- F. Aaron Cruz-Navarrete
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Chemical Biology & Therapeutics, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Wezley C. Griffin
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Chemical Biology & Therapeutics, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Yuk-Cheung Chan
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Maxwell I. Martin
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Chemical Biology & Therapeutics, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Jose L. Alejo
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Chemical Biology & Therapeutics, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - S. Kundhavai Natchiar
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Chemical Biology & Therapeutics, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Isaac J. Knudson
- College of Chemistry, University of California, Berkeley, California, USA
| | - Roger B. Altman
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Chemical Biology & Therapeutics, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Alanna Schepartz
- College of Chemistry, University of California, Berkeley, California, USA
- Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Innovation Investigator, ARC Institute, Palo Alto, CA 94304, USA
| | - Scott J. Miller
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Scott C. Blanchard
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Chemical Biology & Therapeutics, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
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7
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Zafar H, Hassan AH, Demo G. Translation machinery captured in motion. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1792. [PMID: 37132456 DOI: 10.1002/wrna.1792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/14/2023] [Accepted: 04/17/2023] [Indexed: 05/04/2023]
Abstract
Translation accuracy is one of the most critical factors for protein synthesis. It is regulated by the ribosome and its dynamic behavior, along with translation factors that direct ribosome rearrangements to make translation a uniform process. Earlier structural studies of the ribosome complex with arrested translation factors laid the foundation for an understanding of ribosome dynamics and the translation process as such. Recent technological advances in time-resolved and ensemble cryo-EM have made it possible to study translation in real time at high resolution. These methods provided a detailed view of translation in bacteria for all three phases: initiation, elongation, and termination. In this review, we focus on translation factors (in some cases GTP activation) and their ability to monitor and respond to ribosome organization to enable efficient and accurate translation. This article is categorized under: Translation > Ribosome Structure/Function Translation > Mechanisms.
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Affiliation(s)
- Hassan Zafar
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ahmed H Hassan
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Gabriel Demo
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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8
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Majumdar C, Walker JA, Francis MB, Schepartz A, Cate JHD. Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome. ACS CENTRAL SCIENCE 2023; 9:1160-1169. [PMID: 37396857 PMCID: PMC10311655 DOI: 10.1021/acscentsci.3c00153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Indexed: 07/04/2023]
Abstract
The Escherichia coli (E. coli) ribosome can incorporate a variety of non-l-α-amino acid monomers into polypeptide chains in vitro but with poor efficiency. Although these monomers span a diverse set of compounds, there exists no high-resolution structural information regarding their positioning within the catalytic center of the ribosome, the peptidyl transferase center (PTC). Thus, details regarding the mechanism of amide bond formation and the structural basis for differences and defects in incorporation efficiency remain unknown. Within a set of three aminobenzoic acid derivatives-3-aminopyridine-4-carboxylic acid (Apy), ortho-aminobenzoic acid (oABZ), and meta-aminobenzoic acid (mABZ)-the ribosome incorporates Apy into polypeptide chains with the highest efficiency, followed by oABZ and then mABZ, a trend that does not track with the nucleophilicity of the reactive amines. Here, we report high-resolution cryo-EM structures of the ribosome with each of these three aminobenzoic acid derivatives charged on tRNA bound in the aminoacyl-tRNA site (A-site). The structures reveal how the aromatic ring of each monomer sterically blocks the positioning of nucleotide U2506, thereby preventing rearrangement of nucleotide U2585 and the resulting induced fit in the PTC required for efficient amide bond formation. They also reveal disruptions to the bound water network that is believed to facilitate formation and breakdown of the tetrahedral intermediate. Together, the cryo-EM structures reported here provide a mechanistic rationale for differences in reactivity of aminobenzoic acid derivatives relative to l-α-amino acids and each other and identify stereochemical constraints on the size and geometry of non-monomers that can be accepted efficiently by wild-type ribosomes.
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Affiliation(s)
- Chandrima Majumdar
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
| | - Joshua A. Walker
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Matthew B. Francis
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Alanna Schepartz
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Chan
Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Jamie H. D. Cate
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Innovative
Genomics Institute, University of California, Berkeley, California 94720, United States
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9
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Watson ZL, Knudson IJ, Ward FR, Miller SJ, Cate JHD, Schepartz A, Abramyan AM. Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates. Nat Chem 2023:10.1038/s41557-023-01226-w. [PMID: 37308707 DOI: 10.1038/s41557-023-01226-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/28/2023] [Indexed: 06/14/2023]
Abstract
As genetic code expansion advances beyond L-α-amino acids to backbone modifications and new polymerization chemistries, delineating what substrates the ribosome can accommodate remains a challenge. The Escherichia coli ribosome tolerates non-L-α-amino acids in vitro, but few structural insights that explain how are available, and the boundary conditions for efficient bond formation are so far unknown. Here we determine a high-resolution cryogenic electron microscopy structure of the E. coli ribosome containing α-amino acid monomers and use metadynamics simulations to define energy surface minima and understand incorporation efficiencies. Reactive monomers across diverse structural classes favour a conformational space where the aminoacyl-tRNA nucleophile is <4 Å from the peptidyl-tRNA carbonyl with a Bürgi-Dunitz angle of 76-115°. Monomers with free energy minima that fall outside this conformational space do not react efficiently. This insight should accelerate the in vivo and in vitro ribosomal synthesis of sequence-defined, non-peptide heterooligomers.
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Affiliation(s)
- Zoe L Watson
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Isaac J Knudson
- Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
| | - Fred R Ward
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA, USA
| | - Scott J Miller
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA.
- Department of Chemistry, Yale University, New Haven, CT, USA.
| | - Jamie H D Cate
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA.
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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10
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Fu X, Shang Y, Chen S, Dedkova LM, Hecht SM. Activation of d-Asparagine and d-Glutamine Derivatives Using the Mitsunobu Reaction. Org Lett 2023. [PMID: 36800493 DOI: 10.1021/acs.orglett.3c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Seven d-amino acid derivatives having reactive side chains have been activated to afford their respective 3,5-dinitrobenzyl esters using the Mitsunobu reaction. This esterification was found to be difficult using traditional methods involving 3,5-dinitrobenzyl chloride under alkaline conditions. The conversion of a tRNA to the respective d-glutaminyl-tRNA using d-glutamine 3,5-dinitrobenzyl ester was catalyzed by a flexizyme, followed by purification to remove all the unacylated tRNAs and other byproducts. Both d- and l-glutamine were incorporated from their aminoacyl-tRNAs into a model peptide structurally related to IFN-β.
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Affiliation(s)
- Xuan Fu
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Yuqin Shang
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for Bioenergetics, Arizona State University, Tempe, Arizona 85287, United States.,School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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11
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Choi YN, Cho N, Lee K, Gwon DA, Lee JW, Lee J. Programmable Synthesis of Biobased Materials Using Cell-Free Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2203433. [PMID: 36108274 DOI: 10.1002/adma.202203433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Motivated by the intricate mechanisms underlying biomolecule syntheses in cells that chemistry is currently unable to mimic, researchers have harnessed biological systems for manufacturing novel materials. Cell-free systems (CFSs) utilizing the bioactivity of transcriptional and translational machineries in vitro are excellent tools that allow supplementation of exogenous materials for production of innovative materials beyond the capability of natural biological systems. Herein, recent studies that have advanced the ability to expand the scope of biobased materials using CFS are summarized and approaches enabling the production of high-value materials, prototyping of genetic parts and modules, and biofunctionalization are discussed. By extending the reach of chemical and enzymatic reactions complementary to cellular materials, CFSs provide new opportunities at the interface of materials science and synthetic biology.
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Affiliation(s)
- Yun-Nam Choi
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Namjin Cho
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Kanghun Lee
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Da-Ae Gwon
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Joongoo Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
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12
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Lee J, Coronado JN, Cho N, Lim J, Hosford BM, Seo S, Kim DS, Kofman C, Moore JS, Ellington AD, Anslyn EV, Jewett MC. Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro. Nat Commun 2022; 13:6322. [PMID: 36280685 PMCID: PMC9592601 DOI: 10.1038/s41467-022-33701-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 09/28/2022] [Indexed: 12/25/2022] Open
Abstract
The ribosome is a macromolecular machine that catalyzes the sequence-defined polymerization of L-α-amino acids into polypeptides. The catalysis of peptide bond formation between amino acid substrates is based on entropy trapping, wherein the adjacency of transfer RNA (tRNA)-coupled acyl bonds in the P-site and the α-amino groups in the A-site aligns the substrates for coupling. The plasticity of this catalytic mechanism has been observed in both remnants of the evolution of the genetic code and modern efforts to reprogram the genetic code (e.g., ribosomal incorporation of non-canonical amino acids, ribosomal ester formation). However, the limits of ribosome-mediated polymerization are underexplored. Here, rather than peptide bonds, we demonstrate ribosome-mediated polymerization of pyridazinone bonds via a cyclocondensation reaction between activated γ-keto and α-hydrazino ester monomers. In addition, we demonstrate the ribosome-catalyzed synthesis of peptide-hybrid oligomers composed of multiple sequence-defined alternating pyridazinone linkages. Our results highlight the plasticity of the ribosome's ancient bond-formation mechanism, expand the range of non-canonical polymeric backbones that can be synthesized by the ribosome, and open the door to new applications in synthetic biology.
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Affiliation(s)
- Joongoo Lee
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
| | - Jaime N Coronado
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Namjin Cho
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Jongdoo Lim
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Brandon M Hosford
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Sangwon Seo
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Do Soon Kim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Camila Kofman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Jeffrey S Moore
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Andrew D Ellington
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Eric V Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Interdisplinary Biological Sciences Graduate Program, Evanston, IL, 60208, USA.
- Chemistry of Life Processes Institute, Evanston, IL, 60208, USA.
- Robert H. Lurie Comprehensive Cancer Center, Evanston, IL, 60208, USA.
- Simpson Querrey Institute, Evanston, IL, 60208, USA.
- Center for Synthetic Biology, Northwestern University and Biological Engineering, 2145 Sheridan Road, Evanston, IL, 60208, USA.
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13
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Thommen M, Draycheva A, Rodnina MV. Ribosome selectivity and nascent chain context in modulating the incorporation of fluorescent non-canonical amino acid into proteins. Sci Rep 2022; 12:12848. [PMID: 35896582 PMCID: PMC9329280 DOI: 10.1038/s41598-022-16932-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
Fluorescence reporter groups are important tools to study the structure and dynamics of proteins. Genetic code reprogramming allows for cotranslational incorporation of non-canonical amino acids at any desired position. However, cotranslational incorporation of bulky fluorescence reporter groups is technically challenging and usually inefficient. Here we analyze the bottlenecks for the cotranslational incorporation of NBD-, BodipyFL- and Atto520-labeled Cys-tRNACys into a model protein using a reconstituted in-vitro translation system. We show that the modified Cys-tRNACys can be rejected during decoding due to the reduced ribosome selectivity for the modified aa-tRNA and the competition with native near-cognate aminoacyl-tRNAs. Accommodation of the modified Cys-tRNACys in the A site of the ribosome is also impaired, but can be rescued by one or several Gly residues at the positions −1 to −4 upstream of the incorporation site. The incorporation yield depends on the steric properties of the downstream residue and decreases with the distance from the protein N-terminus to the incorporation site. In addition to the full-length translation product, we find protein fragments corresponding to the truncated N-terminal peptide and the C-terminal fragment starting with a fluorescence-labeled Cys arising from a StopGo-like event due to a defect in peptide bond formation. The results are important for understanding the reasons for inefficient cotranslational protein labeling with bulky reporter groups and for designing new approaches to improve the yield of fluorescence-labeled protein.
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Affiliation(s)
- Michael Thommen
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Albena Draycheva
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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14
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Katoh T, Suga H. In Vitro Genetic Code Reprogramming for the Expansion of Usable Noncanonical Amino Acids. Annu Rev Biochem 2022; 91:221-243. [PMID: 35729073 DOI: 10.1146/annurev-biochem-040320-103817] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic code reprogramming has enabled us to ribosomally incorporate various nonproteinogenic amino acids (npAAs) into peptides in vitro. The repertoire of usable npAAs has been expanded to include not only l-α-amino acids with noncanonical sidechains but also those with noncanonical backbones. Despite successful single incorporation of npAAs, multiple and consecutive incorporations often suffer from low efficiency or are even unsuccessful. To overcome this stumbling block, engineering approaches have been used to modify ribosomes, EF-Tu, and tRNAs. Here, we provide an overview of these in vitro methods that are aimed at optimal expansion of the npAA repertoire and their applications for the development of de novo bioactive peptides containing various npAAs.
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Affiliation(s)
- Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan; ,
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan; ,
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15
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Dyakin VV, Uversky VN. Arrow of Time, Entropy, and Protein Folding: Holistic View on Biochirality. Int J Mol Sci 2022; 23:ijms23073687. [PMID: 35409047 PMCID: PMC8998916 DOI: 10.3390/ijms23073687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023] Open
Abstract
Chirality is a universal phenomenon, embracing the space–time domains of non-organic and organic nature. The biological time arrow, evident in the aging of proteins and organisms, should be linked to the prevalent biomolecular chirality. This hypothesis drives our exploration of protein aging, in relation to the biological aging of an organism. Recent advances in the chirality discrimination methods and theoretical considerations of the non-equilibrium thermodynamics clarify the fundamental issues, concerning the biphasic, alternative, and stepwise changes in the conformational entropy associated with protein folding. Living cells represent open, non-equilibrium, self-organizing, and dissipative systems. The non-equilibrium thermodynamics of cell biology are determined by utilizing the energy stored, transferred, and released, via adenosine triphosphate (ATP). At the protein level, the synthesis of a homochiral polypeptide chain of L-amino acids (L-AAs) represents the first state in the evolution of the dynamic non-equilibrium state of the system. At the next step the non-equilibrium state of a protein-centric system is supported and amended by a broad set of posttranslational modifications (PTMs). The enzymatic phosphorylation, being the most abundant and ATP-driven form of PTMs, illustrates the principal significance of the energy-coupling, in maintaining and reshaping the system. However, the physiological functions of phosphorylation are under the permanent risk of being compromised by spontaneous racemization. Therefore, the major distinct steps in protein-centric aging include the biosynthesis of a polypeptide chain, protein folding assisted by the system of PTMs, and age-dependent spontaneous protein racemization and degradation. To the best of our knowledge, we are the first to pay attention to the biphasic, alternative, and stepwise changes in the conformational entropy of protein folding. The broader view on protein folding, including the impact of spontaneous racemization, will help in the goal-oriented experimental design in the field of chiral proteomics.
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Affiliation(s)
- Victor V. Dyakin
- Virtual Reality Perception Lab (VRPL), The Nathan S. Kline Institute for Psychiatric Research (NKI), 140 Old Orangeburg Road, Bldg, 35, Orangeburg, NY 10962, USA
- Correspondence:
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA;
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16
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Jani J, Pappachan A. A review on quality control agents of protein translation - The role of Trans-editing proteins. Int J Biol Macromol 2022; 199:252-263. [PMID: 34995670 DOI: 10.1016/j.ijbiomac.2021.12.176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/18/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022]
Abstract
Translation of RNA to protein is a key feature of cellular life. The fidelity of this process mainly depends on the availability of correctly charged tRNAs. Different domains of tRNA synthetase (aaRS) maintain translation quality by ensuring the proper attachment of particular amino acid with respective tRNA, thus it establishes the rule of genetic code. However occasional errors by aaRS generate mischarged tRNAs, which can become lethal to the cells. Accurate protein synthesis necessitates hydrolysis of mischarged tRNAs. Various cis and trans-editing proteins are identified which recognize these mischarged products and correct them by hydrolysis. Trans-editing proteins are homologs of cis-editing domains of aaRS. The trans-editing proteins work in close association with aaRS, Ef-Tu, and ribosome to prevent global mistranslation and ensures correct charging of tRNA. In this review, we discuss the major trans-editing proteins and compared them with their cis-editing counterparts. We also discuss their structural features, biochemical activity and role in maintaining cellular protein homeostasis.
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Affiliation(s)
- Jaykumar Jani
- School of Life Sciences, Central University of Gujarat, Sector 30, Gandhinagar 382030, Gujarat, India
| | - Anju Pappachan
- School of Life Sciences, Central University of Gujarat, Sector 30, Gandhinagar 382030, Gujarat, India.
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17
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Dyakin VV, Dyakina-Fagnano NV, Mcintire LB, Uversky VN. Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology. Int J Mol Sci 2021; 23:ijms23010285. [PMID: 35008708 PMCID: PMC8745688 DOI: 10.3390/ijms23010285] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/24/2021] [Accepted: 12/22/2021] [Indexed: 12/23/2022] Open
Abstract
In humans, age-associated degrading changes, widely observed in molecular and cellular processes underly the time-dependent decline in spatial navigation, time perception, cognitive and psychological abilities, and memory. Cross-talk of biological, cognitive, and psychological clocks provides an integrative contribution to healthy and advanced aging. At the molecular level, genome, proteome, and lipidome instability are widely recognized as the primary causal factors in aging. We narrow attention to the roles of protein aging linked to prevalent amino acids chirality, enzymatic and spontaneous (non-enzymatic) post-translational modifications (PTMs SP), and non-equilibrium phase transitions. The homochirality of protein synthesis, resulting in the steady-state non-equilibrium condition of protein structure, makes them prone to multiple types of enzymatic and spontaneous PTMs, including racemization and isomerization. Spontaneous racemization leads to the loss of the balanced prevalent chirality. Advanced biological aging related to irreversible PTMs SP has been associated with the nontrivial interplay between somatic (molecular aging) and mental (psychological aging) health conditions. Through stress response systems (SRS), the environmental and psychological stressors contribute to the age-associated “collapse” of protein homochirality. The role of prevalent protein chirality and entropy of protein folding in biological aging is mainly overlooked. In a more generalized context, the time-dependent shift from enzymatic to the non-enzymatic transformation of biochirality might represent an important and yet underappreciated hallmark of aging. We provide the experimental arguments in support of the racemization theory of aging.
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Affiliation(s)
- Victor V. Dyakin
- The Nathan S. Kline Institute for Psychiatric Research (NKI), 140 Old Orangeburg Road, Bldg, 35, Bld. 35. Rom 201-C, Orangeburg, NY 10962, USA
- Correspondence: ; Tel.: +1-845-548-96-94; Fax: +1-845-398-5510
| | - Nuka V. Dyakina-Fagnano
- Child, Adolescent and Young Adult Psychiatry, 36 Franklin Turnpike, Waldwick, NJ 07463, USA;
| | - Laura B. Mcintire
- Department of Pathology and Cell Biology, Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA;
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA;
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18
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Liu X, Gellman SH. Comparisons of β-Hairpin Propensity Among Peptides with Homochiral or Heterochiral Strands. Chembiochem 2021; 22:2772-2776. [PMID: 34288305 PMCID: PMC8486351 DOI: 10.1002/cbic.202100324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/18/2021] [Indexed: 11/10/2022]
Abstract
Assemblies of racemic β-sheet-forming peptides have attracted attention for biomedical applications because racemic forms of peptides can self-associate more avidly than do single enantiomers. In 1953, Pauling and Corey proposed "rippled β-sheet" modes of H-bond-mediated interstrand assembly for alternating L- and D-peptide strands; this structural hypothesis was complementary to their proposal of "pleated β-sheet" assembly for L-peptides. Although no high-resolution structure has been reported for a rippled β-sheet, there is strong evidence for the occurrence of rippled β-sheets in some racemic peptide assemblies. Here we compare propensities of peptide diastereomers in aqueous solution to form a minimum increment of β-sheet in which two antiparallel strands associate. β-Hairpin folding is observed for homochiral peptides with aligned nonpolar side chains, but no β-hairpin population can be detected for diastereomers in which one strand contains L residues and the other contains D residues. These observations suggest that rippled β-sheet assemblies are stabilized by interactions between β-sheet layers rather than interactions within these layers.
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Affiliation(s)
- Xinyu Liu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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19
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Insights into the Interaction of Lysosomal Amino Acid Transporters SLC38A9 and SLC36A1 Involved in mTORC1 Signaling in C2C12 Cells. Biomolecules 2021; 11:biom11091314. [PMID: 34572527 PMCID: PMC8467208 DOI: 10.3390/biom11091314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 08/28/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022] Open
Abstract
Amino acids are critical for mammalian target of rapamycin complex 1 (mTORC1) activation on the lysosomal surface. Amino acid transporters SLC38A9 and SLC36A1 are the members of the lysosomal amino acid sensing machinery that activates mTORC1. The current study aims to clarify the interaction of SLC38A9 and SLC36A1. Here, we discovered that leucine increased expressions of SLC38A9 and SLC36A1, leading to mTORC1 activation. SLC38A9 interacted with SLC36A1 and they enhanced each other's expression levels and locations on the lysosomal surface. Additionally, the interacting proteins of SLC38A9 in C2C12 cells were identified to participate in amino acid sensing mechanism, mTORC1 signaling pathway, and protein synthesis, which provided a resource for future investigations of skeletal muscle mass.
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20
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Abstract
![]()
Since the establishment
of site-specific mutagenesis of single
amino acids to interrogate protein function in the 1970s, biochemists
have sought to tailor protein structure in the native cell environment.
Fine-tuning the chemical properties of proteins is an indispensable
way to address fundamental mechanistic questions. Unnatural amino
acids (UAAs) offer the possibility to expand beyond the 20 naturally
occurring amino acids in most species and install new and useful chemical
functions. Here, we review the literature about advances in UAA incorporation
technology from chemoenzymatic aminoacylation of modified tRNAs to in vitro translation systems to genetic encoding of UAAs
in the native cell environment and whole organisms. We discuss innovative
applications of the UAA technology to challenges in bioengineering
and medicine.
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Affiliation(s)
- Mia A Shandell
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, U.K
| | - Zhongping Tan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Virginia W Cornish
- Department of Chemistry, Columbia University, New York, New York 10027, United States.,Department of Systems Biology, Columbia University, New York, New York 10027, United States
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21
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Abstract
Over the past decade, harnessing the cellular protein synthesis machinery to incorporate non-canonical amino acids (ncAAs) into tailor-made peptides has significantly advanced many aspects of molecular science. More recently, groundbreaking progress in our ability to engineer this machinery for improved ncAA incorporation has led to significant enhancements of this powerful tool for biology and chemistry. By revealing the molecular basis for the poor or improved incorporation of ncAAs, mechanistic studies of ncAA incorporation by the protein synthesis machinery have tremendous potential for informing and directing such engineering efforts. In this chapter, we describe a set of complementary biochemical and single-molecule fluorescence assays that we have adapted for mechanistic studies of ncAA incorporation. Collectively, these assays provide data that can guide engineering of the protein synthesis machinery to expand the range of ncAAs that can be incorporated into peptides and increase the efficiency with which they can be incorporated, thereby enabling the full potential of ncAA mutagenesis technology to be realized.
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22
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Kofman C, Lee J, Jewett MC. Engineering molecular translation systems. Cell Syst 2021; 12:593-607. [PMID: 34139167 DOI: 10.1016/j.cels.2021.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/19/2021] [Accepted: 03/31/2021] [Indexed: 12/16/2022]
Abstract
Molecular translation systems provide a genetically encoded framework for protein synthesis, which is essential for all life. Engineering these systems to incorporate non-canonical amino acids (ncAAs) into peptides and proteins has opened many exciting opportunities in chemical and synthetic biology. Here, we review recent advances that are transforming our ability to engineer molecular translation systems. In cell-based systems, new processes to synthesize recoded genomes, tether ribosomal subunits, and engineer orthogonality with high-throughput workflows have emerged. In cell-free systems, adoption of flexizyme technology and cell-free ribosome synthesis and evolution platforms are expanding the limits of chemistry at the ribosome's RNA-based active site. Looking forward, innovations will deepen understanding of molecular translation and provide a path to polymers with previously unimaginable structures and functions.
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Affiliation(s)
- Camila Kofman
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Joongoo Lee
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA; Department of Chemical Engineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA; Interdisplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA; Simpson Querrey Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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23
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Zhang L, He J, Bai L, Ruan S, Yang T, Luo Y. Ribosome-targeting antibacterial agents: Advances, challenges, and opportunities. Med Res Rev 2021; 41:1855-1889. [PMID: 33501747 DOI: 10.1002/med.21780] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/08/2020] [Accepted: 12/19/2020] [Indexed: 02/05/2023]
Abstract
Ribosomes, which synthesize proteins, are critical organelles for the survival and growth of bacteria. About 60% of approved antibiotics discovered so far combat pathogenic bacteria by targeting ribosomes. However, several issues, such as drug resistance and toxicity, have impeded the clinical use of ribosome-targeting antibiotics. Moreover, the complexity of the bacteria ribosome structure has retarded the discovery of new ribosome-targeting agents that are considered as the key to the drug-resistance and toxicity. To deal with these challenges, efforts such as medicinal chemistry optimization, combination treatment, and new drug delivery system have been developed. But not enough, the development of structural biology and new screening methods bring powerful tools, such as cryo-electron microscopy technology, advanced computer-aided drug design, and cell-free in vitro transcription/translation systems, for the discovery of novel ribosome-targeting antibiotics. Thus, in this paper, we overview the research on different aspects of bacterial ribosomes, especially focus on discussing the challenges in the discovery of ribosome-targeting antibacterial drugs and advances made to address issues such as drug-resistance and selectivity, which, we believe, provide perspectives for the discovery of novel antibiotics.
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Affiliation(s)
- Laiying Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Jun He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Lang Bai
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Shihua Ruan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China.,Laboratory of Human Diseases and Immunotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China.,Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
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24
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Supplementing conjugated and non-conjugated L-methionine and acetate alters expression patterns of CSN2, proteins and metabolites related to protein synthesis in bovine mammary cells. J DAIRY RES 2021; 87:70-77. [PMID: 32114997 DOI: 10.1017/s0022029919000979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The experiments reported in this research paper aimed to determine the effect of supplementing different forms of L-methionine (L-Met) and acetate on protein synthesis in immortalized bovine mammary epithelial cell line (MAC-T cells). Treatments were Control, L-Met, conjugated L-Met and acetate (CMA), and non-conjugated L-Met and Acetate (NMA). Protein synthesis mechanism was determined by omics method. NMA group had the highest protein content in the media and CSN2 mRNA expression levels (P < 0.05). The number of upregulated and downregulated proteins observed were 39 and 77 in L-Met group, 62 and 80 in CMA group and 50 and 81 in NMA group from 448 proteins, respectively (P < 0.05). L-Met, NMA and CMA treatments stimulated pathways related to protein and energy metabolism (P < 0.05). Metabolomic analysis also revealed that L-Met, CMA and NMA treatments resulted in increases of several metabolites (P < 0.05). In conclusion, NMA treatment increased protein concentration and expression level of CSN2 mRNA in MAC-T cells compared to control as well as L-Met and CMA treatments through increased expression of milk protein synthesis-related genes and production of the proteins and metabolites involved in energy and protein synthesis pathways.
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25
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Ward FR, Watson ZL, Ad O, Schepartz A, Cate JHD. Defects in the Assembly of Ribosomes Selected for β-Amino Acid Incorporation. Biochemistry 2019; 58:4494-4504. [PMID: 31607123 PMCID: PMC8435211 DOI: 10.1021/acs.biochem.9b00746] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ribosome engineering has emerged as a promising field in synthetic biology, particularly concerning the production of new sequence-defined polymers. Mutant ribosomes have been developed that improve the incorporation of several nonstandard monomers including d-amino acids, dipeptides, and β-amino acids into polypeptide chains. However, there remains little mechanistic understanding of how these ribosomes catalyze incorporation of these new substrates. Here, we probed the properties of a mutant ribosome-P7A7-evolved for better in vivo β-amino acid incorporation through in vitro biochemistry and cryo-electron microscopy. Although P7A7 is a functional ribosome in vivo, it is inactive in vitro, and assembles poorly into 70S ribosome complexes. Structural characterization revealed large regions of disorder in the peptidyltransferase center and nearby features, suggesting a defect in assembly. Comparison of RNA helix and ribosomal protein occupancy with other assembly intermediates revealed that P7A7 is stalled at a late stage in ribosome assembly, explaining its weak activity. These results highlight the importance of ensuring efficient ribosome assembly during ribosome engineering toward new catalytic abilities.
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Affiliation(s)
- Fred R. Ward
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA
| | - Zoe L. Watson
- Department of Chemistry, University of California-Berkeley, Berkeley, CA
| | - Omer Ad
- Department of Chemistry, Yale University, New Haven, CT
| | - Alanna Schepartz
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA
- Department of Chemistry, University of California-Berkeley, Berkeley, CA
- Department of Chemistry, Yale University, New Haven, CT
| | - Jamie H. D. Cate
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA
- Department of Chemistry, University of California-Berkeley, Berkeley, CA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA
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26
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Kuncha SK, Kruparani SP, Sankaranarayanan R. Chiral checkpoints during protein biosynthesis. J Biol Chem 2019; 294:16535-16548. [PMID: 31591268 DOI: 10.1074/jbc.rev119.008166] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Protein chains contain only l-amino acids, with the exception of the achiral glycine, making the chains homochiral. This homochirality is a prerequisite for proper protein folding and, hence, normal cellular function. The importance of d-amino acids as a component of the bacterial cell wall and their roles in neurotransmission in higher eukaryotes are well-established. However, the wider presence and the corresponding physiological roles of these specific amino acid stereoisomers have been appreciated only recently. Therefore, it is expected that enantiomeric fidelity has to be a key component of all of the steps in translation. Cells employ various molecular mechanisms for keeping d-amino acids away from the synthesis of nascent polypeptide chains. The major factors involved in this exclusion are aminoacyl-tRNA synthetases (aaRSs), elongation factor thermo-unstable (EF-Tu), the ribosome, and d-aminoacyl-tRNA deacylase (DTD). aaRS, EF-Tu, and the ribosome act as "chiral checkpoints" by preferentially binding to l-amino acids or l-aminoacyl-tRNAs, thereby excluding d-amino acids. Interestingly, DTD, which is conserved across all life forms, performs "chiral proofreading," as it removes d-amino acids erroneously added to tRNA. Here, we comprehensively review d-amino acids with respect to their occurrence and physiological roles, implications for chiral checkpoints required for translation fidelity, and potential use in synthetic biology.
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Affiliation(s)
- Santosh Kumar Kuncha
- Council of Scientific and Industrial Research (CSIR)-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana 500007, India.,Academy of Scientific and Innovative Research, CSIR-CCMB Campus, Hyderabad, Telangana 500007, India
| | - Shobha P Kruparani
- Council of Scientific and Industrial Research (CSIR)-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana 500007, India
| | - Rajan Sankaranarayanan
- Council of Scientific and Industrial Research (CSIR)-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana 500007, India
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27
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Engineered ribosomes with tethered subunits for expanding biological function. Nat Commun 2019; 10:3920. [PMID: 31477696 PMCID: PMC6718428 DOI: 10.1038/s41467-019-11427-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 07/10/2019] [Indexed: 01/01/2023] Open
Abstract
Ribo-T is a ribosome with covalently tethered subunits where core 16S and 23S ribosomal RNAs form a single chimeric molecule. Ribo-T makes possible a functionally orthogonal ribosome-mRNA system in cells. Unfortunately, use of Ribo-T has been limited because of low activity of its original version. Here, to overcome this limitation, we use an evolutionary approach to select new tether designs that are capable of supporting faster cell growth and increased protein expression. Further, we evolve new orthogonal Ribo-T/mRNA pairs that function in parallel with, but independent of, natural ribosomes and mRNAs, increasing the efficiency of orthogonal protein expression. The Ribo-T with optimized designs is able to synthesize a diverse set of proteins, and can also incorporate multiple non-canonical amino acids into synthesized polypeptides. The enhanced Ribo-T designs should be useful for exploring poorly understood functions of the ribosome and engineering ribosomes with altered catalytic properties.
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28
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Fujino T, Kondo T, Suga H, Murakami H. Exploring the Minimal RNA Substrate of Flexizymes. Chembiochem 2019; 20:1959-1965. [PMID: 30950544 DOI: 10.1002/cbic.201900150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Indexed: 02/06/2023]
Abstract
Flexizymes are tRNA acylation ribozymes that have been successfully used to facilitate genetic code reprogramming. They are capable of charging acid substrates onto various tRNAs and tRNA analogues. However, their minimal RNA substrate has not been investigated. Here we have designed fluorescently labeled short RNAs corresponding to the four, three, and two bases (4bRNA, 3bRNA, 2bRNA) at the tRNA 3'-end and explored the minimal RNA substrate of flexizymes, dFx and eFx. 3bRNA was the observed minimal RNA substrate of the flexizymes, but the efficiency of acylation of this short RNA was two to three times lower than that of 4bRNA. The efficiency of acylation of 4bRNA was comparable with that of the microhelix, a 22-base RNA conventionally used as a tRNA analogue for analyzing acylation efficiency. We also compared the efficiencies of acylation of the microhelix and 4bRNA with various acid substrates. Thanks to the short length of 4bRNA, its acyl-4bRNA products exhibited larger mobility shifts in gel electrophoresis than those exhibited by acyl-microhelix products with every substrate tested. This indicated that 4bRNA was an ideal RNA substrate for analyzing the efficiency of acylation by flexizymes.
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Affiliation(s)
- Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Taishi Kondo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
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29
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Baiesi M, Orlandini E, Seno F, Trovato A. Sequence and structural patterns detected in entangled proteins reveal the importance of co-translational folding. Sci Rep 2019; 9:8426. [PMID: 31182755 PMCID: PMC6557820 DOI: 10.1038/s41598-019-44928-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/23/2019] [Indexed: 11/09/2022] Open
Abstract
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence of specific patterns adopted by protein sequences and structures to deal with backbone self-entanglement. A large scale analysis of the Protein Data Bank shows that loops significantly intertwined with another chain portion are typically closed by weakly bound amino acids. Why is this energetic frustration maintained? A possible picture is that entangled loops are formed only toward the end of the folding process to avoid kinetic traps. Consistently, these loops are more frequently found to be wrapped around a portion of the chain on their N-terminal side, the one translated earlier at the ribosome. Finally, these motifs are less abundant in natural native states than in simulated protein-like structures, yet they appear in 32% of proteins, which in some cases display an amazingly complex intertwining.
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Affiliation(s)
- Marco Baiesi
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131, Padova, Italy
- INFN, Sezione di Padova, Via Marzolo 8, I-35131, Padova, Italy
| | - Enzo Orlandini
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131, Padova, Italy
- INFN, Sezione di Padova, Via Marzolo 8, I-35131, Padova, Italy
| | - Flavio Seno
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131, Padova, Italy.
- INFN, Sezione di Padova, Via Marzolo 8, I-35131, Padova, Italy.
| | - Antonio Trovato
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131, Padova, Italy
- INFN, Sezione di Padova, Via Marzolo 8, I-35131, Padova, Italy
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30
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Grishin DV, Zhdanov DD, Pokrovskaya MV, Sokolov NN. D-amino acids in nature, agriculture and biomedicine. ALL LIFE 2019. [DOI: 10.1080/21553769.2019.1622596] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
| | - D. D. Zhdanov
- Institute of Biomedical Chemistry, Moscow, Russia
- Peoples Friendship University of Russia, Moscow, Russia
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31
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Dedkova LM, Hecht SM. Expanding the Scope of Protein Synthesis Using Modified Ribosomes. J Am Chem Soc 2019; 141:6430-6447. [PMID: 30901982 DOI: 10.1021/jacs.9b02109] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The ribosome produces all of the proteins and many of the peptides present in cells. As a macromolecular complex composed of both RNAs and proteins, it employs a constituent RNA to catalyze the formation of peptide bonds rapidly and with high fidelity. Thus, the ribosome can be argued to represent the key link between the RNA World, in which RNAs were the primary catalysts, and present biological systems in which protein catalysts predominate. In spite of the well-known phylogenetic conservation of rRNAs through evolutionary history, rRNAs can be altered readily when placed under suitable pressure, e.g. in the presence of antibiotics which bind to functionally critical regions of rRNAs. While the structures of rRNAs have been altered intentionally for decades to enable the study of their role(s) in the mechanism of peptide bond formation, it is remarkable that the purposeful alteration of rRNA structure to enable the elaboration of proteins and peptides containing noncanonical amino acids has occurred only recently. In this Perspective, we summarize the history of rRNA modifications, and demonstrate how the intentional modification of 23S rRNA in regions critical for peptide bond formation now enables the direct ribosomal incorporation of d-amino acids, β-amino acids, dipeptides and dipeptidomimetic analogues of the normal proteinogenic l-α-amino acids. While proteins containing metabolically important functional groups such as carbohydrates and phosphate groups are normally elaborated by the post-translational modification of nascent polypeptides, the use of modified ribosomes to produce such polymers directly is also discussed. Finally, we describe the elaboration of such modified proteins both in vitro and in bacterial cells, and suggest how such novel biomaterials may be exploited in future studies.
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Affiliation(s)
- Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
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32
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Melnikov SV, Khabibullina NF, Mairhofer E, Vargas-Rodriguez O, Reynolds NM, Micura R, Söll D, Polikanov YS. Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site. Nucleic Acids Res 2019; 47:2089-2100. [PMID: 30520988 PMCID: PMC6393236 DOI: 10.1093/nar/gky1211] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/14/2018] [Accepted: 11/20/2018] [Indexed: 12/24/2022] Open
Abstract
During protein synthesis, ribosomes discriminate chirality of amino acids and prevent incorporation of D-amino acids into nascent proteins by slowing down the rate of peptide bond formation. Despite this phenomenon being known for nearly forty years, no structures have ever been reported that would explain the poor reactivity of D-amino acids. Here we report a 3.7Å-resolution crystal structure of a bacterial ribosome in complex with a D-aminoacyl-tRNA analog bound to the A site. Although at this resolution we could not observe individual chemical groups, we could unambiguously define the positions of the D-amino acid side chain and the amino group based on chemical restraints. The structure reveals that similarly to L-amino acids, the D-amino acid binds the ribosome by inserting its side chain into the ribosomal A-site cleft. This binding mode does not allow optimal nucleophilic attack of the peptidyl-tRNA by the reactive α-amino group of a D-amino acid. Also, our structure suggests that the D-amino acid cannot participate in hydrogen-bonding with the P-site tRNA that is required for the efficient proton transfer during peptide bond formation. Overall, our work provides the first mechanistic insight into the ancient mechanism that helps living cells ensure the stereochemistry of protein synthesis.
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Affiliation(s)
- Sergey V Melnikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Nelli F Khabibullina
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Elisabeth Mairhofer
- Institute of Organic Chemistry at Leopold Franzens University, A-6020 Innsbruck, Austria
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Noah M Reynolds
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Ronald Micura
- Institute of Organic Chemistry at Leopold Franzens University, A-6020 Innsbruck, Austria
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607, USA
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33
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Korenić A, Perović S, Ćirković MM, Miquel PA. Symmetry breaking and functional incompleteness in biological systems. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 150:1-12. [PMID: 30776381 DOI: 10.1016/j.pbiomolbio.2019.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/31/2018] [Accepted: 02/05/2019] [Indexed: 12/20/2022]
Abstract
Symmetry-based explanations using symmetry breaking (SB) as the key explanatory tool have complemented and replaced traditional causal explanations in various domains of physics. The process of spontaneous SB is now a mainstay of contemporary explanatory accounts of large chunks of condensed-matter physics, quantum field theory, nonlinear dynamics, cosmology, and other disciplines. A wide range of empirical research into various phenomena related to symmetries and SB across biological scales has accumulated as well. Led by these results, we identify and explain some common features of the emergence, propagation, and cascading of SB-induced layers across the biosphere. These features are predicated on the thermodynamic openness and intrinsic functional incompleteness of the systems at stake and have not been systematically analyzed from a general philosophical and methodological perspective. We also consider possible continuity of SB across the physical and biological world and discuss the connection between Darwinism and SB-based analysis of the biosphere and its history.
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Affiliation(s)
- Andrej Korenić
- The Centre for Laser Microscopy, Institute for Physiology and Biochemistry, Faculty of Biology, University of Belgrade, Serbia
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34
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Liljeruhm J, Wang J, Kwiatkowski M, Sabari S, Forster AC. Kinetics of d-Amino Acid Incorporation in Translation. ACS Chem Biol 2019; 14:204-213. [PMID: 30648860 DOI: 10.1021/acschembio.8b00952] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite the stereospecificity of translation for l-amino acids (l-AAs) in vivo, synthetic biologists have enabled ribosomal incorporation of d-AAs in vitro toward encoding polypeptides with pharmacologically desirable properties. However, the steps in translation limiting d-AA incorporation need clarification. In this work, we compared d- and l-Phe incorporation in translation by quench-flow kinetics, measuring 250-fold slower incorporation into the dipeptide for the d isomer from a tRNAPhe-based adaptor (tRNAPheB). Incorporation was moderately hastened by tRNA body swaps and higher EF-Tu concentrations, indicating that binding by EF-Tu can be rate-limiting. However, from tRNAAlaB with a saturating concentration of EF-Tu, the slow d-Phe incorporation was unexpectedly very efficient in competition with incorporation of the l isomer, indicating fast binding to EF-Tu, fast binding of the resulting complex to the ribosome, and rate-limiting accommodation/peptide bond formation. Subsequent elongation with an l-AA was confirmed to be very slow and inefficient. This understanding helps rationalize incorporation efficiencies in vitro and stereospecific mechanisms in vivo and suggests approaches for improving incorporation.
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Affiliation(s)
- Josefine Liljeruhm
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, 751 24 Uppsala, Sweden
| | - Jinfan Wang
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, 751 24 Uppsala, Sweden
| | - Marek Kwiatkowski
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, 751 24 Uppsala, Sweden
| | - Samudra Sabari
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, 751 24 Uppsala, Sweden
| | - Anthony C. Forster
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, 751 24 Uppsala, Sweden
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35
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Wang J, Forster AC. Ribosomal incorporation of unnatural amino acids: lessons and improvements from fast kinetics studies. Curr Opin Chem Biol 2018; 46:180-187. [DOI: 10.1016/j.cbpa.2018.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 05/21/2018] [Accepted: 07/13/2018] [Indexed: 11/30/2022]
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36
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Kuncha SK, Suma K, Pawar KI, Gogoi J, Routh SB, Pottabathini S, Kruparani SP, Sankaranarayanan R. A discriminator code-based DTD surveillance ensures faithful glycine delivery for protein biosynthesis in bacteria. eLife 2018; 7:38232. [PMID: 30091703 PMCID: PMC6097841 DOI: 10.7554/elife.38232] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/07/2018] [Indexed: 11/13/2022] Open
Abstract
D-aminoacyl-tRNA deacylase (DTD) acts on achiral glycine, in addition to D-amino acids, attached to tRNA. We have recently shown that this activity enables DTD to clear non-cognate Gly-tRNAAla with 1000-fold higher efficiency than its activity on Gly-tRNAGly, indicating tRNA-based modulation of DTD (Pawar et al., 2017). Here, we show that tRNA's discriminator base predominantly accounts for this activity difference and is the key to selection by DTD. Accordingly, the uracil discriminator base, serving as a negative determinant, prevents Gly-tRNAGly misediting by DTD and this protection is augmented by EF-Tu. Intriguingly, eukaryotic DTD has inverted discriminator base specificity and uses only G3•U70 for tRNAGly/Ala discrimination. Moreover, DTD prevents alanine-to-glycine misincorporation in proteins rather than only recycling mischarged tRNAAla. Overall, the study reveals the unique co-evolution of DTD and discriminator base, and suggests DTD's strong selection pressure on bacterial tRNAGlys to retain a pyrimidine discriminator code.
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Affiliation(s)
- Santosh Kumar Kuncha
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Academy of Scientific and Innovative Research, CSIR-CCMB Campus, Hyderabad, India
| | - Katta Suma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Jotin Gogoi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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37
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Fleisher RC, Cornish VW, Gonzalez RL. d-Amino Acid-Mediated Translation Arrest Is Modulated by the Identity of the Incoming Aminoacyl-tRNA. Biochemistry 2018; 57:4241-4246. [PMID: 29979035 DOI: 10.1021/acs.biochem.8b00595] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A complete understanding of the determinants that restrict d-amino acid incorporation by the ribosome, which is of interest to both basic biologists and the protein engineering community, remains elusive. Previously, we demonstrated that d-amino acids are successfully incorporated into the C-terminus of the nascent polypeptide chain. Ribosomes carrying the resulting peptidyl-d-aminoacyl-tRNA (peptidyl-d-aa-tRNA) donor substrate, however, partition into subpopulations that either undergo translation arrest through inactivation of the ribosomal peptidyl-transferase center (PTC) or remain translationally competent. The proportion of each subpopulation is determined by the identity of the d-amino acid side chain. Here, we demonstrate that the identity of the aminoacyl-tRNA (aa-tRNA) acceptor substrate that is delivered to ribosomes carrying a peptidyl-d-aa-tRNA donor further modulates this partitioning. Our discovery demonstrates that it is the pairing of the peptidyl-d-aa-tRNA donor and the aa-tRNA acceptor that determines the activity of the PTC. Moreover, we provide evidence that both the amino acid and tRNA components of the aa-tRNA acceptor contribute synergistically to the extent of arrest. The results of this work deepen our understanding of the mechanism of d-amino acid-mediated translation arrest and how cells avoid this precarious obstacle, reveal similarities to other translation arrest mechanisms involving the PTC, and provide a new route for improving the yields of engineered proteins containing d-amino acids.
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Affiliation(s)
- Rachel C Fleisher
- Department of Chemistry , Columbia University , New York , New York 10027 , United States
| | - Virginia W Cornish
- Department of Chemistry , Columbia University , New York , New York 10027 , United States
| | - Ruben L Gonzalez
- Department of Chemistry , Columbia University , New York , New York 10027 , United States
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38
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Rybak MY, Kovalenko OP, Tukalo MA. The Dual Role of the 2'-OH Group of A76 tRNA Tyr in the Prevention of d-tyrosine Mistranslation. J Mol Biol 2018; 430:2670-2676. [PMID: 29953888 DOI: 10.1016/j.jmb.2018.06.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 06/17/2018] [Accepted: 06/19/2018] [Indexed: 02/02/2023]
Abstract
Aminoacyl-tRNA-synthetases are crucial enzymes for initiation step of translation. Possessing editing activity, they protect living cells from misincorporation of non-cognate and non-proteinogenic amino acids into proteins. Tyrosyl-tRNA synthetase (TyrRS) does not have such editing properties, but it shares weak stereospecificity in recognition of d-/l-tyrosine (Tyr). Nevertheless, an additional enzyme, d-aminoacyl-tRNA-deacylase (DTD), exists to overcome these deficiencies. The precise catalytic role of hydroxyl groups of the tRNATyr A76 in the catalysis by TyrRS and DTD remained unknown. To address this issue, [32P]-labeled tRNATyr substrates have been tested in aminoacylation and deacylation assays. TyrRS demonstrates similar activity in charging the 2' and 3'-OH groups of A76 with l-Tyr. This synthetase can effectively use both OH groups as primary sites for aminoacylation with l-Tyr, but demonstrates severe preference toward 2'-OH, in charging with d-Tyr. In both cases, the catalysis is not substrate-assisted: neither the 2'-OH nor the 3'-OH group assists catalysis. In contrast, DTD catalyzes deacylation of d-Tyr-tRNATyr specifically from the 3'-OH group, while the 2'-OH assists in this hydrolysis.
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Affiliation(s)
- Mariia Yu Rybak
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, 150 Zabolotnogo Str., 03143 Kyiv, Ukraine.
| | - Oksana P Kovalenko
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, 150 Zabolotnogo Str., 03143 Kyiv, Ukraine
| | - Michael A Tukalo
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, 150 Zabolotnogo Str., 03143 Kyiv, Ukraine
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39
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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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40
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A chiral selectivity relaxed paralog of DTD for proofreading tRNA mischarging in Animalia. Nat Commun 2018; 9:511. [PMID: 29410408 PMCID: PMC5802732 DOI: 10.1038/s41467-017-02204-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/13/2017] [Indexed: 01/07/2023] Open
Abstract
D-aminoacyl-tRNA deacylase (DTD), a bacterial/eukaryotic trans-editing factor, removes D-amino acids mischarged on tRNAs and achiral glycine mischarged on tRNAAla. An invariant cross-subunit Gly-cisPro motif forms the mechanistic basis of L-amino acid rejection from the catalytic site. Here, we present the identification of a DTD variant, named ATD (Animalia-specific tRNA deacylase), that harbors a Gly-transPro motif. The cis-to-trans switch causes a "gain of function" through L-chiral selectivity in ATD resulting in the clearing of L-alanine mischarged on tRNAThr(G4•U69) by eukaryotic AlaRS. The proofreading activity of ATD is conserved across diverse classes of phylum Chordata. Animalia genomes enriched in tRNAThr(G4•U69) genes are in strict association with the presence of ATD, underlining the mandatory requirement of a dedicated factor to proofread tRNA misaminoacylation. The study highlights the emergence of ATD during genome expansion as a key event associated with the evolution of Animalia.
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Chin JW. Expanding and reprogramming the genetic code. Nature 2017; 550:53-60. [PMID: 28980641 DOI: 10.1038/nature24031] [Citation(s) in RCA: 504] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022]
Abstract
Nature uses a limited, conservative set of amino acids to synthesize proteins. The ability to genetically encode an expanded set of building blocks with new chemical and physical properties is transforming the study, manipulation and evolution of proteins, and is enabling diverse applications, including approaches to probe, image and control protein function, and to precisely engineer therapeutics. Underpinning this transformation are strategies to engineer and rewire translation. Emerging strategies aim to reprogram the genetic code so that noncanonical biopolymers can be synthesized and evolved, and to test the limits of our ability to engineer the translational machinery and systematically recode genomes.
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Affiliation(s)
- Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.,Department of Chemistry, Cambridge University, Cambridge CB2 1EW, UK
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Jiang Y, Li F, Wu J, Shi Y, Gong Q. Structural insights into substrate selectivity of ribosomal RNA methyltransferase RlmCD. PLoS One 2017; 12:e0185226. [PMID: 28949991 PMCID: PMC5614603 DOI: 10.1371/journal.pone.0185226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/09/2017] [Indexed: 11/22/2022] Open
Abstract
RlmCD has recently been identified as the S-adenosyl methionine (SAM)-dependent methyltransferase responsible for the formation of m5U at U747 and U1939 of 23S ribosomal RNA in Streptococcus pneumoniae. In this research, we determine the high-resolution crystal structures of apo-form RlmCD and its complex with SAH. Using an in-vitro methyltransferase assay, we reveal the crucial residues for its catalytic functions. Furthermore, structural comparison between RlmCD and its structural homologue RumA, which only catalyzes the m5U1939 in Escherichia coli, implicates that a unique long linker in the central domain of RlmCD is the key factor in determining its substrate selectivity. Its significance in the enzyme activity of RlmCD is further confirmed by in-vitro methyltransferase assay.
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Affiliation(s)
- Yiyang Jiang
- Hefei National Laboratory For Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Fudong Li
- Hefei National Laboratory For Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Jihui Wu
- Hefei National Laboratory For Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Yunyu Shi
- Hefei National Laboratory For Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Qingguo Gong
- Hefei National Laboratory For Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
- * E-mail:
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43
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Repurposing ribosomes for synthetic biology. Curr Opin Chem Biol 2017; 40:87-94. [PMID: 28869851 DOI: 10.1016/j.cbpa.2017.07.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 11/21/2022]
Abstract
The translation system is the cell's factory for protein biosynthesis, stitching together hundreds to thousands of amino acids into proteins, which are required for the structure, function, and regulation of living systems. The extraordinary synthetic capability of this system, which includes the ribosome and its associated factors required for polymerization, has driven extensive efforts to harness it for societal use in areas as diverse as energy, materials, and medicine. A powerful example is recombinant protein production, which has impacted the lives of patients through the synthesis of biopharmaceuticals such as insulin. In nature, however, only limited sets of monomers are utilized, thereby resulting in limited sets of biopolymers (i.e., proteins). Expanding nature's repertoire of ribosomal monomers could yield new classes of enzymes, therapeutics, materials, and chemicals with diverse, genetically encoded chemistry. Here, we discuss recent progress towards engineering ribosomes both in vivo and in vitro. These fundamental and technical breakthroughs open doors for advanced applications in biotechnology and synthetic biology.
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De Bo G, Gall MAY, Kitching MO, Kuschel S, Leigh DA, Tetlow DJ, Ward JW. Sequence-Specific β-Peptide Synthesis by a Rotaxane-Based Molecular Machine. J Am Chem Soc 2017; 139:10875-10879. [DOI: 10.1021/jacs.7b05850] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Guillaume De Bo
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Malcolm A. Y. Gall
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Matthew O. Kitching
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Sonja Kuschel
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - David A. Leigh
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Daniel J. Tetlow
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - John W. Ward
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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45
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Exploring sequence space: harnessing chemical and biological diversity towards new peptide leads. Curr Opin Chem Biol 2017; 38:52-61. [DOI: 10.1016/j.cbpa.2017.02.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/18/2017] [Accepted: 02/20/2017] [Indexed: 12/29/2022]
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Mechanistic Insights Into Catalytic RNA-Protein Complexes Involved in Translation of the Genetic Code. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017. [PMID: 28683922 DOI: 10.1016/bs.apcsb.2017.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The contemporary world is an "RNA-protein world" rather than a "protein world" and tracing its evolutionary origins is of great interest and importance. The different RNAs that function in close collaboration with proteins are involved in several key physiological processes, including catalysis. Ribosome-the complex megadalton cellular machinery that translates genetic information encoded in nucleotide sequence to amino acid sequence-epitomizes such an association between RNA and protein. RNAs that can catalyze biochemical reactions are known as ribozymes. They usually employ general acid-base catalytic mechanism, often involving the 2'-OH of RNA that activates and/or stabilizes a nucleophile during the reaction pathway. The protein component of such RNA-protein complexes (RNPCs) mostly serves as a scaffold which provides an environment conducive for the RNA to function, or as a mediator for other interacting partners. In this review, we describe those RNPCs that are involved at different stages of protein biosynthesis and in which RNA performs the catalytic function; the focus of the account is on highlighting mechanistic aspects of these complexes. We also provide a perspective on such associations in the context of proofreading during translation of the genetic code. The latter aspect is not much appreciated and recent works suggest that this is an avenue worth exploring, since an understanding of the subject can provide useful insights into how RNAs collaborate with proteins to ensure fidelity during these essential cellular processes. It may also aid in comprehending evolutionary aspects of such associations.
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Makarov GI, Makarova TM, Sumbatyan NV, Bogdanov AA. Investigation of Ribosomes Using Molecular Dynamics Simulation Methods. BIOCHEMISTRY (MOSCOW) 2017; 81:1579-1588. [PMID: 28260485 DOI: 10.1134/s0006297916130010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The ribosome as a complex molecular machine undergoes significant conformational changes while synthesizing a protein molecule. Molecular dynamics simulations have been used as complementary approaches to X-ray crystallography and cryoelectron microscopy, as well as biochemical methods, to answer many questions that modern structural methods leave unsolved. In this review, we demonstrate that all-atom modeling of ribosome molecular dynamics is particularly useful in describing the process of tRNA translocation, atomic details of behavior of nascent peptides, antibiotics, and other small molecules in the ribosomal tunnel, and the putative mechanism of allosteric signal transmission to functional sites of the ribosome.
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Affiliation(s)
- G I Makarov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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Rewiring protein synthesis: From natural to synthetic amino acids. Biochim Biophys Acta Gen Subj 2017; 1861:3024-3029. [PMID: 28095316 DOI: 10.1016/j.bbagen.2017.01.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 11/21/2022]
Abstract
BACKGROUND The protein synthesis machinery uses 22 natural amino acids as building blocks that faithfully decode the genetic information. Such fidelity is controlled at multiple steps and can be compromised in nature and in the laboratory to rewire protein synthesis with natural and synthetic amino acids. SCOPE OF REVIEW This review summarizes the major quality control mechanisms during protein synthesis, including aminoacyl-tRNA synthetases, elongation factors, and the ribosome. We will discuss evolution and engineering of such components that allow incorporation of natural and synthetic amino acids at positions that deviate from the standard genetic code. MAJOR CONCLUSIONS The protein synthesis machinery is highly selective, yet not fixed, for the correct amino acids that match the mRNA codons. Ambiguous translation of a codon with multiple amino acids or complete reassignment of a codon with a synthetic amino acid diversifies the proteome. GENERAL SIGNIFICANCE Expanding the genetic code with synthetic amino acids through rewiring protein synthesis has broad applications in synthetic biology and chemical biology. Biochemical, structural, and genetic studies of the translational quality control mechanisms are not only crucial to understand the physiological role of translational fidelity and evolution of the genetic code, but also enable us to better design biological parts to expand the proteomes of synthetic organisms. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Wang J, Kwiatkowski M, Forster AC. Ribosomal Peptide Syntheses from Activated Substrates Reveal Rate Limitation by an Unexpected Step at the Peptidyl Site. J Am Chem Soc 2016; 138:15587-15595. [DOI: 10.1021/jacs.6b06936] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jinfan Wang
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan 3, Box
596, Uppsala 75124, Sweden
| | - Marek Kwiatkowski
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan 3, Box
596, Uppsala 75124, Sweden
| | - Anthony C. Forster
- Department of Cell and Molecular
Biology, Uppsala University, Husargatan 3, Box
596, Uppsala 75124, Sweden
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50
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Manuel Carlevaro C, Irastorza RM, Vericat F. Chirality in a quaternionic representation of the genetic code. Biosystems 2016; 150:99-109. [PMID: 27378069 DOI: 10.1016/j.biosystems.2016.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/14/2016] [Accepted: 08/23/2016] [Indexed: 10/21/2022]
Abstract
A quaternionic representation of the genetic code, previously reported by the authors (BioSystems 141 (10-19), 2016), is updated in order to incorporate chirality of nucleotide bases and amino acids. The original representation associates with each nucleotide base a prime integer quaternion of norm 7 and involves a function that assigns to each codon, represented by three of these quaternions, another integer quaternion (amino acid type quaternion). The assignation is such that the essentials of the standard genetic code (particularly its degeneration) are preserved. To show the advantages of such a quaternionic representation we have designed an algorithm to go from the primary to the tertiary structure of the protein. The algorithm uses, besides of the type quaternions, a second kind of quaternions with real components that we additionally associate with the amino acids according to their order along the proteins (order quaternions). In this context, we incorporate chirality in our representation by observing that the set of eight integer quaternions of norm 7 can be partitioned into a pair of subsets of cardinality four each with their elements mutually conjugate and by putting them into correspondence one to one with the two sets of enantiomers (D and L) of the four nucleotide bases adenine, cytosine, guanine and uracil, respectively. We then propose two diagrams in order to describe the hypothetical evolution of the genetic codes corresponding to both of the chiral systems of affinities: D-nucleotide bases/L-amino acids and L-nucleotide bases/D-amino acids at reading frames 5'→3' and 3'→5', respectively. Guided by these diagrams we define functions that in each case assign to the triplets of D- (L-) bases a L- (D-) amino acid type integer quaternion. Specifically, the integer quaternion associated with a given D-amino acid is the conjugate of that one corresponding to the enantiomer L. The chiral type quaternions obtained for the amino acids are used, together with a common set of order quaternions, to describe the folding of the two classes, L and D, of homochiral proteins.
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Affiliation(s)
- C Manuel Carlevaro
- Instituto de Física de Líquidos y Sistemas Biológicos, 59 Nro. 789, 1900 La Plata, Argentina; Universidad Tecnológica Nacional, Facultad Regional Buenos Aires, Mozart Nro. 2300, C14071VT Buenos Aires, Argentina.
| | - Ramiro M Irastorza
- Instituto de Física de Líquidos y Sistemas Biológicos, 59 Nro. 789, 1900 La Plata, Argentina; Instituto de Ingeniería y Agronomía, Universidad Nacional Arturo Jauretche, 1888 Florencio Varela, Buenos Aires, Argentina.
| | - Fernando Vericat
- Instituto de Física de Líquidos y Sistemas Biológicos, 59 Nro. 789, 1900 La Plata, Argentina; Grupo de Aplicaciones Matemáticas y Estadísticas de la Facultad de Ingeniería (GAMEFI), Universidad Nacional de La Plata, Calle 115 y 48, 1900 La Plata, Argentina.
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