1
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Kim J, Jeong KJ, Kim GJ, Choi JI. Engineering of Recombinant Human Papillomavirus 16 L1 Protein for Incorporation with para-Azido- L-Phenylalanine. J Microbiol Biotechnol 2024; 34:1926-1932. [PMID: 39155395 DOI: 10.4014/jmb.2407.07033] [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: 07/19/2024] [Revised: 07/30/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024]
Abstract
Human papillomavirus (HPV) L1 capsid protein were produced in several host systems, but few studies have focused on enhancing the properties of the L1 protein. In this study, we aimed to produce recombinant Human papillomavirus (HPV) L1 capsid protein containing para-azido-L-phenylalanine (pAzF) in Escherichia coli. First, we expressed the maltose-binding protein (MBP)-fused HPV16 L1, and 5 residues in HPV16 L1 protein were selected by the in silico modeling for amber codon substitution. Among the variants of the five locations, we identified a candidate that exhibited significant differences in expression with and without pAzF via genetic code expansion (GCE). The expressed recombinant MBP-HPV16L1 protein was confirmed for incorporation of pAzF and the formation of VLPs was tested in vitro.
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Affiliation(s)
- Jinhyeon Kim
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Geun-Joong Kim
- Department of Biological Sciences and Research Center of Ecomimetics, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jong-Il Choi
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju 61186, Republic of Korea
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2
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Niu W, Guo J. Cellular Site-Specific Incorporation of Noncanonical Amino Acids in Synthetic Biology. Chem Rev 2024; 124:10577-10617. [PMID: 39207844 PMCID: PMC11470805 DOI: 10.1021/acs.chemrev.3c00938] [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] [Indexed: 09/04/2024]
Abstract
Over the past two decades, genetic code expansion (GCE)-enabled methods for incorporating noncanonical amino acids (ncAAs) into proteins have significantly advanced the field of synthetic biology while also reaping substantial benefits from it. On one hand, they provide synthetic biologists with a powerful toolkit to enhance and diversify biological designs beyond natural constraints. Conversely, synthetic biology has not only propelled the development of ncAA incorporation through sophisticated tools and innovative strategies but also broadened its potential applications across various fields. This Review delves into the methodological advancements and primary applications of site-specific cellular incorporation of ncAAs in synthetic biology. The topics encompass expanding the genetic code through noncanonical codon addition, creating semiautonomous and autonomous organisms, designing regulatory elements, and manipulating and extending peptide natural product biosynthetic pathways. The Review concludes by examining the ongoing challenges and future prospects of GCE-enabled ncAA incorporation in synthetic biology and highlighting opportunities for further advancements in this rapidly evolving field.
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Affiliation(s)
- Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
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3
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Sviben I, Glavaš M, Erben A, Bachelart T, Pavlović Saftić D, Piantanida I, Basarić N. Dipeptides Containing Pyrene and Modified Photochemically Reactive Tyrosine: Noncovalent and Covalent Binding to Polynucleotides. Molecules 2023; 28:7533. [PMID: 38005255 PMCID: PMC10672942 DOI: 10.3390/molecules28227533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Dipeptides 1 and 2 were synthesized from unnatural amino acids containing pyrene as a fluorescent label and polynucleotide binding unit, and modified tyrosine as a photochemically reactive unit. Photophysical properties of the peptides were investigated by steady-state and time-resolved fluorescence. Both peptides are fluorescent (Φf = 0.3-0.4) and do not show a tendency to form pyrene excimers in the concentration range < 10-5 M, which is important for their application in the fluorescent labeling of polynucleotides. Furthermore, both peptides are photochemically reactive and undergo deamination delivering quinone methides (QMs) (ΦR = 0.01-0.02), as indicated from the preparative photomethanolysis study of the corresponding N-Boc protected derivatives 7 and 8. Both peptides form stable complexes with polynucleotides (log Ka > 6) by noncovalent interactions and similar affinities, binding to minor grooves, preferably to the AT reach regions. Peptide 2 with a longer spacer between the fluorophore and the photo-activable unit undergoes a more efficient deamination reaction, based on the comparison with the N-Boc protected derivatives. Upon light excitation of the complex 2·oligoAT10, the photo-generation of QM initiates the alkylation, which results in the fluorescent labeling of the oligonucleotide. This study demonstrated, as a proof of principle, that small molecules can combine dual forms of fluorescent labeling of polynucleotides, whereby initial addition of the dye rapidly forms a reversible high-affinity noncovalent complex with ds-DNA/RNA, which can be, upon irradiation by light, converted to the irreversible (covalent) form. Such a dual labeling ability of a dye could have many applications in biomedicinal sciences.
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Affiliation(s)
| | | | | | | | | | - Ivo Piantanida
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (I.S.); (M.G.); (A.E.); (T.B.); (D.P.S.)
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (I.S.); (M.G.); (A.E.); (T.B.); (D.P.S.)
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4
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Do T, Link AJ. Protein Engineering in Ribosomally Synthesized and Post-translationally Modified Peptides (RiPPs). Biochemistry 2023; 62:201-209. [PMID: 35006671 PMCID: PMC9454058 DOI: 10.1021/acs.biochem.1c00714] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) make up a rapidly growing superfamily of natural products. RiPPs exhibit an extraordinary range of structures, but they all begin as gene-encoded precursor peptides that are linear chains of amino acids produced by ribosomes. Given the gene-encoded nature of RiPP precursor peptides, the toolbox of protein engineering can be directly applied to these precursors. This Perspective will discuss examples of site-directed mutagenesis, noncanonical amino acid mutagenesis, and the construction and screening of combinatorial libraries as applied to RiPPs. These studies have led to important insights into the biosynthesis and bioactivity of RiPPs and the reengineering of RiPPs for entirely new functions.
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Affiliation(s)
- Truc Do
- Department of Chemical and Biological Engineering, 207 Hoyt Laboratory Princeton University, Princeton, NJ 08544 USA
| | - A. James Link
- Department of Chemical and Biological Engineering, 207 Hoyt Laboratory Princeton University, Princeton, NJ 08544 USA
- Department of Chemistry, 207 Hoyt Laboratory Princeton University, Princeton, NJ 08544 USA
- Department of Molecular Biology, 207 Hoyt Laboratory Princeton University, Princeton, NJ 08544 USA
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5
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Du Y, Li L, Zheng Y, Liu J, Gong J, Qiu Z, Li Y, Qiao J, Huo YX. Incorporation of Non-Canonical Amino Acids into Antimicrobial Peptides: Advances, Challenges, and Perspectives. Appl Environ Microbiol 2022; 88:e0161722. [PMID: 36416555 PMCID: PMC9746297 DOI: 10.1128/aem.01617-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The emergence of antimicrobial resistance is a global health concern and calls for the development of novel antibiotic agents. Antimicrobial peptides seem to be promising candidates due to their diverse sources, mechanisms of action, and physicochemical characteristics, as well as the relatively low emergence of resistance. The incorporation of noncanonical amino acids into antimicrobial peptides could effectively improve their physicochemical and pharmacological diversity. Recently, various antimicrobial peptides variants with improved or novel properties have been produced by the incorporation of single and multiple distinct noncanonical amino acids. In this review, we summarize strategies for the incorporation of noncanonical amino acids into antimicrobial peptides, as well as their features and suitabilities. Recent applications of noncanonical amino acid incorporation into antimicrobial peptides are also presented. Finally, we discuss the related challenges and prospects.
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Affiliation(s)
- Yuhui Du
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Li Li
- School of Chemical Engineering, Sichuan University (SCU), Chengdu, China
| | - Yue Zheng
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Jiaheng Liu
- School of Chemical Engineering, Sichuan University (SCU), Chengdu, China
| | - Julia Gong
- Marymount High School, Los Angeles, California, USA
| | - Zekai Qiu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Yanni Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Jianjun Qiao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
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6
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Scholz S, Kerestetzopoulou S, Wiebach V, Schnegotzki R, Schmid B, Reyna‐González E, Ding L, Süssmuth RD, Dittmann E, Baunach M. One-Pot Chemoenzymatic Synthesis of Microviridin Analogs Containing Functional Tags. Chembiochem 2022; 23:e202200345. [PMID: 35995730 PMCID: PMC9826346 DOI: 10.1002/cbic.202200345] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/31/2022] [Indexed: 01/11/2023]
Abstract
Microviridins are a prominent family of ribosomally synthesized and posttranslationally modified peptides (RiPPs) featuring characteristic lactone and lactam rings. Their unusual cage-like architecture renders them highly potent serine protease inhibitors of which individual variants specifically inhibit different types of proteases of pharmacological interest. While posttranslational modifications are key for the stability and bioactivity of RiPPs, additional attractive properties can be introduced by functional tags. To date - although highly desirable - no method has been reported to incorporate functional tags in microviridin scaffolds or the overarching class of graspetides. In this study, a chemoenzymatic in vitro platform is used to introduce functional tags in various microviridin variants yielding biotinylated, dansylated or propargylated congeners. This straightforward approach paves the way for customized protease inhibitors with built-in functionalities that can help to unravel the still elusive ecological roles and targets of this remarkable class of compounds and to foster applications based on protease inhibition.
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Affiliation(s)
- Stella Scholz
- Department of MicrobiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Sofia Kerestetzopoulou
- Department of MicrobiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Vincent Wiebach
- Department of Biotechnology and BiomedicineTechnical University of DenmarkSøltofts Plads, Building 221DK-2800 Kgs.LyngbyDenmark
| | - Romina Schnegotzki
- Institute of ChemistryTechnical University BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Bianca Schmid
- Institute of ChemistryTechnical University BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Emmanuel Reyna‐González
- Department of MicrobiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Ling Ding
- Department of Biotechnology and BiomedicineTechnical University of DenmarkSøltofts Plads, Building 221DK-2800 Kgs.LyngbyDenmark
| | - Roderich D. Süssmuth
- Institute of ChemistryTechnical University BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Elke Dittmann
- Department of MicrobiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Martin Baunach
- Department of MicrobiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
- Institute of Pharmaceutical BiologyUniversity of BonnNussallee 653115BonnGermany
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7
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Nguyen DT, Le TT, Rice AJ, Hudson GA, van der Donk WA, Mitchell DA. Accessing Diverse Pyridine-Based Macrocyclic Peptides by a Two-Site Recognition Pathway. J Am Chem Soc 2022; 144:11263-11269. [PMID: 35713415 PMCID: PMC9247985 DOI: 10.1021/jacs.2c02824] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Indexed: 11/29/2022]
Abstract
Macrocyclic peptides are sought-after molecular scaffolds for drug discovery, and new methods to access diverse libraries are of increasing interest. Here, we report the enzymatic synthesis of pyridine-based macrocyclic peptides (pyritides) from linear precursor peptides. Pyritides are a recently described class of ribosomally synthesized and post-translationally modified peptides (RiPPs) and are related to the long-known thiopeptide natural products. RiPP precursors typically contain an N-terminal leader region that is physically engaged by the biosynthetic proteins that catalyze modification of the C-terminal core region of the precursor peptide. We demonstrate that pyritide-forming enzymes recognize both the leader region and a C-terminal tripeptide motif, with each contributing to site-selective substrate modification. Substitutions in the core region were well-tolerated and facilitated the generation of a wide range of pyritide analogues, with variations in macrocycle sequence and size. A combination of the pyritide biosynthetic pathway with azole-forming enzymes was utilized to generate a thiazole-containing pyritide (historically known as a thiopeptide) with no similarity in sequence and macrocycle size to the naturally encoded pyritides. The broad substrate scope of the pyritide biosynthetic enzymes serves as a future platform for macrocyclic peptide lead discovery and optimization.
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Affiliation(s)
- Dinh T. Nguyen
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Howard
Hughes Medical Institute, University of
Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Tung T. Le
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
- Howard
Hughes Medical Institute, University of
Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Andrew J. Rice
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Graham A. Hudson
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Howard
Hughes Medical Institute, University of
Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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8
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Johnston CW, Badran AH. Natural and engineered precision antibiotics in the context of resistance. Curr Opin Chem Biol 2022; 69:102160. [PMID: 35660248 DOI: 10.1016/j.cbpa.2022.102160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/18/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022]
Abstract
Antibiotics are essential weapons in our fight against infectious disease, yet the consequences of broad-spectrum antibiotic use on microbiome stability and pathogen resistance are prompting investigations into more selective alternatives. Echoing the advent of precision medicine in oncology, precision antibiotics with focused activities are emerging as a means of addressing infections without damaging microbiomes or incentivizing resistance. Historically, antibiotic design principles have been gleaned from Nature, and reinvestigation of overlooked antibacterials is now providing scaffolds and targets for the design of pathogen-specific drugs. In this perspective, we summarize the biosynthetic and antibacterial mechanisms used to access these activities, and discuss how such strategies may be co-opted through engineering approaches to afford precision antibiotics.
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Affiliation(s)
- Chad W Johnston
- Department of Pharmacology & Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Ahmed H Badran
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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9
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Tan Y, Wang M, Chen Y. Reprogramming the Biosynthesis of Precursor Peptide to Create a Selenazole-Containing Nosiheptide Analogue. ACS Synth Biol 2022; 11:85-91. [PMID: 35006674 DOI: 10.1021/acssynbio.1c00578] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nosiheptide (NOS), a potent bactericidal thiopeptide, belongs to a class of natural products produced by ribosomal synthesis and post-translational modifications, and its biosynthetic pathway has largely been elucidated. However, the central trithiazolylpyridine structure of NOS remains inaccessible to structural changes. Here we report the creation of a NOS analogue containing a unique selenazole ring by the construction of an artificial system in Streptomyces actuosus ATCC25421, where the genes responsible for the biosynthesis of selenoprotein from Escherichia coli and the biosynthetic gene cluster of NOS were rationally integrated to produce a selenazole-containing analogue of NOS. The thiazole at the fifth position in NOS was specifically replaced by a selenazole to afford the first selenazole-containing "unnatural" natural product. The present strategy is useful for structural manipulation of various RiPP natural products.
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Affiliation(s)
- Yingzi Tan
- State Key Laboratory of Natural Medicines and Laboratory of Chemical Biology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, P. R. China
| | - Miao Wang
- State Key Laboratory of Natural Medicines and Laboratory of Chemical Biology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, P. R. China
| | - Yijun Chen
- State Key Laboratory of Natural Medicines and Laboratory of Chemical Biology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, P. R. China
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10
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Lateef OM, Akintubosun MO, Olaoba OT, Samson SO, Adamczyk M. Making Sense of "Nonsense" and More: Challenges and Opportunities in the Genetic Code Expansion, in the World of tRNA Modifications. Int J Mol Sci 2022; 23:938. [PMID: 35055121 PMCID: PMC8779196 DOI: 10.3390/ijms23020938] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 01/09/2023] Open
Abstract
The evolutional development of the RNA translation process that leads to protein synthesis based on naturally occurring amino acids has its continuation via synthetic biology, the so-called rational bioengineering. Genetic code expansion (GCE) explores beyond the natural translational processes to further enhance the structural properties and augment the functionality of a wide range of proteins. Prokaryotic and eukaryotic ribosomal machinery have been proven to accept engineered tRNAs from orthogonal organisms to efficiently incorporate noncanonical amino acids (ncAAs) with rationally designed side chains. These side chains can be reactive or functional groups, which can be extensively utilized in biochemical, biophysical, and cellular studies. Genetic code extension offers the contingency of introducing more than one ncAA into protein through frameshift suppression, multi-site-specific incorporation of ncAAs, thereby increasing the vast number of possible applications. However, different mediating factors reduce the yield and efficiency of ncAA incorporation into synthetic proteins. In this review, we comment on the recent advancements in genetic code expansion to signify the relevance of systems biology in improving ncAA incorporation efficiency. We discuss the emerging impact of tRNA modifications and metabolism in protein design. We also provide examples of the latest successful accomplishments in synthetic protein therapeutics and show how codon expansion has been employed in various scientific and biotechnological applications.
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Affiliation(s)
- Olubodun Michael Lateef
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | | | - Olamide Tosin Olaoba
- Laboratory of Functional and Structural Biochemistry, Federal University of Sao Carlos, Sao Carlos 13565-905, SP, Brazil;
| | - Sunday Ocholi Samson
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | - Malgorzata Adamczyk
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
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11
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Tang H, Zhang P, Luo X. Recent Technologies for Genetic Code Expansion and their Implications on Synthetic Biology Applications. J Mol Biol 2021; 434:167382. [PMID: 34863778 DOI: 10.1016/j.jmb.2021.167382] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/18/2021] [Accepted: 11/24/2021] [Indexed: 02/03/2023]
Abstract
Genetic code expansion (GCE) enables the site-specific incorporation of non-canonical amino acids as novel building blocks for the investigation and manipulation of proteins. The advancement of genetic code expansion has been benefited from the development of synthetic biology, while genetic code expansion also helps to create more synthetic biology tools. In this review, we summarize recent advances in genetic code expansion brought by synthetic biology progresses, including engineering of the translation machinery, genome-wide codon reassignment, and the biosynthesis of non-canonical amino acids. We highlight the emerging application of this technology in construction of new synthetic biology parts, circuits, chassis, and products.
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Affiliation(s)
- Hongting Tang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Pan Zhang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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12
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Wang M, Fage CD, He Y, Mi J, Yang Y, Li F, An X, Fan H, Song L, Zhu S, Tong Y. Recent Advances and Perspectives on Expanding the Chemical Diversity of Lasso Peptides. Front Bioeng Biotechnol 2021; 9:741364. [PMID: 34631682 PMCID: PMC8498205 DOI: 10.3389/fbioe.2021.741364] [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: 07/14/2021] [Accepted: 09/13/2021] [Indexed: 12/16/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing family of natural products that exhibit a range of structures and bioactivities. Initially assembled from the twenty proteinogenic amino acids in a ribosome-dependent manner, RiPPs assume their peculiar bioactive structures through various post-translational modifications. The essential modifications representative of each subfamily of RiPP are performed on a precursor peptide by the so-called processing enzymes; however, various tailoring enzymes can also embellish the precursor peptide or processed peptide with additional functional groups. Lasso peptides are an interesting subfamily of RiPPs characterized by their unique lariat knot-like structure, wherein the C-terminal tail is inserted through a macrolactam ring fused by an isopeptide bond between the N-terminal amino group and an acidic side chain. Until recently, relatively few lasso peptides were found to be tailored with extra functional groups. Nevertheless, the development of new routes to diversify lasso peptides and thus introduce novel or enhanced biological, medicinally relevant, or catalytic properties is appealing. In this review, we highlight several strategies through which lasso peptides have been successfully modified and provide a brief overview of the latest findings on the tailoring of these peptides. We also propose future directions for lasso peptide tailoring as well as potential applications for these peptides in hybrid catalyst design.
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Affiliation(s)
- Mengjiao Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Christopher D Fage
- Department of Chemistry, University of Warwick, Coventry, United Kingdom
| | - Yile He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jinhui Mi
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yang Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Fei Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.,Clinical Laboratory Center, Taian City Central Hospital, Taian, China
| | - Xiaoping An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shaozhou Zhu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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13
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Stork DA, Squyres GR, Kuru E, Gromek KA, Rittichier J, Jog A, Burton BM, Church GM, Garner EC, Kunjapur AM. Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights. Nat Commun 2021; 12:5429. [PMID: 34521822 PMCID: PMC8440579 DOI: 10.1038/s41467-021-25691-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 08/18/2021] [Indexed: 02/08/2023] Open
Abstract
Bacillus subtilis is a model gram-positive bacterium, commonly used to explore questions across bacterial cell biology and for industrial uses. To enable greater understanding and control of proteins in B. subtilis, here we report broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons. We use these systems to achieve click-labelling, photo-crosslinking, and translational titration. These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression, validate a predicted protein-protein binding interface, and begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo. We expect that the establishment of this simple and easily accessible chemical biology system in B. subtilis will help uncover an abundance of biological insights and aid genetic code expansion in other organisms.
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Affiliation(s)
- Devon A Stork
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Georgia R Squyres
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Erkin Kuru
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Katarzyna A Gromek
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Jonathan Rittichier
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Aditya Jog
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Briana M Burton
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA.
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
| | - Aditya M Kunjapur
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Chemical and Biological Engineering, University of Delaware, Newark, DE, USA.
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14
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Chan DCK, Burrows LL. Thiocillin and micrococcin exploit the ferrioxamine receptor of Pseudomonas aeruginosa for uptake. J Antimicrob Chemother 2021; 76:2029-2039. [PMID: 33907816 DOI: 10.1093/jac/dkab124] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/16/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Thiopeptides are a class of antibiotics that are active against Gram-positive bacteria and inhibit translation. They were considered inactive against Gram-negative bacteria due to their inability to cross the outer membrane. However, we discovered previously that a member of this class, thiostrepton (TS), has activity against Pseudomonas aeruginosa and Acinetobacter baumannii under iron-limiting conditions. TS hijacks the pyoverdine siderophore receptors of P. aeruginosa to cross the outer membrane and synergizes with iron chelators. OBJECTIVES To test other thiopeptides for antimicrobial activity against P. aeruginosa and determine their mechanism of uptake, action and spectrum of activity. METHODS Eight thiopeptides were screened in chequerboard assays against a mutant of P. aeruginosa PA14 lacking both pyoverdine receptors. Thiopeptides that retain activity against a pyoverdine receptor-null mutant may use alternative siderophore receptors for entry. Susceptibility testing against siderophore receptor mutants was used to determine thiopeptide mechanism of uptake. RESULTS The thiopeptides thiocillin (TC) and micrococcin (MC) use the ferrioxamine siderophore receptor (FoxA) for uptake and inhibit the growth of P. aeruginosa at low micromolar concentrations. The activity of TC required the TonB-ExbBD system used to energize siderophore uptake. TC acted through its canonical mechanism of action of translation inhibition. CONCLUSIONS Multiple thiopeptides have antimicrobial activity against P. aeruginosa, countering the historical assumption that they cannot cross the outer membrane. These results demonstrate the potential for thiopeptides to act as antipseudomonal antibiotics.
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Affiliation(s)
- Derek C K Chan
- Department of Biochemistry and Biomedical Sciences, McMaster Children's Hospital, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.,Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Lori L Burrows
- Department of Biochemistry and Biomedical Sciences, McMaster Children's Hospital, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.,Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
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15
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Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep 2021; 38:130-239. [PMID: 32935693 PMCID: PMC7864896 DOI: 10.1039/d0np00027b] [Citation(s) in RCA: 410] [Impact Index Per Article: 136.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
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16
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Chan DCK, Burrows LL. Thiopeptides: antibiotics with unique chemical structures and diverse biological activities. J Antibiot (Tokyo) 2020; 74:161-175. [PMID: 33349675 DOI: 10.1038/s41429-020-00387-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/05/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022]
Abstract
Thiopeptides are a class of natural product antibiotics with diverse structures and functions. Their complex structures and biosynthesis have intrigued researchers since their discovery in 1948, but not a single thiopeptide has been approved for human use. This is mainly due to their poor solubility, challenging synthesis, and low bioavailability. This review summarizes the current research on the biosynthesis and biological activity of thiopeptide antibiotics since 2015. The focus of research since 2015 has been on uncovering biosynthetic routes, developing methods for total synthesis, and understanding the biological activity of thiopeptides. Overall, there is still much to learn about this family of molecules.
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Affiliation(s)
- Derek C K Chan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, ON, Canada
| | - Lori L Burrows
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada. .,Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, ON, Canada.
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17
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Karbalaei-Heidari HR, Budisa N. Combating Antimicrobial Resistance With New-To-Nature Lanthipeptides Created by Genetic Code Expansion. Front Microbiol 2020; 11:590522. [PMID: 33250877 PMCID: PMC7674664 DOI: 10.3389/fmicb.2020.590522] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/13/2020] [Indexed: 01/10/2023] Open
Abstract
Due to the rapid emergence of multi-resistant bacterial strains in recent decades, the commercially available effective antibiotics are becoming increasingly limited. On the other hand, widespread antimicrobial peptides (AMPs) such as the lantibiotic nisin has been used worldwide for more than 40 years without the appearance of significant bacterial resistance. Lantibiotics are ribosomally synthesized antimicrobials generated by posttranslational modifications. Their biotechnological production is of particular interest to redesign natural scaffolds improving their pharmaceutical properties, which has great potential for therapeutic use in human medicine and other areas. However, conventional protein engineering methods are limited to 20 canonical amino acids prescribed by the genetic code. Therefore, the expansion of the genetic code as the most advanced approach in Synthetic Biology allows the addition of new amino acid building blocks (non-canonical amino acids, ncAAs) during protein translation. We now have solid proof-of-principle evidence that bioexpression with these novel building blocks enabled lantibiotics with chemical properties transcending those produced by natural evolution. The unique scaffolds with novel structural and functional properties are the result of this bioengineering. Here we will critically examine and evaluate the use of the expanded genetic code and its alternatives in lantibiotics research over the last 7 years. We anticipate that Synthetic Biology, using engineered lantibiotics and even more complex scaffolds will be a promising tool to address an urgent problem of antibiotic resistance, especially in a class of multi-drug resistant microbes known as superbugs.
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Affiliation(s)
- Hamid Reza Karbalaei-Heidari
- Department of Biology, Faculty of Sciences, Shiraz University, Shiraz, Iran
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
- Institute of Chemistry, Technical University of Berlin, Berlin, Germany
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18
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Takahashi H, Dohmae N, Kim KS, Shimuta K, Ohnishi M, Yokoyama S, Yanagisawa T. Genetic incorporation of non-canonical amino acid photocrosslinkers in Neisseria meningitidis: New method provides insights into the physiological function of the function-unknown NMB1345 protein. PLoS One 2020; 15:e0237883. [PMID: 32866169 PMCID: PMC7458321 DOI: 10.1371/journal.pone.0237883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/04/2020] [Indexed: 02/01/2023] Open
Abstract
Although whole-genome sequencing has provided novel insights into Neisseria meningitidis, many open reading frames have only been annotated as hypothetical proteins with unknown biological functions. Our previous genetic analyses revealed that the hypothetical protein, NMB1345, plays a crucial role in meningococcal infection in human brain microvascular endothelial cells; however, NMB1345 has no homology to any identified protein in databases and its physiological function could not be elucidated using pre-existing methods. Among the many biological technologies to examine transient protein-protein interaction in vivo, one of the developed methods is genetic code expansion with non-canonical amino acids (ncAAs) utilizing a pyrrolysyl-tRNA synthetase/tRNAPyl pair from Methanosarcina species: However, this method has never been applied to assign function-unknown proteins in pathogenic bacteria. In the present study, we developed a new method to genetically incorporate ncAAs-encoded photocrosslinking probes into N. meningitidis by utilizing a pyrrolysyl-tRNA synthetase/tRNAPyl pair and elucidated the biological function(s) of the NMB1345 protein. The results revealed that the NMB1345 protein directly interacts with PilE, a major component of meningococcal pili, and further physicochemical and genetic analyses showed that the interaction between the NMB1345 protein and PilE was important for both functional pilus formation and meningococcal infectious ability in N. meningitidis. The present study using this new methodology for N. meningitidis provides novel insights into meningococcal pathogenesis by assigning the function of a hypothetical protein.
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Affiliation(s)
- Hideyuki Takahashi
- National Institute of Infectious Diseases, Department of Bacteriology I, Shinjuku-ku, Japan
- * E-mail:
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Kwang Sik Kim
- Division of Pediatric Infectious Diseases, Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Ken Shimuta
- National Institute of Infectious Diseases, Department of Bacteriology I, Shinjuku-ku, Japan
| | - Makoto Ohnishi
- National Institute of Infectious Diseases, Department of Bacteriology I, Shinjuku-ku, Japan
| | - Shigeyuki Yokoyama
- RIKEN Structural Biology Laboratory, Yokohama, Japan
- RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama, Japan
| | - Tatsuo Yanagisawa
- RIKEN Structural Biology Laboratory, Yokohama, Japan
- RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama, Japan
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19
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Bogart JW, Kramer NJ, Turlik A, Bleich RM, Catlin DS, Schroeder FC, Nair SK, Williamson RT, Houk KN, Bowers AA. Interception of the Bycroft-Gowland Intermediate in the Enzymatic Macrocyclization of Thiopeptides. J Am Chem Soc 2020; 142:13170-13179. [PMID: 32609512 PMCID: PMC7429253 DOI: 10.1021/jacs.0c05639] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Thiopeptides are a broad class of macrocyclic, heavily modified peptide natural products that are unified by the presence of a substituted, nitrogen-containing heterocycle core. Early work indicated that this core might be fashioned from two dehydroalanines by an enzyme-catalyzed aza-[4 + 2] cycloaddition to give a cyclic-hemiaminal intermediate. This common intermediate could then follow a reductive path toward a dehydropiperidine, as in the thiopeptide thiostrepton, or an aromatization path to yield the pyridine groups observed in many other thiopeptides. Although several of the enzymes proposed to perform this cycloaddition have been reconstituted, only pyridine products have been isolated and any hemiaminal intermediates have yet to be observed. Here, we identify the conditions and substrates that decouple the cycloaddition from subsequent steps and allow interception and characterization of this long hypothesized intermediate. Transition state modeling indicates that the key amide-iminol tautomerization is the major hurdle in an otherwise energetically favorable cycloaddition. An anionic model suggests that deprotonation and polarization of this amide bond by TbtD removes this barrier and provides a sufficient driving force for facile (stepwise) cycloaddition. This work provides evidence for a mechanistic link between disparate cyclases in thiopeptide biosynthesis.
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Affiliation(s)
- Jonathan W. Bogart
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Nicholas J. Kramer
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Aneta Turlik
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Rachel M. Bleich
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Daniel S. Catlin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Frank C. Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Ithaca, New York 14853, USA
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - R. Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, USA
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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20
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Vinogradov AA, Suga H. Introduction to Thiopeptides: Biological Activity, Biosynthesis, and Strategies for Functional Reprogramming. Cell Chem Biol 2020; 27:1032-1051. [PMID: 32698017 DOI: 10.1016/j.chembiol.2020.07.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/21/2020] [Accepted: 07/01/2020] [Indexed: 12/16/2022]
Abstract
Thiopeptides (also known as thiazolyl peptides) are structurally complex natural products with rich biological activities. Known for over 70 years for potent killing of Gram-positive bacteria, thiopeptides are experiencing a resurgence of interest in the last decade, primarily brought about by the genomic revolution of the 21st century. Every area of thiopeptide research-from elucidating their biological function and biosynthesis to expanding their structural diversity through genome mining-has made great strides in recent years. These advances lay the foundation for and inspire novel strategies for thiopeptide engineering. Accordingly, a number of diverse approaches are being actively pursued in the hope of developing the next generation of natural-product-inspired therapeutics. Here, we review the contemporary understanding of thiopeptide biological activities, biosynthetic pathways, and approaches to structural and functional reprogramming, with a special focus on the latter.
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Affiliation(s)
- Alexander A Vinogradov
- 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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21
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Rahman IR, Acedo JZ, Liu XR, Zhu L, Arrington J, Gross ML, van der Donk WA. Substrate Recognition by the Class II Lanthipeptide Synthetase HalM2. ACS Chem Biol 2020; 15:1473-1486. [PMID: 32293871 DOI: 10.1021/acschembio.0c00127] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Class II lanthipeptides belong to a diverse group of natural products known as ribosomally synthesized and post-translationally modified peptides (RiPPs). Most RiPP precursor peptides contain an N-terminal recognition sequence known as the leader peptide, which is typically recognized by biosynthetic enzymes that catalyze modifications on the C-terminal core peptide. For class II lanthipeptides, these are carried out by a bifunctional lanthipeptide synthetase (LanM) that catalyzes dehydration and cyclization reactions on peptidic substrates to generate thioether-containing, macrocyclic molecules. Some lanthipeptide synthetases are extraordinarily substrate tolerant, making them promising candidates for biotechnological applications such as combinatorial biosynthesis and cyclic peptide library construction. In this study, we characterized the mode of leader peptide recognition by HalM2, the lanthipeptide synthetase responsible for the production of the antimicrobial peptide haloduracin β. Using NMR spectroscopic techniques, in vitro binding assays, and enzyme activity assays, we identified substrate residues that are important for binding to HalM2 and for post-translational modification of the peptide substrates. Additionally, we provide evidence of the binding site on the enzyme using binding assays with truncated enzyme variants, hydrogen-deuterium exchange mass spectrometry, and photoaffinity labeling. Understanding the mechanism by which lanthipeptide synthetases recognize their substrate will facilitate their use in biotechnology, as well as further our general understanding of how RiPP enzymes recognize their substrates.
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Affiliation(s)
- Imran R. Rahman
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jeella Z. Acedo
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Xiaoran Roger Liu
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Lingyang Zhu
- School of Chemical Sciences NMR Laboratory, Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Justine Arrington
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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22
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Minimal lactazole scaffold for in vitro thiopeptide bioengineering. Nat Commun 2020; 11:2272. [PMID: 32385237 PMCID: PMC7210931 DOI: 10.1038/s41467-020-16145-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/06/2020] [Indexed: 12/16/2022] Open
Abstract
Lactazole A is a cryptic thiopeptide from Streptomyces lactacystinaeus, encoded by a compact 9.8 kb biosynthetic gene cluster. Here, we establish a platform for in vitro biosynthesis of lactazole A, referred to as the FIT-Laz system, via a combination of the flexible in vitro translation (FIT) system with recombinantly produced lactazole biosynthetic enzymes. Systematic dissection of lactazole biosynthesis reveals remarkable substrate tolerance of the biosynthetic enzymes and leads to the development of the minimal lactazole scaffold, a construct requiring only 6 post-translational modifications for macrocyclization. Efficient assembly of such minimal thiopeptides with FIT-Laz opens access to diverse lactazole analogs with 10 consecutive mutations, 14- to 62-membered macrocycles, and 18 amino acid-long tail regions, as well as to hybrid thiopeptides containing non-proteinogenic amino acids. This work suggests that the minimal lactazole scaffold is amenable to extensive bioengineering and opens possibilities to explore untapped chemical space of thiopeptides. Lactazole A is a thiopeptide from Streptomyces lactacystinaeus, encoded by a compact 9.8 kb biosynthetic gene cluster. Here, the authors show a platform for in vitro biosynthesis of lactazole A via a combination of a flexible in vitro translation system with recombinantly produced lactazole biosynthetic enzymes.
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23
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Scheidler CM, Vrabel M, Schneider S. Genetic Code Expansion, Protein Expression, and Protein Functionalization in Bacillus subtilis. ACS Synth Biol 2020; 9:486-493. [PMID: 32053368 DOI: 10.1021/acssynbio.9b00458] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The site-specific chemical modification of proteins through incorporation of noncanonical amino acids enables diverse applications, such as imaging, probing, and expanding protein functions, as well as to precisely engineer therapeutics. Here we report a general strategy that allows the incorporation of noncanonical amino acids into target proteins using the amber suppression method and their efficient secretion in the biotechnological relevant expression host Bacillus subtilis. This facilitates efficient purification of target proteins directly from the supernatant, followed by their functionalization using click chemistry. We used this strategy to site-specifically introduce norbornene lysine into a single chain antibody and functionalize it with fluorophores for the detection of human target proteins.
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Affiliation(s)
- Christopher M. Scheidler
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians University Munich, Butenandtstraße 5-13, Munich, 81377, Germany
| | - Milan Vrabel
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, Prague 6, CZ-166 10, Czech Republic
| | - Sabine Schneider
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians University Munich, Butenandtstraße 5-13, Munich, 81377, Germany
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24
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Natural thiopeptides as a privileged scaffold for drug discovery and therapeutic development. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02361-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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25
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Characterization of Nocardithiocin Derivatives Produced by Amino Acid Substitution of Precursor Peptide notG. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09836-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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26
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Akasapu S, Hinds AB, Powell WC, Walczak MA. Total synthesis of micrococcin P1 and thiocillin I enabled by Mo(vi) catalyst. Chem Sci 2019; 10:1971-1975. [PMID: 30881626 PMCID: PMC6383332 DOI: 10.1039/c8sc04885a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/03/2018] [Indexed: 12/05/2022] Open
Abstract
Thiopeptides are a class of potent antibiotics with promising therapeutic potential. We developed a novel Mo(vi)-oxide/picolinic acid catalyst for the cyclodehydration of cysteine peptides to form thiazoline heterocycles. With this powerful tool in hand, we completed the total syntheses of two representative thiopeptide antibiotics: micrococcin P1 and thiocillin I. These two concise syntheses (15 steps, longest linear sequence) feature a C-H activation strategy to install the trisubstituted pyridine core and thiazole groups. The synthetic material displays promising antimicrobial properties measured against a series of Gram-positive bacteria.
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Affiliation(s)
- Siddhartha Akasapu
- Department of Chemistry , University of Colorado , Boulder , CO 80309 , USA .
| | - Aaron B Hinds
- Department of Chemistry , University of Colorado , Boulder , CO 80309 , USA .
| | - Wyatt C Powell
- Department of Chemistry , University of Colorado , Boulder , CO 80309 , USA .
| | - Maciej A Walczak
- Department of Chemistry , University of Colorado , Boulder , CO 80309 , USA .
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27
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Zhang R, Li C, Wang J, Yang Y, Yan Y. Microbial production of small medicinal molecules and biologics: From nature to synthetic pathways. Biotechnol Adv 2018; 36:2219-2231. [DOI: 10.1016/j.biotechadv.2018.10.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/02/2018] [Accepted: 10/15/2018] [Indexed: 01/07/2023]
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28
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Geninthiocins C and D from Streptomyces as 35-membered macrocyclic thiopeptides with modified tail moiety. J Antibiot (Tokyo) 2018; 72:106-110. [PMID: 30479394 DOI: 10.1038/s41429-018-0127-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/01/2018] [Accepted: 11/12/2018] [Indexed: 11/09/2022]
Abstract
Geninthiocin is a thiopeptide with 35-membered macrocyclic core moiety. It has potent anti-Gram-positive (G+) bacteria activity. Herein, we reported two new congeners (2-3) of geninthiocin (geninthiocin A, 1) from Streptomyces sp. CPCC 200267, and designated them as geninthiocins C and D, whose structures were determined by NMR. Geninthiocins A, C and D had the same 35-membered macrocyclic core moiety, but possessed a -Dha-Dha-NH2, -Dha-Ala-NH2, and -NH2 tail, respectively. Besides, the Ala residue in geninthiocin C was determined as L- configuration by C3 Marfey's method. In vitro assays indicated that geninthiocins C-D showed no antibacterial activity, in contrast to the potent anti-G+ bacteria activity displayed by geninthiocin A. Therefore, the -Dha-Dha-NH2 tail of geninthiocin A played an important role in its potent activity against G+ bacteria.
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Thinking Outside the Box-Novel Antibacterials To Tackle the Resistance Crisis. Angew Chem Int Ed Engl 2018; 57:14440-14475. [PMID: 29939462 DOI: 10.1002/anie.201804971] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Indexed: 12/13/2022]
Abstract
The public view on antibiotics as reliable medicines changed when reports about "resistant superbugs" appeared in the news. While reasons for this resistance development are easily spotted, solutions for re-establishing effective antibiotics are still in their infancy. This Review encompasses several aspects of the antibiotic development pipeline from very early strategies to mature drugs. An interdisciplinary overview is given of methods suitable for mining novel antibiotics and strategies discussed to unravel their modes of action. Select examples of antibiotics recently identified by using these platforms not only illustrate the efficiency of these measures, but also highlight promising clinical candidates with therapeutic potential. Furthermore, the concept of molecules that disarm pathogens by addressing gatekeepers of virulence will be covered. The Review concludes with an evaluation of antibacterials currently in clinical development. Overall, this Review aims to connect select innovative antimicrobial approaches to stimulate interdisciplinary partnerships between chemists from academia and industry.
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Affiliation(s)
- Markus Lakemeyer
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Weining Zhao
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Franziska A Mandl
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases, Sanofi-Aventis (Deutschland) GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
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30
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Über bisherige Denkweisen hinaus - neue Wirkstoffe zur Überwindung der Antibiotika-Krise. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804971] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Markus Lakemeyer
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Weining Zhao
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Franziska A. Mandl
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases; Sanofi-Aventis (Deutschland) GmbH; Industriepark Höchst 65926 Frankfurt am Main Deutschland
| | - Stephan A. Sieber
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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31
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Huang Y, Liu T. Therapeutic applications of genetic code expansion. Synth Syst Biotechnol 2018; 3:150-158. [PMID: 30345400 PMCID: PMC6190509 DOI: 10.1016/j.synbio.2018.09.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/16/2018] [Accepted: 09/18/2018] [Indexed: 12/05/2022] Open
Abstract
In nature, a limited, conservative set of amino acids are utilized to synthesize proteins. Genetic code expansion technique reassigns codons and incorporates noncanonical amino acids (ncAAs) through orthogonal aminoacyl-tRNA synthetase (aaRS)/tRNA pairs. The past decade has witnessed the rapid growth in diversity and scope for therapeutic applications of this technology. Here, we provided an update on the recent progress using genetic code expansion in the following areas: antibody-drug conjugates (ADCs), bispecific antibodies (BsAb), immunotherapies, long-lasting protein therapeutics, biosynthesized peptides, engineered viruses and cells, as well as other therapeutic related applications, where the technique was used to elucidate the mechanisms of biotherapeutics and drug targets.
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Affiliation(s)
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
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32
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Zhang J, Yan S, He Z, Ding C, Zhai T, Chen Y, Li H, Yang G, Zhou X, Wang P. Small Unnatural Amino Acid Carried Raman Tag for Molecular Imaging of Genetically Targeted Proteins. J Phys Chem Lett 2018; 9:4679-4685. [PMID: 30067370 DOI: 10.1021/acs.jpclett.8b01991] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Raman has been implemented to image biological systems for decades. However, Raman microscopy along with Raman probes is restricted to image metabolites or a few intracellular organelles so far and lacks genetic specificity for imaging proteins of interest, which significantly hinders their application. Here, we report the Raman spectra-based protein imaging method, which incorporates a small phenyl ring enhanced Raman tag (total of ∼0.55 kDa) with a single unnatural amino acid (UAA) to genetically label specific proteins. We further demonstrate hyperspectral stimulated Raman scattering (SRS) imaging of the Histone3.3 protein in the nucleus, Sec61β protein in the endoplasmic reticulum of HeLa cells, and Huntingtin protein Htt74Q in mutant huntingtin-induced cells. Genetic encoding of a small, stable, sensitive, and narrow-band Raman tag took one key step forward to enable SRS or Raman imaging of specific proteins and could further facilitate quantitative Raman spectra-based supermultiplexing microscopy in the future.
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Affiliation(s)
- Jing Zhang
- Britton Chance Center for Biomedical Photonics , Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Shuai Yan
- Britton Chance Center for Biomedical Photonics , Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Zhiyong He
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of the Ministry of Education , Wuhan University , Wuhan , Hubei 430072 , China
| | - Cong Ding
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of the Ministry of Education , Wuhan University , Wuhan , Hubei 430072 , China
| | - Tianxing Zhai
- Britton Chance Center for Biomedical Photonics , Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Yage Chen
- Britton Chance Center for Biomedical Photonics , Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Haozheng Li
- Britton Chance Center for Biomedical Photonics , Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Guang Yang
- Britton Chance Center for Biomedical Photonics , Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of the Ministry of Education , Wuhan University , Wuhan , Hubei 430072 , China
| | - Ping Wang
- Britton Chance Center for Biomedical Photonics , Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
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33
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Weaver JB, Boxer SG. Genetic Code Expansion in Rhodobacter sphaeroides to Incorporate Noncanonical Amino Acids into Photosynthetic Reaction Centers. ACS Synth Biol 2018; 7:1618-1628. [PMID: 29763307 DOI: 10.1021/acssynbio.8b00100] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photosynthetic reaction centers (RCs) are the membrane proteins responsible for the initial charge separation steps central to photosynthesis. As a complex and spectroscopically complicated membrane protein, the RC (and other associated photosynthetic proteins) would benefit greatly from the insight offered by site-specifically encoded noncanonical amino acids in the form of probes and an increased chemical range in key amino acid analogues. Toward that goal, we developed a method to transfer amber codon suppression machinery developed for E. coli into the model bacterium needed to produce RCs, Rhodobacter sphaeroides. Plasmids were developed and optimized to incorporate 3-chlorotyrosine, 3-bromotyrosine, and 3-iodotyrosine into RCs. Multiple challenges involving yield and orthogonality were overcome to implement amber suppression in R. sphaeroides, providing insights into the hurdles that can be involved in host transfer of amber suppression systems from E. coli. In the process of verifying noncanonical amino acid incorporation, characterization of this membrane protein via mass spectrometry (which has been difficult previously) was substantially improved. Importantly, the ability to incorporate noncanonical amino acids in R. sphaeroides expands research capabilities in the photosynthetic field.
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Affiliation(s)
- Jared Bryce Weaver
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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34
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Abstract
Our understanding of the complex molecular processes of living organisms at the molecular level is growing exponentially. This knowledge, together with a powerful arsenal of tools for manipulating the structures of macromolecules, is allowing chemists to to harness and reprogram the cellular machinery in ways previously unimaged. Here we review one example in which the genetic code itself has been expanded with new building blocks that allow us to probe and manipulate the structures and functions of proteins with unprecedented precision.
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Affiliation(s)
- Douglas D. Young
- Department of Chemistry, College of William & Mary,
P.O. Box 8795, Williamsburg, VA 23187 (USA)
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute,
La Jolla, CA 92037 (USA),
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35
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Kakkar N, Perez JG, Liu WR, Jewett MC, van der Donk WA. Incorporation of Nonproteinogenic Amino Acids in Class I and II Lantibiotics. ACS Chem Biol 2018; 13:951-957. [PMID: 29439566 PMCID: PMC5910287 DOI: 10.1021/acschembio.7b01024] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Lantibiotics are ribosomally synthesized and post-translationally modified peptide natural products that contain thioether cross-links formed by lanthionine and methyllanthionine residues. They exert potent antimicrobial activity against Gram-positive bacteria. We herein report production of analogues of two lantibiotics, lacticin 481 and nisin, that contain nonproteinogenic amino acids using two different strategies involving amber stop codon suppression technology. These methods complement recent alternative approaches to incorporate nonproteinogenic amino acids into lantibiotics.
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Affiliation(s)
- Nidhi Kakkar
- Howard Hughes Medical Institute and Roger Adams Laboratory, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jessica G. Perez
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Wenshe R. Liu
- Department of Chemistry, Texas A&M University, College Station, TX 77843m United States
| | - Michael C. Jewett
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Howard Hughes Medical Institute and Roger Adams Laboratory, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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36
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Bartholomae M, Baumann T, Nickling JH, Peterhoff D, Wagner R, Budisa N, Kuipers OP. Expanding the Genetic Code of Lactococcus lactis and Escherichia coli to Incorporate Non-canonical Amino Acids for Production of Modified Lantibiotics. Front Microbiol 2018; 9:657. [PMID: 29681891 PMCID: PMC5897534 DOI: 10.3389/fmicb.2018.00657] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/21/2018] [Indexed: 12/19/2022] Open
Abstract
The incorporation of non-canonical amino acids (ncAAs) into ribosomally synthesized and post-translationally modified peptides, e.g., nisin from the Gram-positive bacterium Lactococcus lactis, bears great potential to expand the chemical space of various antimicrobials. The ncAA Nε-Boc-L-lysine (BocK) was chosen for incorporation into nisin using the archaeal pyrrolysyl-tRNA synthetase–tRNAPyl pair to establish orthogonal translation in L. lactis for read-through of in-frame amber stop codons. In parallel, recombinant nisin production and orthogonal translation were combined in Escherichia coli cells. Both organisms synthesized bioactive nisin(BocK) variants. Screening of a nisin amber codon library revealed suitable sites for ncAA incorporation and two variants displayed high antimicrobial activity. Orthogonal translation in E. coli and L. lactis presents a promising tool to create new-to-nature nisin derivatives.
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Affiliation(s)
- Maike Bartholomae
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Tobias Baumann
- Biocatalysis Group, Department of Chemistry, Technische Universität Berlin (Berlin Institute of Technology), Berlin, Germany
| | - Jessica H Nickling
- Biocatalysis Group, Department of Chemistry, Technische Universität Berlin (Berlin Institute of Technology), Berlin, Germany
| | - David Peterhoff
- Institute of Medical Microbiology and Hygiene, Universität Regensburg, Regensburg, Germany
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, Universität Regensburg, Regensburg, Germany
| | - Nediljko Budisa
- Biocatalysis Group, Department of Chemistry, Technische Universität Berlin (Berlin Institute of Technology), Berlin, Germany
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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37
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Xuan W, Collins D, Koh M, Shao S, Yao A, Xiao H, Garner P, Schultz PG. Site-Specific Incorporation of a Thioester Containing Amino Acid into Proteins. ACS Chem Biol 2018; 13:578-581. [PMID: 29360343 PMCID: PMC5856652 DOI: 10.1021/acschembio.7b00998] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Here,
we report the site-specific incorporation of a thioester
containing noncanonical amino acid (ncAA) into recombinantly expressed
proteins. Specifically, we genetically encoded a thioester-activated
aspartic acid (ThioD) in bacteria in good yield and with high fidelity
using an orthogonal nonsense suppressor tRNA/aminoacyl-tRNA synthetase
(aaRS) pair. To demonstrate the utility of ThioD, we used native chemical
ligation to label green fluorescent protein with a fluorophore in
good yield.
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Affiliation(s)
- Weimin Xuan
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - Daniel Collins
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, United States
| | - Minseob Koh
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - Sida Shao
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - Anzhi Yao
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - Han Xiao
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - Philip Garner
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, United States
| | - Peter G. Schultz
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
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38
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Zheng Q, Fang H, Liu W. Post-translational modifications involved in the biosynthesis of thiopeptide antibiotics. Org Biomol Chem 2018; 15:3376-3390. [PMID: 28358161 DOI: 10.1039/c7ob00466d] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thiopeptide antibiotics are a class of typical ribosomally synthesized and post-translationally modified peptides (RiPPs) with complex chemical structures that are difficult to construct via chemical synthesis. To date, more than 100 thiopeptides have been discovered, and most of these compounds exhibit remarkable biological activities, such as antibacterial, antitumor and immunosuppressive activities. Therefore, studies of the biosynthesis of thiopeptides can contribute to the development of new drug leads and facilitate the understanding of the complex post-translational modifications (PTMs) of peptides and/or proteins. Since the biosynthetic gene clusters of thiopeptides were first discovered in 2009, several research studies regarding the biochemistry and enzymology of thiopeptide biosyntheses have been reported, indicating that their characteristic framework is constructed via a cascade of common PTMs and that additional specific PTMs diversify the molecules. In this review, we primarily summarize recent advances in understanding the biosynthesis of thiopeptide antibiotics and propose some potential applications based on our insights into the biosynthetic logic and machinery.
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Affiliation(s)
- Qingfei Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
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39
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Sharma V, Zeng Y, Wang WW, Qiao Y, Kurra Y, Liu WR. Evolving the N-Terminal Domain of Pyrrolysyl-tRNA Synthetase for Improved Incorporation of Noncanonical Amino Acids. Chembiochem 2017; 19:26-30. [PMID: 29096043 DOI: 10.1002/cbic.201700268] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Indexed: 11/10/2022]
Abstract
By evolving the N-terminal domain of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) that directly interacts with tRNAPyl , a mutant clone displaying improved amber-suppression efficiency for the genetic incorporation of Nϵ -(tert-butoxycarbonyl)-l-lysine threefold more than the wild type was identified. The identified mutations were R19H/H29R/T122S. Direct transfer of these mutations to two other PylRS mutants that were previously evolved for the genetic incorporation of Nϵ -acetyl-l-lysine and Nϵ -(4-azidobenzoxycarbonyl)-l-δ,ϵ-dehydrolysine also improved the incorporation efficiency of these two noncanonical amino acids. As the three identified mutations were found in the N-terminal domain of PylRS that was separated from its catalytic domain for charging tRNAPyl with a noncanonical amino acid, they could potentially be introduced to all other PylRS mutants to improve the incorporation efficiency of their corresponding noncanonical amino acids. Therefore, it represents a general strategy to optimize the pyrrolysine incorporation system-based noncanonical amino-acid mutagenesis.
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Affiliation(s)
- Vangmayee Sharma
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yu Zeng
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - W Wesley Wang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yuchen Qiao
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yadagiri Kurra
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Wenshe R Liu
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
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40
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Lopatniuk M, Myronovskyi M, Luzhetskyy A. Streptomyces albus: A New Cell Factory for Non-Canonical Amino Acids Incorporation into Ribosomally Synthesized Natural Products. ACS Chem Biol 2017; 12:2362-2370. [PMID: 28758722 DOI: 10.1021/acschembio.7b00359] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The incorporation of noncanonical amino acids (ncAAs) with different side chains into a peptide is a promising technique for changing the functional properties of that peptide. Of particular interest is the incorporation of ncAAs into peptide-derived natural products to optimize their biophysical properties for medical and industrial applications. Here, we present the first instance of ncAA incorporation into the natural product cinnamycin in streptomycetes using the orthogonal pyrrolysyl-tRNA synthetase/tRNAPyl pair from Methanosarcina barkeri. This approach allows site-specific incorporation of ncAAs via the read-through of a stop codon by the suppressor tRNAPyl, which can carry different pyrrolysine analogues. Five new deoxycinnamycin derivatives were obtained with three distinct pyrrolysine analogues incorporated into diverse positions of the antibiotic. The combination of partial hydrolysis and MS/MS fragmentation analysis was used to verify the exact position of the incorporation events. The introduction of ncAAs into different positions of the peptide had opposite effects on the peptide's biological activity.
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Affiliation(s)
- Mariia Lopatniuk
- Department
of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Maksym Myronovskyi
- Department
of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Department
of Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
- Helmholtz-Institute for Pharmaceutical Research, Saarland Campus, Building C2.3, 66123 Saarbrücken, Germany
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41
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Lin Z, He Q, Liu W. Bio-inspired engineering of thiopeptide antibiotics advances the expansion of molecular diversity and utility. Curr Opin Biotechnol 2017; 48:210-219. [PMID: 28672170 DOI: 10.1016/j.copbio.2017.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/14/2017] [Accepted: 06/14/2017] [Indexed: 02/08/2023]
Abstract
Thiopeptide antibiotics, which are a class of sulfur-rich and highly modified peptide natural products, exhibit a wide variety of important biological properties. These antibiotics are ribosomally synthesized and arise from post-translational modifications, exemplifying a process through which nature develops the structural complexity from Ser/Thr and Cys-rich precursor peptides. Following a brief review of the knowledge gained from nature in terms of the formation of a common thiopeptide scaffold and its specialization to individual members, we highlight the significance of bio-inspired engineering, which has greatly expanded the molecular diversity and utility of thiopeptide antibiotics regarding the search for clinically useful agents, investigation into new mechanisms of action and access to typically 'inaccessible' biosynthetic processes over the past two years.
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Affiliation(s)
- Zhi Lin
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Qingli He
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China.
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42
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Elucidating and engineering thiopeptide biosynthesis. World J Microbiol Biotechnol 2017; 33:119. [DOI: 10.1007/s11274-017-2283-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/03/2017] [Indexed: 01/15/2023]
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43
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Zhang F, Sun Y, Tian D, Li H. Chiral Selective Transport of Proteins by Cysteine-Enantiomer-Modified Nanopores. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701255] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Fan Zhang
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry; Central China Normal University; Wuhan 430079 P.R. China
| | - Yue Sun
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry; Central China Normal University; Wuhan 430079 P.R. China
| | - Demei Tian
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry; Central China Normal University; Wuhan 430079 P.R. China
| | - Haibing Li
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry; Central China Normal University; Wuhan 430079 P.R. China
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Zhang F, Sun Y, Tian D, Li H. Chiral Selective Transport of Proteins by Cysteine-Enantiomer-Modified Nanopores. Angew Chem Int Ed Engl 2017; 56:7186-7190. [DOI: 10.1002/anie.201701255] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/07/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Fan Zhang
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry; Central China Normal University; Wuhan 430079 P.R. China
| | - Yue Sun
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry; Central China Normal University; Wuhan 430079 P.R. China
| | - Demei Tian
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry; Central China Normal University; Wuhan 430079 P.R. China
| | - Haibing Li
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry; Central China Normal University; Wuhan 430079 P.R. China
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45
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Xuan W, Shao S, Schultz PG. Protein Crosslinking by Genetically Encoded Noncanonical Amino Acids with Reactive Aryl Carbamate Side Chains. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611841] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Weimin Xuan
- Department of Chemistry; the Scripps Research Institute; 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Sida Shao
- Department of Chemistry; the Scripps Research Institute; 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Peter G. Schultz
- Department of Chemistry; the Scripps Research Institute; 10550 N. Torrey Pines Road La Jolla CA 92037 USA
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46
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Xuan W, Shao S, Schultz PG. Protein Crosslinking by Genetically Encoded Noncanonical Amino Acids with Reactive Aryl Carbamate Side Chains. Angew Chem Int Ed Engl 2017; 56:5096-5100. [PMID: 28371162 DOI: 10.1002/anie.201611841] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/06/2017] [Indexed: 01/08/2023]
Abstract
The use of genetically encoded noncanonical amino acids (ncAAs) to construct crosslinks within or between proteins has emerged as a useful method to enhance protein stability, investigate protein-protein interactions, and improve the pharmacological properties of proteins. We report ncAAs with aryl carbamate side chains (PheK and FPheK) that can react with proximal nucleophilic residues to form intra- or intermolecular protein crosslinks. We evolved a pyrrolysyl-tRNA synthetase that incorporates site-specifically PheK and FPheK into proteins in both E. coli and mammalian cells. PheK and FPheK when incorporated into proteins showed good stability during protein expression and purification. FPheK reacted with adjacent Lys, Cys, and Tyr residues in thioredoxin in high yields. In addition, crosslinks could be formed between FPheK and Lys residue of two interacting proteins, including the heavy chain and light chain of an antibody Fab.
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Affiliation(s)
- Weimin Xuan
- Department of Chemistry, the Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Sida Shao
- Department of Chemistry, the Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter G Schultz
- Department of Chemistry, the Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
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47
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Burkhart BJ, Schwalen CJ, Mann G, Naismith JH, Mitchell DA. YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function. Chem Rev 2017; 117:5389-5456. [PMID: 28256131 DOI: 10.1021/acs.chemrev.6b00623] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
With advances in sequencing technology, uncharacterized proteins and domains of unknown function (DUFs) are rapidly accumulating in sequence databases and offer an opportunity to discover new protein chemistry and reaction mechanisms. The focus of this review, the formerly enigmatic YcaO superfamily (DUF181), has been found to catalyze a unique phosphorylation of a ribosomal peptide backbone amide upon attack by different nucleophiles. Established nucleophiles are the side chains of Cys, Ser, and Thr which gives rise to azoline/azole biosynthesis in ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products. However, much remains unknown about the potential for YcaO proteins to collaborate with other nucleophiles. Recent work suggests potential in forming thioamides, macroamidines, and possibly additional post-translational modifications. This review covers all knowledge through mid-2016 regarding the biosynthetic gene clusters (BGCs), natural products, functions, mechanisms, and applications of YcaO proteins and outlines likely future research directions for this protein superfamily.
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Affiliation(s)
| | | | - Greg Mann
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom
| | - James H Naismith
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom.,State Key Laboratory of Biotherapy, Sichuan University , Sichuan, China
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48
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Tran HL, Lexa KW, Julien O, Young TS, Walsh CT, Jacobson MP, Wells JA. Structure-Activity Relationship and Molecular Mechanics Reveal the Importance of Ring Entropy in the Biosynthesis and Activity of a Natural Product. J Am Chem Soc 2017; 139:2541-2544. [PMID: 28170244 DOI: 10.1021/jacs.6b10792] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Macrocycles are appealing drug candidates due to their high affinity, specificity, and favorable pharmacological properties. In this study, we explored the effects of chemical modifications to a natural product macrocycle upon its activity, 3D geometry, and conformational entropy. We chose thiocillin as a model system, a thiopeptide in the ribosomally encoded family of natural products that exhibits potent antimicrobial effects against Gram-positive bacteria. Since thiocillin is derived from a genetically encoded peptide scaffold, site-directed mutagenesis allows for rapid generation of analogues. To understand thiocillin's structure-activity relationship, we generated a site-saturation mutagenesis library covering each position along thiocillin's macrocyclic ring. We report the identification of eight unique compounds more potent than wild-type thiocillin, the best having an 8-fold improvement in potency. Computational modeling of thiocillin's macrocyclic structure revealed a striking requirement for a low-entropy macrocycle for activity. The populated ensembles of the active mutants showed a rigid structure with few adoptable conformations while inactive mutants showed a more flexible macrocycle which is unfavorable for binding. This finding highlights the importance of macrocyclization in combination with rigidifying post-translational modifications to achieve high-potency binding.
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Affiliation(s)
| | | | | | - Travis S Young
- Department of Biology, California Institute for Biomedical Research , La Jolla, California 92037, United States
| | - Christopher T Walsh
- Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University , Stanford, California 94305, United States
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49
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Baumann T, Nickling JH, Bartholomae M, Buivydas A, Kuipers OP, Budisa N. Prospects of In vivo Incorporation of Non-canonical Amino Acids for the Chemical Diversification of Antimicrobial Peptides. Front Microbiol 2017; 8:124. [PMID: 28210246 PMCID: PMC5288337 DOI: 10.3389/fmicb.2017.00124] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/18/2017] [Indexed: 12/14/2022] Open
Abstract
The incorporation of non-canonical amino acids (ncAA) is an elegant way for the chemical diversification of recombinantly produced antimicrobial peptides (AMPs). Residue- and site-specific installation methods in several bacterial production hosts hold great promise for the generation of new-to-nature AMPs, and can contribute to tackle the ongoing emergence of antibiotic resistance in pathogens. Especially from a pharmacological point of view, desirable improvements span pH and protease resistance, solubility, oral availability and circulation half-life. Although the primary focus of this report is on ribosomally synthesized and post-translationally modified peptides (RiPPs), we have included selected cases of peptides produced by solid phase peptide synthesis to comparatively show the potential and impact of ncAA introduction. Generally speaking, the introduction of ncAAs in recombinant AMPs delivers novel levels of chemical diversification. Cotranslationally incorporated, they can take part in AMP biogenesis either through direction interaction with elements of the post-translational modification (PTM) machinery or as untargeted sites with unique physicochemical properties and chemical handles for further modification. Together with genetic libraries, genome mining and processing by PTM machineries, ncAAs present not a mere addition to this process, but a highly diverse pool of building blocks to significantly broaden the chemical space of this valuable class of molecules. This perspective summarizes new developments of ncAA containing peptides. Challenges to be resolved in order to reach large-scale pharmaceutical production of these promising compounds and prospects for future developments are discussed.
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Affiliation(s)
- Tobias Baumann
- Biocatalysis Group, Department of Chemistry, Technische Universität Berlin (Berlin Institute of Technology) Berlin, Germany
| | - Jessica H Nickling
- Biocatalysis Group, Department of Chemistry, Technische Universität Berlin (Berlin Institute of Technology) Berlin, Germany
| | - Maike Bartholomae
- Molecular Genetics Group, Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Rijksuniversiteit Groningen (University of Groningen) Groningen, Netherlands
| | - Andrius Buivydas
- Molecular Genetics Group, Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Rijksuniversiteit Groningen (University of Groningen) Groningen, Netherlands
| | - Oscar P Kuipers
- Molecular Genetics Group, Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Rijksuniversiteit Groningen (University of Groningen) Groningen, Netherlands
| | - Nediljko Budisa
- Biocatalysis Group, Department of Chemistry, Technische Universität Berlin (Berlin Institute of Technology) Berlin, Germany
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50
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Wever WJ, Bogart JW, Bowers AA. Identification of Pyridine Synthase Recognition Sequences Allows a Modular Solid-Phase Route to Thiopeptide Variants. J Am Chem Soc 2016; 138:13461-13464. [DOI: 10.1021/jacs.6b05389] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Walter J. Wever
- Division of Chemical Biology
and Medicinal Chemistry, University of North Carolina at Chapel Hill, Eshelman School of Pharmacy, Chapel Hill, North Carolina 27599, United States
| | - Jonathan W. Bogart
- Division of Chemical Biology
and Medicinal Chemistry, University of North Carolina at Chapel Hill, Eshelman School of Pharmacy, Chapel Hill, North Carolina 27599, United States
| | - Albert A. Bowers
- Division of Chemical Biology
and Medicinal Chemistry, University of North Carolina at Chapel Hill, Eshelman School of Pharmacy, Chapel Hill, North Carolina 27599, United States
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