1
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Alexander AK, Elshahawi SI. Promiscuous Enzymes for Residue-Specific Peptide and Protein Late-Stage Functionalization. Chembiochem 2023; 24:e202300372. [PMID: 37338668 PMCID: PMC10496146 DOI: 10.1002/cbic.202300372] [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: 05/18/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 06/21/2023]
Abstract
The late-stage functionalization of peptides and proteins holds significant promise for drug discovery and facilitates bioorthogonal chemistry. This selective functionalization leads to innovative advances in in vitro and in vivo biological research. However, it is a challenging endeavor to selectively target a certain amino acid or position in the presence of other residues containing reactive groups. Biocatalysis has emerged as a powerful tool for selective, efficient, and economical modifications of molecules. Enzymes that have the ability to modify multiple complex substrates or selectively install nonnative handles have wide applications. Herein, we highlight enzymes with broad substrate tolerance that have been demonstrated to modify a specific amino acid residue in simple or complex peptides and/or proteins at late-stage. The different substrates accepted by these enzymes are mentioned together with the reported downstream bioorthogonal reactions that have benefited from the enzymatic selective modifications.
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Affiliation(s)
- Ashley K Alexander
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618, USA
| | - Sherif I Elshahawi
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618, USA
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2
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Schipp CJ, Ma Y, Al‐Shameri A, D'Alessio F, Neubauer P, Contestabile R, Budisa N, di Salvo ML. An Engineered Escherichia coli Strain with Synthetic Metabolism for in-Cell Production of Translationally Active Methionine Derivatives. Chembiochem 2020; 21:3525-3538. [PMID: 32734669 PMCID: PMC7756864 DOI: 10.1002/cbic.202000257] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/28/2020] [Indexed: 01/26/2023]
Abstract
In the last decades, it has become clear that the canonical amino acid repertoire codified by the universal genetic code is not up to the needs of emerging biotechnologies. For this reason, extensive genetic code re-engineering is essential to expand the scope of ribosomal protein translation, leading to reprogrammed microbial cells equipped with an alternative biochemical alphabet to be exploited as potential factories for biotechnological purposes. The prerequisite for this to happen is a continuous intracellular supply of noncanonical amino acids through synthetic metabolism from simple and cheap precursors. We have engineered an Escherichia coli bacterial system that fulfills these requirements through reconfiguration of the methionine biosynthetic pathway and the introduction of an exogenous direct trans-sulfuration pathway. Our metabolic scheme operates in vivo, rescuing intermediates from core cell metabolism and combining them with small bio-orthogonal compounds. Our reprogrammed E. coli strain is capable of the in-cell production of l-azidohomoalanine, which is directly incorporated into proteins in response to methionine codons. We thereby constructed a prototype suitable for economic, versatile, green sustainable chemistry, pushing towards enzyme chemistry and biotechnology-based production.
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Affiliation(s)
- Christian Johannes Schipp
- Chair of Bioprocess Engineering, Institute of BiotechnologyTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
| | - Ying Ma
- Paraxel International GmbH, Berlin, Campus DRK Kliniken Berlin Westend Haus 18Spandauer Damm 13014050BerlinGermany
| | - Ammar Al‐Shameri
- Institut für ChemieTechnische Universität BerlinMüller-Breslau-Straße. 1010623BerlinGermany
| | - Federico D'Alessio
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”Sapienza Università di RomaPiazzale Aldo Moro, 5 – Edificio CU2000185RomaItaly
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of BiotechnologyTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”Sapienza Università di RomaPiazzale Aldo Moro, 5 – Edificio CU2000185RomaItaly
| | - Nediljko Budisa
- Institut für ChemieTechnische Universität BerlinMüller-Breslau-Straße. 1010623BerlinGermany
- Department of ChemistryUniversity of ManitobaWinnipegMB, R3T 2N2Canada
| | - Martino Luigi di Salvo
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”Sapienza Università di RomaPiazzale Aldo Moro, 5 – Edificio CU2000185RomaItaly
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3
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Liu M, Thijssen V, Jongkees SAK. Suppression of Formylation Provides an Alternative Approach to Vacant Codon Creation in Bacterial In Vitro Translation. Angew Chem Int Ed Engl 2020; 59:21870-21874. [PMID: 32840944 PMCID: PMC7756408 DOI: 10.1002/anie.202003779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/04/2020] [Indexed: 11/22/2022]
Abstract
Genetic code reprogramming is a powerful approach to controlled protein modification. A remaining challenge, however, is the generation of vacant codons. We targeted the initiation machinery of E. coli, showing that restriction of the formyl donor or inhibition of the formyl transferase during in vitro translation is sufficient to prevent formylation of the acylated initiating tRNA and thereby create a vacant initiation codon that can be reprogrammed by exogenously charged tRNA. Our approach conveniently generates peptides and proteins tagged N‐terminally with non‐canonical functional groups at up to 99 % reprogramming efficiency, in combination with decoding the AUG elongation codons either with native methionine or with further reprogramming with azide‐ and alkyne‐containing cognates. We further show macrocyclization and intermolecular modifications with these click handles, thus emphasizing the applicability of our method to current challenges in peptide and protein chemistry.
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Affiliation(s)
- Minglong Liu
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| | - Vito Thijssen
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| | - Seino A K Jongkees
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
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4
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Liu M, Thijssen V, Jongkees SAK. Suppression of Formylation Provides an Alternative Approach to Vacant Codon Creation in Bacterial In Vitro Translation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Minglong Liu
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3584CG Utrecht The Netherlands
| | - Vito Thijssen
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3584CG Utrecht The Netherlands
| | - Seino A. K. Jongkees
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3584CG Utrecht The Netherlands
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5
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Identification and biochemical characterisation of a novel methionine aminopeptidase from the taiga tick Ixodes persulcatus. Ticks Tick Borne Dis 2020; 12:101554. [PMID: 33002807 DOI: 10.1016/j.ttbdis.2020.101554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/05/2020] [Accepted: 09/14/2020] [Indexed: 11/22/2022]
Abstract
Methionine aminopeptidases (MetAPs), which remove the initiator methionine from nascent peptides, are essential in all organisms and considered to be a valuable targets for the treatment of various diseases, including cancer, malaria, and bacterial infections. However, MetAPs have not been reported in hard ticks (family Ixodidae), and their bioinformatics characterisation in tick's genome sequences is limited. In this study, we cloned, identified, and characterised a novel MetAP from Ixodes persulcatus, a vector for pathogens causing Lyme borreliosis and tick-borne encephalitis. The sequence analysis showed that I. persulcatus MetAP was a type 1 enzyme carrying C-terminal motifs conserved in the M24A family of metallopeptidases. Protein-protein docking simulations using human MetAP revealed conservation of substrate and metal-binding residues in the catalytic site cleft of the novel enzyme, which was designated IpMetAP. Recombinant IpMetAP expressed in Escherichia coli revealed its significant enzymatic activity with the synthetic substrate H-Met-4-methyl-coumaryl-7-amide at pH 7.5 with Km of 0.014 mM, kcat of 0.25 s-1, and overall catalytic efficiency (kcat/Km) of 18.36 mM-1 s-1. The activity of IpMetAP was enhanced by the addition of divalent cations Mn2+ and Co2+ and significantly inhibited by EDTA and bestatin. Site-directed mutagenesis of conserved amino acids indicated that the substitution of metal-binding residues D226 and H288 completely abolished the IpMetAP enzymatic activity, whereas that of the other sites had only moderate effects on substrate hydrolysis. The catalytic properties of IpMetAP suggest that the enzyme behaves similar to other MetAPs and such characterization expands our knowledge of aminopeptidases and protein metabolism of tick.
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6
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Tharp JM, Krahn N, Varshney U, Söll D. Hijacking Translation Initiation for Synthetic Biology. Chembiochem 2020; 21:1387-1396. [PMID: 32023356 PMCID: PMC7237318 DOI: 10.1002/cbic.202000017] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Indexed: 12/17/2022]
Abstract
Genetic code expansion (GCE) has revolutionized the field of protein chemistry. Over the past several decades more than 150 different noncanonical amino acids (ncAAs) have been co-translationally installed into proteins within various host organisms. The vast majority of these ncAAs have been incorporated between the start and stop codons within an open reading frame. This requires that the ncAA be able to form a peptide bond at the α-amine, limiting the types of molecules that can be genetically encoded. In contrast, the α-amine of the initiating amino acid is not required for peptide bond formation. Therefore, including the initiator position in GCE allows for co-translational insertion of more diverse molecules that are modified, or completely lacking an α-amine. This review explores various methods which have been used to initiate protein synthesis with diverse molecules both in vitro and in vivo.
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Affiliation(s)
- Jeffery M Tharp
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
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7
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Kadunc L, Svetličič M, Forstnerič V, Hafner Bratkovič I, Jerala R. Increased gene translation stringency in mammalian cells by nonsense suppression at multiple permissive sites with a single noncanonical amino acid. FEBS Lett 2020; 594:2452-2461. [PMID: 32401336 DOI: 10.1002/1873-3468.13810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/15/2020] [Accepted: 04/27/2020] [Indexed: 11/10/2022]
Abstract
The considerable potential of engineered cells compels the development of strategies for the stringent control of gene expression. A promising approach is the introduction of a premature stop codon (PTC) into a selected gene that is expressed only in the presence of noncanonical amino acids through nonsense suppression. Here, different strategies of amber PTC readthrough in mammalian cells were tested. The use of a tRNA synthetase together with a TAG codon-specific tRNA achieved PTC readthrough depending on the addition of a noncanonical amino acid (4-benzoyl-L-phenylalanine; Bpa). While single TAG codon incorporation exhibited detectable expression of the reporter protein even in the absence of Bpa, the use of a double PTC enabled virtually leakage-free functional gene translation. The introduction of an additional 5'-PTC, therefore, represents a generally applicable strategy to increase stringency in gene translation.
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Affiliation(s)
- Lucija Kadunc
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,Graduate School of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Svetličič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Vida Forstnerič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Iva Hafner Bratkovič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
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8
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In-Cell Synthesis of Bioorthogonal Alkene Tag S-Allyl-Homocysteine and Its Coupling with Reprogrammed Translation. Int J Mol Sci 2019; 20:ijms20092299. [PMID: 31075919 PMCID: PMC6539321 DOI: 10.3390/ijms20092299] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/05/2019] [Accepted: 05/07/2019] [Indexed: 12/22/2022] Open
Abstract
In this study, we report our initial results on in situ biosynthesis of S-allyl-l-homocysteine (Sahc) by simple metabolic conversion of allyl mercaptan in Escherichia coli, which served as the host organism endowed with a direct sulfhydration pathway. The intracellular synthesis we describe in this study is coupled with the direct incorporation of Sahc into proteins in response to methionine codons. Together with O-acetyl-homoserine, allyl mercaptan was added to the growth medium, followed by uptake and intracellular reaction to give Sahc. Our protocol efficiently combined the in vivo synthesis of Sahc via metabolic engineering with reprogrammed translation, without the need for a major change in the protein biosynthesis machinery. Although the system needs further optimisation to achieve greater intracellular Sahc production for complete protein labelling, we demonstrated its functional versatility for photo-induced thiol-ene coupling and the recently developed phosphonamidate conjugation reaction. Importantly, deprotection of Sahc leads to homocysteine-containing proteins-a potentially useful approach for the selective labelling of thiols with high relevance in various medical settings.
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9
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Flood DT, Yan NL, Dawson PE. Post-Translational Backbone Engineering through Selenomethionine-Mediated Incorporation of Freidinger Lactams. Angew Chem Int Ed Engl 2018; 57:8697-8701. [PMID: 29797386 DOI: 10.1002/anie.201804885] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/16/2018] [Indexed: 11/11/2022]
Abstract
Amino-γ-lactam (Agl) bridged dipeptides, commonly known as Freidinger lactams, have been shown to constrain peptide backbone topology and stabilize type II' β-turns. The utility of these links as peptide constraints has inspired new approaches to their incorporation into complex peptides and peptoids, all of which require harsh reaction conditions or protecting groups that limit their use on unprotected peptides and proteins. Herein, we employ a mild and selective alkylation of selenomethionine in acidic aqueous solution, followed by immobilization of the alkylated peptide on to bulk reverse-phase C18 silica and base-induced lactamization in DMSO. The utilization of selenomethionine, which is readily introduced by synthesis or expression, and the mild conditions enable selective backbone engineering in complex peptide and protein systems.
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Affiliation(s)
- Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Nicholas L Yan
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
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10
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Flood DT, Yan NL, Dawson PE. Post‐Translational Backbone Engineering through Selenomethionine‐Mediated Incorporation of Freidinger Lactams. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804885] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Dillon T. Flood
- Department of Chemistry The Scripps Research Institute 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Nicholas L. Yan
- Department of Chemistry The Scripps Research Institute 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Philip E. Dawson
- Department of Chemistry The Scripps Research Institute 10550 N. Torrey Pines Road La Jolla CA 92037 USA
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11
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Identification of methionine aminopeptidase 2 as a molecular target of the organoselenium drug ebselen and its derivatives/analogues: Synthesis, inhibitory activity and molecular modeling study. Bioorg Med Chem Lett 2016; 26:5254-5259. [DOI: 10.1016/j.bmcl.2016.09.050] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/16/2016] [Accepted: 09/17/2016] [Indexed: 11/19/2022]
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12
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Radchenko DS, Kattge S, Kara S, Ulrich AS, Afonin S. Does a methionine-to-norleucine substitution in PGLa influence peptide-membrane interactions? BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2019-2027. [DOI: 10.1016/j.bbamem.2016.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 05/13/2016] [Accepted: 06/02/2016] [Indexed: 12/17/2022]
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13
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Acevedo-Rocha CG, Budisa N. Xenomicrobiology: a roadmap for genetic code engineering. Microb Biotechnol 2016; 9:666-76. [PMID: 27489097 PMCID: PMC4993186 DOI: 10.1111/1751-7915.12398] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 07/12/2016] [Indexed: 11/27/2022] Open
Abstract
Biology is an analytical and informational science that is becoming increasingly dependent on chemical synthesis. One example is the high‐throughput and low‐cost synthesis of DNA, which is a foundation for the research field of synthetic biology (SB). The aim of SB is to provide biotechnological solutions to health, energy and environmental issues as well as unsustainable manufacturing processes in the frame of naturally existing chemical building blocks. Xenobiology (XB) goes a step further by implementing non‐natural building blocks in living cells. In this context, genetic code engineering respectively enables the re‐design of genes/genomes and proteins/proteomes with non‐canonical nucleic (XNAs) and amino (ncAAs) acids. Besides studying information flow and evolutionary innovation in living systems, XB allows the development of new‐to‐nature therapeutic proteins/peptides, new biocatalysts for potential applications in synthetic organic chemistry and biocontainment strategies for enhanced biosafety. In this perspective, we provide a brief history and evolution of the genetic code in the context of XB. We then discuss the latest efforts and challenges ahead for engineering the genetic code with focus on substitutions and additions of ncAAs as well as standard amino acid reductions. Finally, we present a roadmap for the directed evolution of artificial microbes for emancipating rare sense codons that could be used to introduce novel building blocks. The development of such xenomicroorganisms endowed with a ‘genetic firewall’ will also allow to study and understand the relation between code evolution and horizontal gene transfer.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- Biosyntia ApS, 2970, Hørsholm, Denmark.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark
| | - Nediljko Budisa
- Department of Chemistry, Technical University Berlin, Müller-Breslau-Str. 10, Berlin, 10623, Germany
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14
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Mühlberg M, Hoesl MG, Kuehne C, Dernedde J, Budisa N, Hackenberger CPR. Orthogonal dual-modification of proteins for the engineering of multivalent protein scaffolds. Beilstein J Org Chem 2015; 11:784-791. [PMID: 26124880 PMCID: PMC4464295 DOI: 10.3762/bjoc.11.88] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/05/2015] [Indexed: 01/12/2023] Open
Abstract
To add new tools to the repertoire of protein-based multivalent scaffold design, we have developed a novel dual-labeling strategy for proteins that combines residue-specific incorporation of unnatural amino acids with chemical oxidative aldehyde formation at the N-terminus of a protein. Our approach relies on the selective introduction of two different functional moieties in a protein by mutually orthogonal copper-catalyzed azide-alkyne cycloaddition (CuAAC) and oxime ligation. This method was applied to the conjugation of biotin and β-linked galactose residues to yield an enzymatically active thermophilic lipase, which revealed specific binding to Erythrina cristagalli lectin by SPR binding studies.
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Affiliation(s)
- Michaela Mühlberg
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany
- Freie Universität Berlin, Institut für Chemie und Biochemie, Takustr. 3, 14195 Berlin, Germany
| | - Michael G Hoesl
- Technische Universität Berlin, AK Biokatalyse, Institut für Chemie, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| | - Christian Kuehne
- Charité - Universitätsmedizin Berlin, Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Jens Dernedde
- Charité - Universitätsmedizin Berlin, Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Nediljko Budisa
- Technische Universität Berlin, AK Biokatalyse, Institut für Chemie, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| | - Christian P R Hackenberger
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany
- Humboldt Universität zu Berlin, Institut für Organische und Bioorganische Chemie, Institut für Chemie, Brook-Taylor-Str. 2, 12489 Berlin, Germany
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15
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Mutant methionyl-tRNA synthetase from bacteria enables site-selective N-terminal labeling of proteins expressed in mammalian cells. Proc Natl Acad Sci U S A 2013; 110:4992-7. [PMID: 23479642 DOI: 10.1073/pnas.1216375110] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Newly synthesized cellular proteins can be tagged with a variety of metabolic labels that distinguish them from preexisting proteins and allow them to be identified and tracked. Many such labels are incorporated into proteins via the endogenous cellular machinery and can be used in numerous cell types and organisms. Though broad applicability has advantages, we aimed to develop a strategy to restrict protein labeling to specified mammalian cells that express a transgene. Here we report that heterologous expression of a mutant methionyl-tRNA synthetase from Escherichia coli permits incorporation of azidonorleucine (Anl) into proteins made in mammalian (HEK293) cells. Anl is incorporated site-selectively at N-terminal positions (in competition with initiator methionines) and is not found at internal sites. Site selectivity is enabled by the fact that the bacterial synthetase aminoacylates mammalian initiator tRNA, but not elongator tRNA. N-terminally labeled proteins can be selectively conjugated to a variety of useful probes; here we demonstrate use of this system in enrichment and visualization of proteins made during various stages of the cell cycle. N-terminal incorporation of Anl may also be used to engineer modified proteins for therapeutic and other applications.
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16
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Acevedo-Rocha CG, Geiermann AS, Budisa N, Merkel L. Design of protein congeners containing β-cyclopropylalanine. MOLECULAR BIOSYSTEMS 2013; 8:2719-23. [PMID: 22833107 DOI: 10.1039/c2mb25193k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The non-canonical amino acid (ncAA) analogue of methionine (Met), β-cyclopropylalanine (Cpa), was successfully incorporated into recombinant proteins expressed in Escherichia coli in a residue-specific manner. Proteins substituted in this way are congeners because they derive from the same gene sequence as the parent protein but contain a fraction of ncAAs. We have expressed congeners using parent and mutant gene sequences of various proteins (lipase, annexin A5, enhanced green fluorescent protein, and barstar) and found that Cpa incorporation is highly dependent on the protein sequence composition. These results indicate that the global amino acid composition of proteins might be a crucial parameter that influences the outcome of unnatural translation. In addition, we could also demonstrate that the chemical nature of the second residue could be essential for successful ncAA incorporation.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany.
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17
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Xu J, Qian Y, Skonezny PM, You L, Xing Z, Meyers DS, Stankavage RJ, Pan SH, Li ZJ. Reduction of N-terminal methionylation while increasing titer by lowering metabolic and protein production rates in E. coli auto-induced fed-batch fermentation. ACTA ACUST UNITED AC 2012; 39:1199-208. [DOI: 10.1007/s10295-012-1127-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 03/30/2012] [Indexed: 11/29/2022]
Abstract
Abstract
A standard fed-batch fermentation process using 1 mM isopropyl-β-d-thiogalactopyranoside (IPTG) induction at 37 °C in complex batch and feed media had been developed for manufacturing of a therapeutic protein (TP) expressed in inclusion bodies (IBs) by E. coli BL21 (DE3) driven by T7 promoter. Six unauthentic TP N-terminal variants were identified, of which methionylated TP (Met-TP) ratio was predominant. We hypothesized that lowering metabolic and protein production rates would reduce the Met-TP ratio while improving TP titer. The standard process was surprisingly auto-induced without added IPTG due to galactose in the complex media. Without changing either the clone or the batch medium, a new process was developed using lower feed rates and auto-induction at 29 °C after glucose depletion while increasing induction duration. In comparison to the standard process, the new process reduced the unauthentic Met-TP ratio from 23.6 to 9.6 %, increased the TP titer by 85 %, and the specific production yield from 210 to 330 mg TP per gram of dry cell weight. Furthermore, the TP recovery yield in the purified IBs was improved by ~20 %. Adding together, ~105 % more TP recovered in the purified IBs from per liter of fermentation broth for the new process than the standard process. The basic principles of lowering metabolic and production rates should be applicable to other recombinant protein production in IBs by fed-batch fermentations.
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Affiliation(s)
- Jianlin Xu
- grid.419971.3 Biologics Process Science, Global Manufacturing and Supply Bristol-Myers Squibb 6000 Thompson Road 13057 Syracuse NY USA
| | - Yueming Qian
- grid.419971.3 Biologics Process Science, Global Manufacturing and Supply Bristol-Myers Squibb 6000 Thompson Road 13057 Syracuse NY USA
| | - Paul M Skonezny
- grid.419971.3 Biologics Process Science, Global Manufacturing and Supply Bristol-Myers Squibb 6000 Thompson Road 13057 Syracuse NY USA
| | - Li You
- grid.419971.3 Biologics Process Science, Global Manufacturing and Supply Bristol-Myers Squibb 6000 Thompson Road 13057 Syracuse NY USA
| | - Zizhuo Xing
- grid.419971.3 Biologics Process Science, Global Manufacturing and Supply Bristol-Myers Squibb 6000 Thompson Road 13057 Syracuse NY USA
| | - David S Meyers
- grid.419971.3 Biologics Process Science, Global Manufacturing and Supply Bristol-Myers Squibb 6000 Thompson Road 13057 Syracuse NY USA
| | - Robert J Stankavage
- grid.419971.3 Biologics Process Science, Global Manufacturing and Supply Bristol-Myers Squibb 6000 Thompson Road 13057 Syracuse NY USA
| | - Shih-Hsie Pan
- grid.419971.3 Biologics Process Science, Global Manufacturing and Supply Bristol-Myers Squibb 6000 Thompson Road 13057 Syracuse NY USA
| | - Zheng Jian Li
- grid.419971.3 Biologics Process Science, Global Manufacturing and Supply Bristol-Myers Squibb 6000 Thompson Road 13057 Syracuse NY USA
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Poreba M, Gajda A, Picha J, Jiracek J, Marschner A, Klein CD, Salvesen GS, Drag M. S1 pocket fingerprints of human and bacterial methionine aminopeptidases determined using fluorogenic libraries of substrates and phosphorus based inhibitors. Biochimie 2012; 94:704-10. [DOI: 10.1016/j.biochi.2011.10.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Accepted: 10/25/2011] [Indexed: 10/15/2022]
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Abstract
In a chemical screening, we tested the antiangiogenic effects of fumagillin derivatives and identified fumagillin as an inhibitor of definitive hematopoiesis in zebrafish embryos. Fumagillin is known to target methionine aminopeptidase II (MetAP2), an enzyme whose function in hematopoiesis is unknown. We investigated the role of MetAP2 in hematopoiesis by using zebrafish embryo and human umbilical cord blood models. Zebrafish metap2 was expressed ubiquitously during early embryogenesis and later in the somitic region, the caudal hematopoietic tissue, and pronephric duct. metap2 was inhibited by morpholino and fumagillin treatment, resulting in increased mpo expression at 18 hours postfertilization and reduced c-myb expression along the ventral wall of dorsal aorta at 36 hours postfertilization. It also disrupted intersegmental vessels in Tg(fli1:gfp) embryos without affecting development of major axial vasculatures. Inhibition of MetAP2 in CB CD34(+) cells by fumagillin had no effect on overall clonogenic activity but significantly reduced their engraftment into immunodeficient nonobese diabetes/severe combined immunodeficiency mice. metap2 knock-down in zebrafish and inhibition by fumagillin in zebrafish and human CB CD34(+) cells inhibited Calmodulin Kinase II activity and induced ERK phosphorylation. This study demonstrated a hitherto-undescribed role of MetAP2 in definitive hematopoiesis and a possible link to noncanonical Wnt and ERK signaling.
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20
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Kanudia P, Mittal M, Kumaran S, Chakraborti PK. Amino-terminal extension present in the methionine aminopeptidase type 1c of Mycobacterium tuberculosis is indispensible for its activity. BMC BIOCHEMISTRY 2011; 12:35. [PMID: 21729287 PMCID: PMC3154147 DOI: 10.1186/1471-2091-12-35] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2011] [Accepted: 07/05/2011] [Indexed: 01/07/2023]
Abstract
Background Methionine aminopeptidase (MetAP) is a ubiquitous enzyme in both prokaryotes and eukaryotes, which catalyzes co-translational removal of N-terminal methionine from elongating polypeptide chains during protein synthesis. It specifically removes the terminal methionine in all organisms, if the penultimate residue is non-bulky and uncharged. The MetAP action for exclusion of N-terminal methionine is mandatory in 50-70% of nascent proteins. Such an activity is required for proper sub cellular localization, additional processing and eventually for the degradation of proteins. Results We cloned genes encoding two such metalloproteases (MtMetAP1a and MtMetAP1c) present in Mycobacterium tuberculosis and expressed them as histidine-tagged proteins in Escherichia coli. Although they have different substrate preferences, for Met-Ala-Ser, we found, MtMetAP1c had significantly high enzyme turnover rate as opposed to MtMetAP1a. Circular dichroism spectroscopic studies as well as monitoring of enzyme activity indicated high temperature stability (up to 50°C) of MtMetAP1a compared to that of the MtMetAP1c. Modelling of MtMetAP1a based on MtMetAP1c crystal structure revealed the distinct spatial arrangements of identical active site amino acid residues and their mutations affected the enzymatic activities of both the proteins. Strikingly, we observed that 40 amino acid long N-terminal extension of MtMetAP1c, compared to its other family members, contributes towards the activity and stability of this enzyme, which has never been reported for any methionine aminopeptidase. Furthermore, mutational analysis revealed that Val-18 and Pro-19 of MtMetAP1c are crucial for its enzymatic activity. Consistent with this observation, molecular dynamic simulation studies of wild-type and these variants strongly suggest their involvement in maintaining active site conformation of MtMetAP1c. Conclusion Our findings unequivocally emphasized that N-terminal extension of MtMetAP1c contributes towards the functionality of the enzyme presumably by regulating active site residues through "action-at-a-distance" mechanism and we for the first time are reporting this unique function of the enzyme.
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Affiliation(s)
- Pavitra Kanudia
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39A, Chandigarh 160 036, India
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21
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Abstract
A concise and highly efficient synthetic route to L-azidohomoalanine (L-Aha) and its homologues is presented here. These chemically modified amino acids are used for the introduction of bioorthogonal handles into proteins. The described route avoids major problems of previously reported methods including expensive starting materials, low efficiency, and lack of scalability. Starting from inexpensive N-Boc-O-Bn-L-aspartic acid, gram quantities of L-Aha hydrochloride can be prepared with high purity. The reactions can be completed within 1 week and the products can be incorporated into proteins using L-methionine auxotrophs.
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22
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Wolschner C, Giese A, Kretzschmar HA, Huber R, Moroder L, Budisa N. Design of anti- and pro-aggregation variants to assess the effects of methionine oxidation in human prion protein. Proc Natl Acad Sci U S A 2009; 106:7756-61. [PMID: 19416900 PMCID: PMC2674404 DOI: 10.1073/pnas.0902688106] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Indexed: 01/09/2023] Open
Abstract
Prion disease is characterized by the alpha-->beta structural conversion of the cellular prion protein (PrP(C)) into the misfolded and aggregated "scrapie" (PrP(Sc)) isoform. It has been speculated that methionine (Met) oxidation in PrP(C) may have a special role in this process, but has not been detailed and assigned individually to the 9 Met residues of full-length, recombinant human PrP(C) [rhPrP(C)(23-231)]. To better understand this oxidative event in PrP aggregation, the extent of periodate-induced Met oxidation was monitored by electrospray ionization-MS and correlated with aggregation propensity. Also, the Met residues were replaced with isosteric and chemically stable, nonoxidizable analogs, i.e., with the more hydrophobic norleucine (Nle) and the highly hydrophilic methoxinine (Mox). The Nle-rhPrP(C) variant is an alpha-helix rich protein (like Met-rhPrP(C)) resistant to oxidation that lacks the in vitro aggregation properties of the parent protein. Conversely, the Mox-rhPrP(C) variant is a beta-sheet rich protein that features strong proaggregation behavior. In contrast to the parent Met-rhPrP(C), the Nle/Mox-containing variants are not sensitive to periodate-induced in vitro aggregation. The experimental results fully support a direct correlation of the alpha-->beta secondary structure conversion in rhPrP(C) with the conformational preferences of Met/Nle/Mox residues. Accordingly, sporadic prion and other neurodegenerative diseases, as well as various aging processes, might also be caused by oxidative stress leading to Met oxidation.
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Affiliation(s)
- Christina Wolschner
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Armin Giese
- Zentrum für Neuropathologie und Prionforschung, Ludwig-Maximilians-Universität, Feodor-Lynen-Strasse 23, 81377 Munich, Germany
| | - Hans A. Kretzschmar
- Zentrum für Neuropathologie und Prionforschung, Ludwig-Maximilians-Universität, Feodor-Lynen-Strasse 23, 81377 Munich, Germany
| | - Robert Huber
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18, D-82152 Martinsried, Germany
- School of Biosciences, Cardiff University, Cardiff CF10 3US, United Kingdom; and
- Zentrum für Medizinische Biotechnologie, Universität Duisburg-Essen, D-45117 Essen, Germany
| | - Luis Moroder
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Nediljko Budisa
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18, D-82152 Martinsried, Germany
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23
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The N-terminal penultimate residue of 20S proteasome alpha1 influences its N(alpha) acetylation and protein levels as well as growth rate and stress responses of Haloferax volcanii. J Bacteriol 2009; 191:3794-803. [PMID: 19376868 DOI: 10.1128/jb.00090-09] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Proteasomes are energy-dependent proteolytic machines. We elaborate here on the previously observed N(alpha) acetylation of the initiator methionine of the alpha1 protein of 20S core particles (CPs) of Haloferax volcanii proteasomes. Quantitative mass spectrometry revealed this was the dominant N-terminal form of alpha1 in H. volcanii cells. To further examine this, alpha1 proteins with substitutions in the N-terminal penultimate residue as well as deletion of the CP "gate" formed by the alpha1 N terminus were examined for their N(alpha) acetylation. Both the "gate" deletion and Q2A substitution completely altered the N(alpha)-acetylation pattern of alpha1, with the deletion rendering alpha1 unavailable for N(alpha) acetylation and the Q2A modification apparently enhancing cleavage of alpha1 by methionine aminopeptidase (MAP), resulting in acetylation of the N-terminal alanine. Cells expressing these two alpha1 variants were less tolerant of hypoosmotic stress than the wild type and produced CPs with enhanced peptidase activity. Although alpha1 proteins with Q2D, Q2P, and Q2T substitutions were N(alpha) acetylated in CPs similar to the wild type, cells expressing these variants accumulated unusually high levels of alpha1 as rings in N(alpha)-acetylated, unmodified, and/or MAP-cleaved forms. More detailed examination of this group revealed that while CP peptidase activity was not impaired, cells expressing these alpha1 variants displayed higher growth rates and were more tolerant of hypoosmotic and high-temperature stress than the wild type. Overall, these results suggest that N(alpha) acetylation of alpha1 is important in CP assembly and activity, high levels of alpha1 rings enhance cell proliferation and stress tolerance, and unregulated opening of the CP "gate" impairs the ability of cells to overcome salt stress.
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