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Bharathi M, Chellapandi P. Intergenomic evolution and metabolic cross-talk between rumen and thermophilic autotrophic methanogenic archaea. Mol Phylogenet Evol 2016; 107:293-304. [PMID: 27864137 DOI: 10.1016/j.ympev.2016.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 09/17/2016] [Accepted: 11/13/2016] [Indexed: 02/01/2023]
Abstract
Methanobrevibacter ruminantium M1 (MRU) is a rumen methanogenic archaean that can be able to utilize formate and CO2/H2 as growth substrates. Extensive analysis on the evolutionary genomic contexts considered herein to unravel its intergenomic relationship and metabolic adjustment acquired from the genomic content of Methanothermobacter thermautotrophicus ΔH. We demonstrated its intergenomic distance, genome function, synteny homologs and gene families, origin of replication, and methanogenesis to reveal the evolutionary relationships between Methanobrevibacter and Methanothermobacter. Comparison of the phylogenetic and metabolic markers was suggested for its archaeal metabolic core lineage that might have evolved from Methanothermobacter. Orthologous genes involved in its hydrogenotrophic methanogenesis might be acquired from intergenomic ancestry of Methanothermobacter via Methanobacterium formicicum. Formate dehydrogenase (fdhAB) coding gene cluster and carbon monoxide dehydrogenase (cooF) coding gene might have evolved from duplication events within Methanobrevibacter-Methanothermobacter lineage, and fdhCD gene cluster acquired from bacterial origins. Genome-wide metabolic survey found the existence of four novel pathways viz. l-tyrosine catabolism, mevalonate pathway II, acyl-carrier protein metabolism II and glutathione redox reactions II in MRU. Finding of these pathways suggested that MRU has shown a metabolic potential to tolerate molecular oxygen, antimicrobial metabolite biosynthesis and atypical lipid composition in cell wall, which was acquainted by metabolic cross-talk with mammalian bacterial origins. We conclude that coevolution of genomic contents between Methanobrevibacter and Methanothermobacter provides a clue to understand the metabolic adaptation of MRU in the rumen at different environmental niches.
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Affiliation(s)
- M Bharathi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
| | - P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India.
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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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Coupling bioorthogonal chemistries with artificial metabolism: intracellular biosynthesis of azidohomoalanine and its incorporation into recombinant proteins. Molecules 2014; 19:1004-22. [PMID: 24434673 PMCID: PMC6271081 DOI: 10.3390/molecules19011004] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 01/07/2014] [Accepted: 01/09/2014] [Indexed: 11/17/2022] Open
Abstract
In this paper, we present a novel, “single experiment” methodology based on genetic engineering of metabolic pathways for direct intracellular production of non-canonical amino acids from simple precursors, coupled with expanded genetic code. In particular, we engineered the intracellular biosynthesis of l-azidohomoalanine from O-acetyl-l-homoserine and NaN3, and achieved its direct incorporation into recombinant target proteins by AUG codon reassignment in a methionine-auxotroph E. coli strain. In our system, the host’s methionine biosynthetic pathway was first diverted towards the production of the desired non-canonical amino acid by exploiting the broad reaction specificity of recombinant pyridoxal phosphate-dependent O-acetylhomoserine sulfhydrylase from Corynebacterium glutamicum. Then, the expression of the target protein barstar, accompanied with efficient l-azidohomoalanine incorporation in place of l-methionine, was accomplished. This work stands as proof-of-principle and paves the way for additional work towards intracellular production and site-specific incorporation of biotechnologically relevant non-canonical amino acids directly from common fermentable sources.
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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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Soundrarajan N, Sokalingam S, Raghunathan G, Budisa N, Paik HJ, Yoo TH, Lee SG. Conjugation of proteins by installing BIO-orthogonally reactive groups at their N-termini. PLoS One 2012; 7:e46741. [PMID: 23056430 PMCID: PMC3466299 DOI: 10.1371/journal.pone.0046741] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 09/04/2012] [Indexed: 01/25/2023] Open
Abstract
N-terminal site-specific modification of a protein has many advantages over methods targeting internal positions, but it is not easy to install reactive groups onto a protein in an N-terminal specific manner. We here report a strategy to incorporate amino acid analogues specifically in the N-terminus of a protein in vivo and demonstrate it by preparing green fluorescent protein (GFP) having bio-orthogonally reactive groups at its N-terminus. In the first step, GFP was engineered to be a foldable, internal methionine-free sequence via the semi-rational mutagenesis of five internal methionine residues and the introduction of mutations for GFP folding enhancement. In the second step, the N-terminus of the engineered protein was modified in vivo with bio-orthogonally functional groups by reassigning functional methionine surrogates such as L-homopropargylglycine and L-azidohomoalanine into the first methionine codon of the engineered internal methionine-free GFP. The N-terminal specific incorporation of unnatural amino acids was confirmed by ESI-MS analysis and the incorporation did not affect significantly the specific activity, refolding rate and folding robustness of the protein. The two proteins which have alkyne or azide groups at their N-termini were conjugated each other by bio-orthogonal Cu(I)-catalyzed click chemistry. The strategy used in this study is expected to facilitate bio-conjugation applications of proteins such as N-terminal specific glycosylation, labeling of fluorescent dyes, and immobilization on solid surfaces.
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Affiliation(s)
| | - Sriram Sokalingam
- Department of Polymer Science and Chemical Engineering, Pusan National University, Busan, South Korea
| | - Govindan Raghunathan
- Department of Polymer Science and Chemical Engineering, Pusan National University, Busan, South Korea
| | - Nediljko Budisa
- Department of Chemistry, Technische Universität Berlin, Franklinstrasse, Berlin, Germany
| | - Hyun-Jong Paik
- Department of Polymer Science and Chemical Engineering, Pusan National University, Busan, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
| | - Sun-Gu Lee
- Department of Polymer Science and Chemical Engineering, Pusan National University, Busan, South Korea
- * E-mail:
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Nehring S, Budisa N, Wiltschi B. Performance analysis of orthogonal pairs designed for an expanded eukaryotic genetic code. PLoS One 2012; 7:e31992. [PMID: 22493661 PMCID: PMC3320878 DOI: 10.1371/journal.pone.0031992] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 01/17/2012] [Indexed: 12/02/2022] Open
Abstract
Background The suppression of amber stop codons with non-canonical amino acids (ncAAs) is used for the site-specific introduction of many unusual functions into proteins. Specific orthogonal aminoacyl-tRNA synthetase (o-aaRS)/amber suppressor tRNACUA pairs (o-pairs) for the incorporation of ncAAs in S. cerevisiae were previously selected from an E. coli tyrosyl-tRNA synthetase/tRNACUA mutant library. Incorporation fidelity relies on the specificity of the o-aaRSs for their ncAAs and the ability to effectively discriminate against their natural substrate Tyr or any other canonical amino acid. Methodology/Principal Findings We used o-pairs previously developed for ncAAs carrying reactive alkyne-, azido-, or photocrosslinker side chains to suppress an amber mutant of human superoxide dismutase 1 in S. cerevisiae. We found worse incorporation efficiencies of the alkyne- and the photocrosslinker ncAAs than reported earlier. In our hands, amber suppression with the ncAA containing the azido group did not occur at all. In addition to the incorporation experiments in S. cerevisiae, we analyzed the catalytic properties of the o-aaRSs in vitro. Surprisingly, all o-aaRSs showed much higher preference for their natural substrate Tyr than for any of the tested ncAAs. While it is unclear why efficiently recognized Tyr is not inserted at amber codons, we speculate that metabolically inert ncAAs accumulate in the cell, and for this reason they are incorporated despite being weak substrates for the o-aaRSs. Conclusions/Significance O-pairs have been developed for a whole plethora of ncAAs. However, a systematic and detailed analysis of their catalytic properties is still missing. Our study provides a comprehensive scrutiny of o-pairs developed for the site-specific incorporation of reactive ncAAs in S. cerevisiae. It suggests that future development of o-pairs as efficient biotechnological tools will greatly benefit from sound characterization in vivo and in vitro in parallel to monitoring intracellular ncAA levels.
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Affiliation(s)
- Sebastian Nehring
- Department of Biocatalysis, Technical University of Berlin, Berlin, Germany
| | - Nediljko Budisa
- Department of Biocatalysis, Technical University of Berlin, Berlin, Germany
| | - Birgit Wiltschi
- BIOSS - Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- * E-mail:
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Abstract
Many proteins are post-translationally modified by the attachment of poly-ubiquitin (Ub) chains. Notably, the biological function of the attached Ub chain depends on the specific lysine residue used for conjugate formation. Here, we report an easy and efficient method to synthesize site-specifically linked Ub dimers by click reaction between two artificial amino acids. In fact, we were able to synthesize all seven naturally occurring Ub connectivities, providing the first example of a method that gives access to all Ub dimers. Furthermore, these synthetic Ub dimers are recognized by the natural ubiquitination machinery and are proteolytically stable, making them optimal candidates to further investigate the function of differently linked Ub chains.
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Affiliation(s)
- Silvia Eger
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
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Hoesl MG, Acevedo-Rocha CG, Nehring S, Royter M, Wolschner C, Wiltschi B, Budisa N, Antranikian G. Lipase Congeners Designed by Genetic Code Engineering. ChemCatChem 2010. [DOI: 10.1002/cctc.201000253] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Selvakumar E, Rameshkumar N, Lee SG, Lee SJ, Park HS. In vivo Production of Functional Single-Chain Fv Fragment with an N-Terminal-Specific Bio-orthogonal Reactive Group. Chembiochem 2010; 11:498-501. [DOI: 10.1002/cbic.200900685] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Wiltschi B, Merkel L, Budisa N. Fine tuning the N-terminal residue excision with methionine analogues. Chembiochem 2009; 10:217-20. [PMID: 19067457 DOI: 10.1002/cbic.200800605] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Birgit Wiltschi
- Max Planck Institute of Biochemistry, Molecular Biotechnology, Am Klopferspitz 18, 82152 Martinsried, Germany
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Wiltschi B, Wenger W, Nehring S, Budisa N. Expanding the genetic code ofSaccharomyces cerevisiaewith methionine analogues. Yeast 2008; 25:775-86. [DOI: 10.1002/yea.1632] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Dong S, Merkel L, Moroder L, Budisa N. Convenient syntheses of homopropargylglycine. J Pept Sci 2008; 14:1148-50. [DOI: 10.1002/psc.1065] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Merkel L, Beckmann HSG, Wittmann V, Budisa N. Efficient N-Terminal Glycoconjugation of Proteins by the N-End Rule. Chembiochem 2008; 9:1220-4. [DOI: 10.1002/cbic.200800050] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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