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Mycobacterium tuberculosis Shikimate Pathway Enzymes as Targets for the Rational Design of Anti-Tuberculosis Drugs. Molecules 2020; 25:molecules25061259. [PMID: 32168746 PMCID: PMC7144000 DOI: 10.3390/molecules25061259] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/06/2020] [Accepted: 02/10/2020] [Indexed: 12/17/2022] Open
Abstract
Roughly a third of the world’s population is estimated to have latent Mycobacterium tuberculosis infection, being at risk of developing active tuberculosis (TB) during their lifetime. Given the inefficacy of prophylactic measures and the increase of drug-resistant M. tuberculosis strains, there is a clear and urgent need for the development of new and more efficient chemotherapeutic agents, with selective toxicity, to be implemented on patient treatment. The component enzymes of the shikimate pathway, which is essential in mycobacteria and absent in humans, stand as attractive and potential targets for the development of new drugs to treat TB. This review gives an update on published work on the enzymes of the shikimate pathway and some insight on what can be potentially explored towards selective drug development.
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Unthan S, Baumgart M, Radek A, Herbst M, Siebert D, Brühl N, Bartsch A, Bott M, Wiechert W, Marin K, Hans S, Krämer R, Seibold G, Frunzke J, Kalinowski J, Rückert C, Wendisch VF, Noack S. Chassis organism from Corynebacterium glutamicum--a top-down approach to identify and delete irrelevant gene clusters. Biotechnol J 2015; 10:290-301. [PMID: 25139579 PMCID: PMC4361050 DOI: 10.1002/biot.201400041] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/25/2014] [Accepted: 08/19/2014] [Indexed: 01/05/2023]
Abstract
For synthetic biology applications, a robust structural basis is required, which can be constructed either from scratch or in a top-down approach starting from any existing organism. In this study, we initiated the top-down construction of a chassis organism from Corynebacterium glutamicum ATCC 13032, aiming for the relevant gene set to maintain its fast growth on defined medium. We evaluated each native gene for its essentiality considering expression levels, phylogenetic conservation, and knockout data. Based on this classification, we determined 41 gene clusters ranging from 3.7 to 49.7 kbp as target sites for deletion. 36 deletions were successful and 10 genome-reduced strains showed impaired growth rates, indicating that genes were hit, which are relevant to maintain biological fitness at wild-type level. In contrast, 26 deleted clusters were found to include exclusively irrelevant genes for growth on defined medium. A combinatory deletion of all irrelevant gene clusters would, in a prophage-free strain, decrease the size of the native genome by about 722 kbp (22%) to 2561 kbp. Finally, five combinatory deletions of irrelevant gene clusters were investigated. The study introduces the novel concept of relevant genes and demonstrates general strategies to construct a chassis suitable for biotechnological application.
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Affiliation(s)
- Simon Unthan
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems BiotechnologyForschungszentrum Jülich, Jülich, Germany
| | - Meike Baumgart
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systemic MicrobiologyForschungszentrum Jülich, Jülich, Germany
| | - Andreas Radek
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems BiotechnologyForschungszentrum Jülich, Jülich, Germany
| | - Marius Herbst
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld UniversityBielefeld, Germany
| | - Daniel Siebert
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld UniversityBielefeld, Germany
| | - Natalie Brühl
- Institute of Biochemistry, University of CologneCologne, Germany
| | - Anna Bartsch
- Institute of Biochemistry, University of CologneCologne, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systemic MicrobiologyForschungszentrum Jülich, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems BiotechnologyForschungszentrum Jülich, Jülich, Germany
| | - Kay Marin
- Evonik Degussa GmbHHalle/Westphalia, Germany
| | | | - Reinhard Krämer
- Institute of Biochemistry, University of CologneCologne, Germany
| | - Gerd Seibold
- Institute of Biochemistry, University of CologneCologne, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systemic MicrobiologyForschungszentrum Jülich, Jülich, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld UniversityBielefeld, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld UniversityBielefeld, Germany
| | - Volker F Wendisch
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld UniversityBielefeld, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems BiotechnologyForschungszentrum Jülich, Jülich, Germany
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Peek J, Christendat D. The shikimate dehydrogenase family: functional diversity within a conserved structural and mechanistic framework. Arch Biochem Biophys 2014; 566:85-99. [PMID: 25524738 DOI: 10.1016/j.abb.2014.12.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 11/19/2014] [Accepted: 12/07/2014] [Indexed: 11/19/2022]
Abstract
Shikimate dehydrogenase (SDH) catalyzes the NADPH-dependent reduction of 3-deydroshikimate to shikimate, an essential reaction in the biosynthesis of the aromatic amino acids and a large number of other secondary metabolites in plants and microbes. The indispensible nature of this enzyme makes it a potential target for herbicides and antimicrobials. SDH is the archetypal member of a large protein family, which contains at least four additional functional classes with diverse metabolic roles. The different members of the SDH family share a highly similar three-dimensional structure and utilize a conserved catalytic mechanism, but exhibit distinct substrate preferences, making the family a particularly interesting system for studying modes of substrate recognition used by enzymes. Here, we review our current understanding of the biochemical and structural properties of each of the five previously identified SDH family functional classes.
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Affiliation(s)
- James Peek
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Dinesh Christendat
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada.
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Reimer LC, Spura J, Schmidt-Hohagen K, Schomburg D. High-throughput screening of a Corynebacterium glutamicum mutant library on genomic and metabolic level. PLoS One 2014; 9:e86799. [PMID: 24504095 PMCID: PMC3913579 DOI: 10.1371/journal.pone.0086799] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 12/13/2013] [Indexed: 12/02/2022] Open
Abstract
Due to impressive achievements in genomic research, the number of genome sequences has risen quickly, followed by an increasing number of genes with unknown or hypothetical function. This strongly calls for development of high-throughput methods in the fields of transcriptomics, proteomics and metabolomics. Of these platforms, metabolic profiling has the strongest correlation with the phenotype. We previously published a high-throughput metabolic profiling method for C. glutamicum as well as the automatic GC/MS processing software MetaboliteDetector. Here, we added a high-throughput transposon insertion determination for our C. glutamicum mutant library. The combination of these methods allows the parallel analysis of genotype/phenotype correlations for a large number of mutants. In a pilot project we analyzed the insertion points of 722 transposon mutants and found that 36% of the affected genes have unknown functions. This underlines the need for further information gathered by high-throughput techniques. We therefore measured the metabolic profiles of 258 randomly chosen mutants. The MetaboliteDetector software processed this large amount of GC/MS data within a few hours with a low relative error of 11.5% for technical replicates. Pairwise correlation analysis of metabolites over all genotypes showed dependencies of known and unknown metabolites. For a first insight into this large data set, a screening for interesting mutants was done by a pattern search, focusing on mutants with changes in specific pathways. We show that our transposon mutant library is not biased with respect to insertion points. A comparison of the results for specific mutants with previously published metabolic results on a deletion mutant of the same gene confirmed the concept of high-throughput metabolic profiling. Altogether the described method could be applied to whole mutant libraries and thereby help to gain comprehensive information about genes with unknown, hypothetical and known functions.
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Affiliation(s)
- Lorenz C. Reimer
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jana Spura
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kerstin Schmidt-Hohagen
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
- * E-mail:
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