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Tseduliak VM, Dolia B, Ostash I, Lopatniuk M, Busche T, Ochi K, Kalinowski J, Luzhetskyy A, Fedorenko V, Ostash B. Mutations within gene XNR_2147 for TetR-like protein enhance lincomycin resistance and endogenous specialized metabolism of Streptomyces albus J1074. J Appl Genet 2023; 64:185-195. [PMID: 36417169 DOI: 10.1007/s13353-022-00738-4] [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: 08/28/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022]
Abstract
Streptomyces albus J1074 is one of the most popular heterologous expression platforms among streptomycetes. Identification of new genes and mutations that influence specialized metabolism in this species is therefore of great applied interest. Here, we describe S. albus KO-1304 that was isolated as a spontaneous lincomycin-resistant variant of double rpsLR94G rsmGR15SG40E mutant KO-1295. Besides altered antibiotic resistance profile, KO-1304 exhibited increased antibiotic activity as compared to its parental strains. KO-1304 genome sequencing revealed mutations within gene XNR_2147 encoding putative TetR-like protein. Gene XNR_2146 for efflux protein is the most likely target of repressing action of Xnr_2147. Our data agree with the scenario where lincomycin resistance phenotype of KO-1304 arose from inability of mutated Xnr_2147 protein to repress XNR_2146. Introduction of additional copy of XNR_2146 into wild type strain increased antibiotic activity of the latter, attesting to the practical value of transporter genes for strain improvement.
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Affiliation(s)
- Vasylyna-Marta Tseduliak
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine
| | - Borys Dolia
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine
| | - Iryna Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine
| | - Maria Lopatniuk
- Helmholtz Institute for Pharmaceutical Research, Saarland Campus, Building C2.3, 66123, Saarbrucken, Germany
| | - Tobias Busche
- Technology Platform Genomics, CeBiTec, Bielefeld University, Sequenz 1, 33615, Bielefeld, Germany
| | - Kozo Ochi
- Department of Life Sciences, Hiroshima Institute of Technology, Saeki-Ku, Hiroshima, 731-5193, Japan
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Sequenz 1, 33615, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research, Saarland Campus, Building C2.3, 66123, Saarbrucken, Germany
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho St. 4, Lviv, 79005, Ukraine.
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Sivapragasam S, Deochand DK, Meariman JK, Grove A. The Stringent Response Induced by Phosphate Limitation Promotes Purine Salvage in Agrobacterium fabrum. Biochemistry 2017; 56:5831-5843. [DOI: 10.1021/acs.biochem.7b00844] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Smitha Sivapragasam
- Department of Biological
Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Dinesh K. Deochand
- Department of Biological
Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Jacob K. Meariman
- Department of Biological
Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Anne Grove
- Department of Biological
Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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Sivapragasam S, Grove A. Streptomyces coelicolor XdhR is a direct target of (p)ppGpp that controls expression of genes encoding xanthine dehydrogenase to promote purine salvage. Mol Microbiol 2016; 100:701-18. [PMID: 26833627 DOI: 10.1111/mmi.13342] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2016] [Indexed: 12/20/2022]
Abstract
The gene encoding Streptomyces coelicolor xanthine dehydrogenase regulator (XdhR) is divergently oriented from xdhABC, which encodes xanthine dehydrogenase (Xdh). Xdh is required for purine salvage pathways. XdhR was previously shown to repress xdhABC expression. We show that XdhR binds the xdhABC-xdhR intergenic region with high affinity (Kd ∼ 0.5 nM). DNaseI footprinting reveals that this complex formation corresponds to XdhR binding the xdhR gene promoter at two adjacent sites; at higher protein concentrations, protection expands to a region that overlaps the transcriptional and translational start sites of xdhABC. While substrates for Xdh have little effect on DNA binding, GTP and ppGpp dissociate the DNA-XdhR complex. Progression of cells to stationary phase, a condition associated with increased (p)ppGpp production, leads to elevated xdhB expression; in contrast, inhibition of Xdh by allopurinol results in xdhB repression. We propose that XdhR is a direct target of (p)ppGpp, and that expression of xdhABC is upregulated during the stringent response to promote purine salvage pathways, maintain GTP homeostasis and ensure continued (p)ppGpp synthesis. During exponential phase growth, basal levels of xdhABC expression may be achieved by GTP serving as a lower-affinity XdhR ligand.
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Affiliation(s)
- Smitha Sivapragasam
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Anne Grove
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
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Crystal Structure of Fad35R from Mycobacterium tuberculosis H37Rv in the Apo-State. PLoS One 2015; 10:e0124333. [PMID: 25938298 PMCID: PMC4418694 DOI: 10.1371/journal.pone.0124333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 03/04/2015] [Indexed: 11/19/2022] Open
Abstract
Fad35R from Mycobacterium tuberculosis binds to the promoter site of Fad35 operon and its DNA binding activities are reduced in the presence of tetracycline and palmitoyl-CoA. We resolved the crystal structure of Fad35R using single-wavelength anomalous diffraction method (SAD). Fad35R comprises canonical DNA binding domain (DBD) and ligand binding domain (LBD), but displays several distinct structural features. Two recognition helices of two monomers in the homodimer are separated by ~ 48 Å and two core triangle-shaped ligand binding cavities are well exposed to solvent. Structural comparison with DesT and QacR structures suggests that ligand binding-induced movement of α7, which adopts a straight conformation in the Fad35R, may be crucial to switch the conformational states between repressive and derepressive forms. Two DBDs are packed asymmetrically, creating an alternative dimer interface which coincides with the possible tetramer interface that connects the two canonical dimers. Quaternary state of alternative dimer mimics a closed-state structure in which two recognition helices are distanced at ~ 35 Å and ligand binding pockets are inaccessible. Results of biophysical studies indicate that Fad35R has the propensity to oligomerize in solution in the presence of tetracycline. We present the first structure of a FadR homologue from mycobacterium and the structure reveals DNA and ligand binding features of Fad35R and also provides a view on alternative quaternary states that mimic open and closed forms of the regulator.
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Deng W, Li C, Xie J. The underling mechanism of bacterial TetR/AcrR family transcriptional repressors. Cell Signal 2013; 25:1608-13. [PMID: 23602932 DOI: 10.1016/j.cellsig.2013.04.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 03/31/2013] [Accepted: 04/02/2013] [Indexed: 11/27/2022]
Abstract
Bacteria transcriptional regulators are classified by their functional and sequence similarities. Member of the TetR/AcrR family is two-domain proteins including an N-terminal HTH DNA-binding motif and a C-terminal ligand recognition domain. The C-terminal ligand recognition domain can recognize the very same compounds as their target transporters transferred. TetRs act as chemical sensors to monitor both the cellular environmental dynamics and their regulated genes underlying many events, such as antibiotics production, osmotic stress, efflux pumps, multidrug resistance, metabolic modulation, and pathogenesis. Compounds targeting Mycobacterium tuberculosis ethR represent promising novel antibiotic potentiater. TetR-mediated multidrug efflux pumps regulation might be good target candidate for the discovery of better new antibiotics against drug resistance.
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Affiliation(s)
- Wanyan Deng
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
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