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Fan C, Wu YH, Decker CM, Rohani R, Gesell Salazar M, Ye H, Cui Z, Schmidt F, Huang WE. Defensive Function of Transposable Elements in Bacteria. ACS Synth Biol 2019; 8:2141-2151. [PMID: 31375026 DOI: 10.1021/acssynbio.9b00218] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
It has been widely debated whether transposable elements have a positive or a negative effect on their host cells. This study demonstrated that transposable elements, specifically insertion sequences (ISs), can adopt a defensive role in Escherichia coli. In three different E. coli strains (S17, DH5α, and Nissle 1917), IS1 and IS10 rapidly disrupted the I-CeuI gene (encoding I-CeuI endonuclease) on the plasmid pLO11-ICeuI as early as the first generation, despite the gene-circuit being under control of an arabinose promoter. Proteomics analysis showed that the protein abundance profile of E. coli DH5α with pLO11-ICeuI in the fifth generation was nearly opposite to that of control strain (E. coli with pLO11, no I-CeuI). The DNA damage caused by the leaky expression of I-CeuI was enough to trigger a SOS response and alter lipid synthesis, ribosomal activity, RNA/DNA metabolism, central dogma and cell cycle processes in E. coli DH5α. After the ISs disrupted the expression of I-CeuI, cells fully recovered by the 31st generation had a protein abundance profile similar to that of the control strain. This study showed that ISs readily mutated a harmful gene which subsequently restored host fitness. These observations have implications for the stability of designed gene circuits in synthetic biology.
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Affiliation(s)
- Catherine Fan
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
| | - Yin-Hu Wu
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Christoph M. Decker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Reza Rohani
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
| | - Manuela Gesell Salazar
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Hua Ye
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
| | - Zhanfeng Cui
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
| | - Frank Schmidt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
- Proteomics Core, Weill Cornel Medicine-Qatar, Education City, PO 24144 Doha, Qatar
| | - Wei E. Huang
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
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Alonso CA, Cortés-Cortés G, Maamar E, Massó M, Rocha-Gracia RDC, Torres C, Centrón D, Quiroga MP. Molecular diversity and conjugal transferability of class 2 integrons among Escherichia coli isolates from food, animal and human sources. Int J Antimicrob Agents 2018; 51:905-911. [DOI: 10.1016/j.ijantimicag.2018.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/21/2017] [Accepted: 02/03/2018] [Indexed: 01/03/2023]
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Substrate translocation involves specific lysine residues of the central channel of the conjugative coupling protein TrwB. Mol Genet Genomics 2017; 292:1037-1049. [PMID: 28597316 DOI: 10.1007/s00438-017-1331-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/01/2017] [Indexed: 10/19/2022]
Abstract
Conjugative transfer of plasmid R388 requires the coupling protein TrwB for protein and DNA transport, but their molecular role in transport has not been deciphered. We investigated the role of residues protruding into the central channel of the TrwB hexamer by a mutational analysis. Mutations affecting lysine residues K275, K398, and K421, and residue S441, all facing the internal channel, affected transport of both DNA and the relaxase protein in vivo. The ATPase activity of the purified soluble variants was affected significantly in the presence of accessory protein TrwA or DNA, correlating with their behaviour in vivo. Alteration of residues located at the cytoplasmic or the inner membrane interface resulted in lower activity in vivo and in vitro, while variants affecting residues in the central region of the channel showed increased DNA and protein transfer efficiency and higher ATPase activity, especially in the absence of TrwA. In fact, these variants could catalyze DNA transfer in the absence of TrwA under conditions in which the wild-type system was transfer deficient. Our results suggest that protein and DNA molecules have the same molecular requirements for translocation by Type IV secretion systems, with residues at both ends of the TrwB channel controlling the opening-closing mechanism, while residues embedded in the channel would set the pace for substrate translocation (both protein and DNA) in concert with TrwA.
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