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Maviza TP, Zarechenskaia AS, Burmistrova NR, Tchoub AS, Dontsova OA, Sergiev PV, Osterman IA. RtcB2-PrfH Operon Protects E. coli ATCC25922 Strain from Colicin E3 Toxin. Int J Mol Sci 2022; 23:ijms23126453. [PMID: 35742896 PMCID: PMC9223846 DOI: 10.3390/ijms23126453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/28/2022] [Accepted: 06/07/2022] [Indexed: 02/01/2023] Open
Abstract
In the bid to survive and thrive in an environmental setting, bacterial species constantly interact and compete for resources and space in the microbial ecosystem. Thus, they have adapted to use various antibiotics and toxins to fight their rivals. Simultaneously, they have evolved an ability to withstand weapons that are directed against them. Several bacteria harbor colicinogenic plasmids which encode toxins that impair the translational apparatus. One of them, colicin E3 ribotoxin, mediates cleavage of the 16S rRNA in the decoding center of the ribosome. In order to thrive upon deployment of such ribotoxins, competing bacteria may have evolved counter-conflict mechanisms to prevent their demise. A recent study demonstrated the role of PrfH and the RtcB2 module in rescuing a damaged ribosome and the subsequent re-ligation of the cleaved 16S rRNA by colicin E3 in vitro. The rtcB2-prfH genes coexist as gene neighbors in an operon that is sporadically spread among different bacteria. In the current study, we report that the RtcB2-PrfH module confers resistance to colicin E3 toxicity in E. coli ATCC25922 cells in vivo. We demonstrated that the viability of E. coli ATCC25922 strain that is devoid of rtcB2 and prfH genes is impaired upon action of colicin E3, in contrast to the parental strain which has intact rtcB2 and prfH genes. Complementation of the rtcB2 and prfH gene knockout with a high copy number-plasmid (encoding either rtcB2 alone or both rtcB2-prfH operon) restored resistance to colicin E3. These results highlight a counter-conflict system that may have evolved to thwart colicin E3 activity.
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Affiliation(s)
- Tinashe P. Maviza
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; (T.P.M.); (A.S.Z.); (O.A.D.); (P.V.S.)
| | - Anastasiia S. Zarechenskaia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; (T.P.M.); (A.S.Z.); (O.A.D.); (P.V.S.)
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
| | - Nadezhda R. Burmistrova
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
| | - Andrey S. Tchoub
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
| | - Olga A. Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; (T.P.M.); (A.S.Z.); (O.A.D.); (P.V.S.)
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 119992, Russia
| | - Petr V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; (T.P.M.); (A.S.Z.); (O.A.D.); (P.V.S.)
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
| | - Ilya A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; (T.P.M.); (A.S.Z.); (O.A.D.); (P.V.S.)
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
- Genetics and Life Sciences Research Center, Sirius University of Science and Technology, 1 Olympic Ave., Sochi 354340, Russia
- Correspondence:
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Quintero D, Carrafa J, Vincent L, Kim HJ, Wohlschlegel J, Bermudes D. Co-Expression of a Chimeric Protease Inhibitor Secreted by a Tumor-Targeted Salmonella Protects Therapeutic Proteins from Proteolytic Degradation. J Microbiol Biotechnol 2018; 28:2079-2094. [PMID: 30661346 PMCID: PMC6883771 DOI: 10.4014/jmb.1807.08036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Sunflower trypsin inhibitor (SFTI) is a 14-amino-acid bicyclic peptide that contains a single internal disulfide bond. We initially constructed chimeras of SFTI with N-terminal secretion signals from the Escherichia coli OmpA and Pseudomonas aeruginosa ToxA, but only detected small amounts of protease inhibition resulting from these constructs. A substantially higher degree of protease inhibition was detected from a C-terminal SFTI fusion with E. coli YebF, which radiated more than a centimeter from an individual colony of E. coli using a culture-based inhibitor assay. Inhibitory activity was further improved in YebF-SFTI fusions by the addition of a trypsin cleavage signal immediately upstream of SFTI, and resulted in production of a 14-amino-acid, disulfide-bonded SFTI free in the culture supernatant. To assess the potential of the secreted SFTI to protect the ability of a cytotoxic protein to kill tumor cells, we utilized a tumor-selective form of the Pseudomonas ToxA (OTG-PE38K) alone and expressed as a polycistronic construct with YebF-SFTI in the tumor-targeted Salmonella VNP20009. When we assessed the ability of toxin-containing culture supernatants to kill MDA-MB-468 breast cancer cells, the untreated OTG-PE38K was able to eliminate all detectable tumor cells, while pretreatment with trypsin resulted in the complete loss of anticancer cytotoxicity. However, when OTG-PE38K was co-expressed with YebF-SFTI, cytotoxicity was completely retained in the presence of trypsin. These data demonstrate SFTI chimeras are secreted in a functional form and that co-expression of protease inhibitors with therapeutic proteins by tumor-targeted bacteria has the potential to enhance the activity of therapeutic proteins by suppressing their degradation within a proteolytic environment.
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Affiliation(s)
- David Quintero
- Department of Biology, California State University Northridge, Northridge, CA 91330-8303, USA
- Interdisciplinary Research Institute for the Sciences (IRIS), California State University, College of Science and Math, California State University, Northridge, Northridge, CA 91330-8303
| | - Jamie Carrafa
- Department of Biology, California State University Northridge, Northridge, CA 91330-8303, USA
| | - Lena Vincent
- Department of Biology, California State University Northridge, Northridge, CA 91330-8303, USA
- Current Address, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hee Jong Kim
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California at Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California at Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - David Bermudes
- Department of Biology, California State University Northridge, Northridge, CA 91330-8303, USA
- Interdisciplinary Research Institute for the Sciences (IRIS), California State University, College of Science and Math, California State University, Northridge, Northridge, CA 91330-8303
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CsrA and its regulators control the time-point of ColicinE2 release in Escherichia coli. Sci Rep 2018; 8:6537. [PMID: 29695793 PMCID: PMC5916893 DOI: 10.1038/s41598-018-24699-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/09/2018] [Indexed: 01/09/2023] Open
Abstract
The bacterial SOS response is a cellular reaction to DNA damage, that, among other actions, triggers the expression of colicin - toxic bacteriocins in Escherichia coli that are released to kill close relatives competing for resources. However, it is largely unknown, how the complex network regulating toxin expression controls the time-point of toxin release to prevent premature release of inefficient protein concentrations. Here, we study how different regulatory mechanisms affect production and release of the bacteriocin ColicinE2 in Escherichia coli. Combining experimental and theoretical approaches, we demonstrate that the global carbon storage regulator CsrA controls the duration of the delay between toxin production and release and emphasize the importance of CsrA sequestering elements for the timing of ColicinE2 release. In particular, we show that ssDNA originating from rolling-circle replication of the toxin-producing plasmid represents a yet unknown additional CsrA sequestering element, which is essential in the ColicinE2-producing strain to enable toxin release by reducing the amount of free CsrA molecules in the bacterial cell. Taken together, our findings show that CsrA times ColicinE2 release and reveal a dual function for CsrA as an ssDNA and mRNA-binding protein, introducing ssDNA as an important post-transcriptional gene regulatory element.
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Calcuttawala F, Hariharan C, Pazhani GP, Saha DR, Ramamurthy T. Characterization of E-type colicinogenic plasmids from Shigella sonnei. FEMS Microbiol Lett 2017; 364:3071828. [DOI: 10.1093/femsle/fnx060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 03/14/2017] [Indexed: 12/14/2022] Open
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Quintero D, Carrafa J, Vincent L, Bermudes D. EGFR-targeted Chimeras of Pseudomonas ToxA released into the extracellular milieu by attenuated Salmonella selectively kill tumor cells. Biotechnol Bioeng 2016; 113:2698-2711. [PMID: 27260220 PMCID: PMC5083144 DOI: 10.1002/bit.26026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/25/2016] [Accepted: 05/29/2016] [Indexed: 02/06/2023]
Abstract
Tumor-targeted Salmonella VNP20009 preferentially replicate within tumor tissue and partially suppress tumor growth in murine tumor models. These Salmonella have the ability to locally induce apoptosis when they are in direct contact with cancer cells but they lack significant bystander killing, which may correlate with their overall lack of antitumor activity in human clinical studies. In order to compensate for this deficiency without enhancing overall toxicity, we engineered the bacteria to express epidermal growth factor receptor (EGFR)-targeted cytotoxic proteins that are released into the extracellular milieu. In this study, we demonstrate the ability of the Salmonella strain VNP20009 to produce three different forms of the Pseudomonas exotoxin A (ToxA) chimeric with a tumor growth factor alpha (TGFα) which results in its producing culture supernatants that are cytotoxic and induce apoptosis in EGFR positive cancer cells as measured by the tetrazolium dye reduction, and Rhodamine 123 and JC-10 mitochondrial depolarization assays. In addition, exchange of the ToxA REDLK endoplasmic reticulum retention signal for KDEL and co-expression of the ColE3 lysis protein resulted in an overall increased cytotoxicity compared to the wild type toxin. This approach has the potential to significantly enhance the antitumor activity of VNP20009 while maintaining its previously established safety profile. Biotechnol. Bioeng. 2016;113: 2698-2711. © 2016 The Authors. Biotechnology and Bioengineering published by Wiley Periodicals, Inc.
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Affiliation(s)
- David Quintero
- Department of Biology, California State University Northridge, Northridge, California, 91330-8303
- Interdisciplinary Research Institute for the Sciences (IRIS), California State University Northridge, Northridge, California, 91330-8303
| | - Jamie Carrafa
- Department of Biology, California State University Northridge, Northridge, California, 91330-8303
| | - Lena Vincent
- Department of Biology, California State University Northridge, Northridge, California, 91330-8303
| | - David Bermudes
- Department of Biology, California State University Northridge, Northridge, California, 91330-8303.
- Interdisciplinary Research Institute for the Sciences (IRIS), California State University Northridge, Northridge, California, 91330-8303.
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Yang C, Li P, Su W, Li H, Liu H, Yang G, Xie J, Yi S, Wang J, Cui X, Wu Z, Wang L, Hao R, Jia L, Qiu S, Song H. Polymorphism of CRISPR shows separated natural groupings of Shigella subtypes and evidence of horizontal transfer of CRISPR. RNA Biol 2015; 12:1109-20. [PMID: 26327282 PMCID: PMC4829275 DOI: 10.1080/15476286.2015.1085150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/30/2015] [Accepted: 08/15/2015] [Indexed: 10/23/2022] Open
Abstract
Clustered, regularly interspaced, short palindromic repeats (CRISPR) act as an adaptive RNA-mediated immune mechanism in bacteria. They can also be used for identification and evolutionary studies based on polymorphisms within the CRISPR locus. We amplified and analyzed 6 CRISPR loci from 237 Shigella strains belonging to the 4 species groups, as well as 13 Escherichia coli strains. The CRISPR-associated (cas) gene sequence arrays of these strains were screened and compared. The CRISPR sequences from Shigella were conserved among subtypes, suggesting that CRISPR may represent a new identification tool for the detection and discrimination of Shigella species. Secondary structure analysis showed a different stem-loop structure at the terminal repeat, suggesting a distinct recognition mechanism in the formation of crRNA. In addition, the presence of "self-target" spacers and polymorphisms within CRISPR in Shigella indicated a selective pressure for inhibition of this system, which has the potential to damage "self DNA." Homology analysis of spacers showed that CRISPR might be involved in the regulation of virulence transmission. Phylogenetic analysis based on CRISPR sequences from Shigella and E. coli indicated that although phenotypic properties maintain convergent evolution, the 4 Shigella species do not represent natural groupings. Surprisingly, comparative analysis of Shigella repeats with other species provided new evidence for CRISPR horizontal transfer. Our results suggested that CRISPR analysis is applicable for the detection of Shigella species and for investigation of evolutionary relationships.
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Affiliation(s)
- Chaojie Yang
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Peng Li
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Wenli Su
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Hao Li
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Hongbo Liu
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Guang Yang
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Jing Xie
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Shengjie Yi
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Jian Wang
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Xianyan Cui
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Zhihao Wu
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Ligui Wang
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Rongzhang Hao
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Leili Jia
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Shaofu Qiu
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Hongbin Song
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
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