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Xu Y, Liu J, You G, Yang Z, Miao L, Wu J, Yang G, Hou J. A quaternary ammonium salt grafted tannin-based flocculant boosts the conjugative transfer of plasmid-born antibiotic resistance genes: The nonnegligible side of their flocculation-sterilization properties. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:166515. [PMID: 37619725 DOI: 10.1016/j.scitotenv.2023.166515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/07/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
This study developed dual-function tannin-based flocculants, namely tannin-graft-acrylamide-diallyl dimethyl ammonium chloride (TGCC-A/TGCC-C), endowed with enhanced flocculation-sterilization properties. The impacts of these flocculants on proliferation and transformation of antibiotic resistance genes (ARGs) among bacteria during the flocculation-deposition process were examined. TGCC-A/TGCC-C exhibited remarkable flocculation capacities towards both Escherichia coli and Staphylococcus aureus, encompassing a logarithmic range of initial cell density (108-109 CFU/mL) and a broad pH spectrum (pH 2-11). The grafted quaternary ammonium salt groups played pivotal parts in flocculation through charge neutralization and bridging mechanisms, concurrently contributing to sterilization by disrupting cellular membranes. The correlation between flocculation and sterilization entails a sequential progression, where an excess of TGCC, initially employed for flocculation, is subsequently consumed for sterilization purposes. The frequencies of ARGs conjugative transfer were enhanced in bacterial flocs across all TGCC treatments, stemming from augmented bacterial aggregation and cell membrane permeability, elicited stress response, and up-regulated genes encoding plasmid transfer. These findings underscore the indispensable role of flocculation-sterilization effects in mediating the propagation of ARGs, consequently providing substantial support for the scientific evaluation of the environmental risks associated with flocculants in the context of ARGs dissemination during the treatment of raw water featuring high bacterial density.
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Affiliation(s)
- Yi Xu
- College of Agricultural Science and Engineering, Hohai University, Nanjing 210098, People's Republic of China
| | - Jialin Liu
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Guoxiang You
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China.
| | - Zijun Yang
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Lingzhan Miao
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Jun Wu
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Guang Yang
- Chinese Acad Sci, Res Ctr Ecoenvironm Sci, State Key Lab Urban & Reg Ecol, Beijing 100085, People's Republic of China
| | - Jun Hou
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
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2
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Xiao Y, Zhang Y, Xie F, Olsen RH, Shi L, Li L. Inhibition of Plasmid Conjugation in Escherichia coli by Targeting rbsB Gene Using CRISPRi System. Int J Mol Sci 2023; 24:10585. [PMID: 37445761 DOI: 10.3390/ijms241310585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Bacterial conjugation constitutes a major horizontal gene transfer mechanism for the dissemination of antibiotic-resistant genes (ARGs) among human pathogens. The spread of ARGs can be halted or diminished by interfering with the conjugation process. In this study, we explored the possibility of using an rbsB gene as a single target to inhibit plasmid-mediated horizontal gene transfer in Escherichia coli by CRISPR interference (CRISPRi) system. Three single-guide RNAs (sgRNAs) were designed to target the rbsB gene. The transcriptional levels of the rbsB gene, the conjugation-related genes, and the conjugation efficiency in the CRISPRi strain were tested. We further explored the effect of the repressed expression of the rbsB gene on the quorum sensing (QS) system and biofilm formation. The results showed that the constructed CRISPRi system was effective in repressing the transcriptional level of the rbsB gene at a rate of 66.4%. The repressed expression of the rbsB gene resulted in the reduced conjugation rate of RP4 plasmid by 88.7%, which significantly inhibited the expression of the conjugation-related genes (trbBp, trfAp, traF and traJ) and increased the global regulator genes (korA, korB and trbA). The repressed rbsB gene expression reduced the depletion of autoinducer 2 signals (AI-2) by 12.8% and biofilm formation by a rate of 68.2%. The results of this study indicated the rbsB gene could be used as a universal target for the inhibition of conjugation. The constructed conjugative CRISPRi system has the potential to be used in ARG high-risk areas.
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Affiliation(s)
- Yawen Xiao
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Yan Zhang
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Fengjun Xie
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Rikke Heidemann Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Lili Li
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
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3
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Huang H, Lin L, Bu F, Su Y, Zheng X, Chen Y. Reductive Stress Boosts the Horizontal Transfer of Plasmid-Borne Antibiotic Resistance Genes: The Neglected Side of the Intracellular Redox Spectrum. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15594-15606. [PMID: 36322896 DOI: 10.1021/acs.est.2c04276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The dissemination of plasmid-borne antibiotic resistance genes (ARGs) among bacteria is becoming a global challenge to the "One Health" concept. During conjugation, the donor/recipient usually encounter diverse stresses induced by the surrounding environment. Previous studies mainly focused on the effects of oxidative stress on plasmid conjugation, but ignored the potential contribution of reductive stress (RS), the other side of the intracellular redox spectrum. Herein, we demonstrated for the first time that RS induced by dithiothreitol could significantly boost the horizontal transfer of plasmid RP4 from Escherichia coli K12 to different recipients (E. coli HB101, Salmonella Typhimurium, and Pseudomonas putida KT2440). Phenotypic and genotypic tests confirmed that RS upregulated genes encoding the transfer apparatus of plasmid RP4, which was attributed to the promoted consumption of intracellular glutamine in the donor rather than the widely reported SOS response. Moreover, RS was verified to benefit ATP supply by activating glycolysis (e.g., GAPDH) and the respiratory chain (e.g., appBC), triggering the deficiency of intracellular free Mg2+ by promoting its binding, and reducing membrane permeability by stimulating cardiolipin biosynthesis, all of which were beneficial to the functioning of transfer apparatus. Overall, our findings uncovered the neglected risks of RS in ARG spreading and updated the regulatory mechanism of plasmid conjugation.
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Affiliation(s)
- Haining Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Lin Lin
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Fan Bu
- Shanghai Electric Environmental Protection Group, Shanghai Electric Group Co. Ltd, Shanghai 200092, China
| | - Yinglong Su
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200092, China
| | - Xiong Zheng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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4
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Fernandez-Lopez R, Ruiz R, del Campo I, Gonzalez-Montes L, Boer D, de la Cruz F, Moncalian G. Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors. Nucleic Acids Res 2022; 50:11938-11947. [PMID: 36370103 PMCID: PMC9723621 DOI: 10.1093/nar/gkac1024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 10/13/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022] Open
Abstract
Some transcription factors bind DNA motifs containing direct or inverted sequence repeats. Preference for each of these DNA topologies is dictated by structural constraints. Most prokaryotic regulators form symmetric oligomers, which require operators with a dyad structure. Binding to direct repeats requires breaking the internal symmetry, a property restricted to a few regulators, most of them from the AraC family. The KorA family of transcriptional repressors, involved in plasmid propagation and stability, includes members that form symmetric dimers and recognize inverted repeats. Our structural analyses show that ArdK, a member of this family, can form a symmetric dimer similar to that observed for KorA, yet it binds direct sequence repeats as a non-symmetric dimer. This is possible by the 180° rotation of one of the helix-turn-helix domains. We then probed and confirmed that ArdK shows affinity for an inverted repeat, which, surprisingly, is also recognized by a non-symmetrical dimer. Our results indicate that structural flexibility at different positions in the dimerization interface constrains transcription factors to bind DNA sequences with one of these two alternative DNA topologies.
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Affiliation(s)
- Raul Fernandez-Lopez
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011, Santander, Spain
| | - Raul Ruiz
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011, Santander, Spain
| | - Irene del Campo
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011, Santander, Spain
| | - Lorena Gonzalez-Montes
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011, Santander, Spain
| | - D Roeland Boer
- Alba Synchrotron, Cerdanyola del Vallès, 08290, Barcelona, Spain
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Wu Y, Yan H, Zhu X, Liu C, Chu C, Zhu X, Chen B. Biochar Effectively Inhibits the Horizontal Transfer of Antibiotic Resistance Genes via Restraining the Energy Supply for Conjugative Plasmid Transfer. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:12573-12583. [PMID: 35944241 DOI: 10.1021/acs.est.2c02701] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) through plasmid-mediated conjugation poses a major threat to global public health. Biochar, a widely used environmental remediation material, has remarkable impacts on the fate of ARGs. However, although biochar was reported being able to inhibit the HGT of ARGs via conjugation and transformation, little is known about the intracellular process that mediates the inhibition effects. On the other hand, as typical natural organic matter, fulvic acid is a common environmental influencer, and how it interferes with the effect of biochar on the HGT of ARGs is unknown. Therefore, this study investigated the effects on the conjugative transfer of ARGs between Escherichia coli MG1655 and E. coli HB101 carrying plasmid RP4, with biochars pyrolyzed at three temperatures and with the corresponding biochars coating with fulvic acid. Results showed that biochar with higher pyrolyzed temperature had a more substantial inhibitory effect on the conjugative transfer of the RP4 plasmid. The inhibitory effect of biochar was mainly attributed to (i) down-regulation of plasmid transfer gene expression, including the formation of conjugative transfer channel and plasmid replication, due to restrained adenosine triphosphate (ATP) energy supply and (ii) decreased cell membrane permeability. Conversely, the fulvic acid coating diminished this inhibition effect of biochar, mainly by providing more ATP and strengthening intracellular reactive oxygen species (ROS) defense. Our findings shed light on the intracellular process that mediates the effects of biochar on the conjugative transfer of ARGs, which would provide support for using biochar to reduce the spread of ARGs.
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Affiliation(s)
- Yajing Wu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Huicong Yan
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Xiaomin Zhu
- College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Congcong Liu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Chiheng Chu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Xiaoying Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Baoliang Chen
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
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Yu Z, Wang Y, Lu J, Bond PL, Guo J. Nonnutritive sweeteners can promote the dissemination of antibiotic resistance through conjugative gene transfer. THE ISME JOURNAL 2021; 15:2117-2130. [PMID: 33589766 PMCID: PMC8245538 DOI: 10.1038/s41396-021-00909-x] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/12/2021] [Accepted: 01/21/2021] [Indexed: 02/08/2023]
Abstract
Antimicrobial resistance (AMR) poses a worldwide threat to human health and biosecurity. The spread of antibiotic resistance genes (ARGs) via conjugative plasmid transfer is a major contributor to the evolution of this resistance. Although permitted as safe food additives, compounds such as saccharine, sucralose, aspartame, and acesulfame potassium that are commonly used as nonnutritive sweeteners have recently been associated with shifts in the gut microbiota similar to those caused by antibiotics. As antibiotics can promote the spread of antibiotic resistance genes (ARGs), we hypothesize that these nonnutritive sweeteners could have a similar effect. Here, we demonstrate for the first time that saccharine, sucralose, aspartame, and acesulfame potassium could promote plasmid-mediated conjugative transfer in three established conjugation models between the same and different phylogenetic strains. The real-time dynamic conjugation process was visualized at the single-cell level. Bacteria exposed to the tested compounds exhibited increased reactive oxygen species (ROS) production, the SOS response, and gene transfer. In addition, cell membrane permeability increased in both parental bacteria under exposure to the tested compounds. The expression of genes involved in ROS detoxification, the SOS response, and cell membrane permeability was significantly upregulated under sweetener treatment. In conclusion, exposure to nonnutritive sweeteners enhances conjugation in bacteria. Our findings provide insight into AMR spread and indicate the potential risk associated with the presence of nonnutritive sweeteners.
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Affiliation(s)
- Zhigang Yu
- grid.1003.20000 0000 9320 7537Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD Australia
| | - Yue Wang
- grid.1003.20000 0000 9320 7537Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD Australia
| | - Ji Lu
- grid.1003.20000 0000 9320 7537Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD Australia
| | - Philip L. Bond
- grid.1003.20000 0000 9320 7537Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD Australia
| | - Jianhua Guo
- grid.1003.20000 0000 9320 7537Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD Australia
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7
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Zhu L, Chen T, Xu L, Zhou Z, Feng W, Liu Y, Chen H. Effect and mechanism of quorum sensing on horizontal transfer of multidrug plasmid RP4 in BAC biofilm. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 698:134236. [PMID: 31493577 DOI: 10.1016/j.scitotenv.2019.134236] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/28/2019] [Accepted: 08/31/2019] [Indexed: 06/10/2023]
Abstract
The widespread emergence of antibiotic resistance genes (ARGs) in drinking water systems endangers human health, and may be exacerbated by their horizontal gene transfer (HGT) among microbiota. In our previous study, Quorum sensing (QS) molecules produced by bacteria from biological activated carbon (BAC) biofilms were demonstrated to influence the transfer efficiency of a model conjugative plasmid, here RP4. In this study, we further explored the effect and mechanism of QS on conjugation transfer. The results revealed that Acyl-homoserine lactones producing (AHL-producing) bacteria isolated from BAC biofilm play a role in the propagation of ARGs. We selected several quorum sensing inhibitors (QSIs) to study their effects on AHL-producing bacteria, including the formation of biofilm and the regulating effect on conjugation transfer. In addition, the possible molecular mechanisms for AHLs that promote conjugative transfer were attributable to enhancing the mRNA expression, which involved altered expressions of conjugation-related genes. We also found that QSIs could inhibit conjugative transfer by downregulating the conjugation-relevant genes. We believe that this is the first insightful exploration of the mechanism by which AHLs will facilitate and QSIs will inhibit the conjugative transfer of ARGs. These results provide creative insight into ARG pollution control that involves blocking QS during BAC treatment in drinking water systems.
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Affiliation(s)
- Lin Zhu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Tao Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lan Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhenchao Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wanqiu Feng
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yang Liu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hong Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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Liao J, Huang H, Chen Y. CO 2 promotes the conjugative transfer of multiresistance genes by facilitating cellular contact and plasmid transfer. ENVIRONMENT INTERNATIONAL 2019; 129:333-342. [PMID: 31150975 DOI: 10.1016/j.envint.2019.05.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/23/2019] [Accepted: 05/23/2019] [Indexed: 06/09/2023]
Abstract
The dissemination of antibiotic resistance genes (ARGs), especially via the plasmid-mediated conjugation, is becoming a pervasive global health threat. This study reported that this issue can be worse by CO2, as increased CO2 was found to facilitate the conjugative transfer of ARGs carried on plasmid RP4 by 2.4-9.0 and 1.3-3.8 fold within and across genera, respectively. Mechanistic studies revealed that CO2 benefitted the cell-to-cell contact by increasing cell surface hydrophobicity and decreasing cell surface charge, both of which resulted in the reduced intercellular repulsion. Besides, the transcriptional expression of genes responsible for global regulator (korA, korB and trbA), plasmid transfer and replication system (trfAp), and mating pair formation system (traF and traG) were all influenced by CO2, facilitating the mobilization and channel transfer of plasmid. Furthermore, the presence of CO2 induced the release of intracellular Ca2+ and increased the transmembrane potential of recipients, which contributed to the increased proton motive force (PMF), providing more power for DNA uptake. This is the first study addressing the potential risks of increased CO2 on the propagation of ARGs, which provides a new insight into the concerns of anthropogenic CO2 emissions and CO2 storage.
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Affiliation(s)
- Junqi Liao
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Haining Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
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9
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Zhou X, Yan Q, Wang N. Deciphering the regulon of a GntR family regulator via transcriptome and ChIP-exo analyses and its contribution to virulence in Xanthomonas citri. MOLECULAR PLANT PATHOLOGY 2017; 18:249-262. [PMID: 26972728 PMCID: PMC6638223 DOI: 10.1111/mpp.12397] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/08/2016] [Accepted: 03/07/2016] [Indexed: 05/14/2023]
Abstract
Xanthomonas contains a large group of plant-associated species, many of which cause severe diseases on important crops worldwide. Six gluconate-operon repressor (GntR) family transcriptional regulators are predicted in Xanthomonas, one of which, belonging to the YtrA subfamily, plays a prominent role in bacterial virulence. However, the direct targets and comprehensive regulatory profile of YtrA remain unknown. Here, we performed microarray and high-resolution chromatin immunoprecipitation-exonuclease (ChIP-exo) experiments to identify YtrA direct targets and its DNA binding motif in X. citri ssp. citri (Xac), the causal agent of citrus canker. Integrative microarray and ChIP-exo data analysis revealed that YtrA directly regulates three operons by binding to a palindromic motif GGTG-N16 -CACC at the promoter region. A similar palindromic motif and YtrA homologues were also identified in many other bacteria, including Stenotrophomonas, Pseudoxanthomonas and Frateuria, indicating a widespread phenomenon. Deletion of ytrA in Xac abolishes bacterial virulence and induction of the hypersensitive response (HR). We found that YtrA regulates the expression of hrp/hrc genes encoding the bacterial type III secretion system (T3SS) and controls multiple biological processes, including motility and adhesion, oxidative stress, extracellular enzyme production and iron uptake. YtrA represses the expression of its direct targets in artificial medium or in planta. Importantly, over-expression of yro3, one of the YtrA directly regulated operons which contains trmL and XAC0231, induced weaker canker symptoms and down-regulation of hrp/hrc gene expression, suggesting a negative regulation in Xac virulence and T3SS. Our study has significantly advanced the mechanistic understanding of YtrA regulation and its contribution to bacterial virulence.
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Affiliation(s)
- Xiaofeng Zhou
- Citrus Research and Education CenterDepartment of Microbiology and Cell Science, IFAS, University of Florida700 Experiment Station RoadLake AlfredFL33850USA
| | - Qing Yan
- Citrus Research and Education CenterDepartment of Microbiology and Cell Science, IFAS, University of Florida700 Experiment Station RoadLake AlfredFL33850USA
| | - Nian Wang
- Citrus Research and Education CenterDepartment of Microbiology and Cell Science, IFAS, University of Florida700 Experiment Station RoadLake AlfredFL33850USA
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10
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Zhang Y, Gu AZ, He M, Li D, Chen J. Subinhibitory Concentrations of Disinfectants Promote the Horizontal Transfer of Multidrug Resistance Genes within and across Genera. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:570-580. [PMID: 27997135 DOI: 10.1021/acs.est.6b03132] [Citation(s) in RCA: 253] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The greater abundances of antibiotic resistance genes (ARGs) in point-of-use tap and reclaimed water than that in freshly treated water raise the question whether residual disinfectants in distribution systems facilitate the spread of ARGs. This study investigated three widely used disinfectants (free chlorine, chloramine, and hydrogen peroxide) on promoting ARGs transfer within Escherichia coli strains and across genera from Escherichia coli to Salmonella typhimurium. The results demonstrated that subinhibitory concentrations (lower than minimum inhibitory concentrations [MICs]) of these disinfectants, namely 0.1-1 mg/L Cl2 for free chlorine, 0.1-1 mg/L Cl2 for chloramine, and 0.24-3 mg/L H2O2, led to concentration-dependent increases in intragenera conjugative transfer by 3.4-6.4, 1.9-7.5, and 1.4-5.4 folds compared with controls, respectively. By comparison, the intergenera conjugative frequencies were slightly increased by approximately 1.4-2.3 folds compared with controls. However, exposure to disinfectants concentrations higher than MICs significantly suppressed conjugative transfer. This study provided evidence and insights into possible underlying mechanisms for enhanced conjugative transfer, which involved intracellular reactive oxygen species formation, SOS response, increased cell membrane permeability, and altered expressions of conjugation-relevant genes. The results suggest that certain oxidative chemicals, such as disinfectants, accelerate ARGs transfer and therefore justify motivations in evaluating disinfection alternatives for controlling antibiotic resistance. This study also triggers questions regarding the potential role of environmental chemicals in the global spread of antibiotic resistance.
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Affiliation(s)
- Ye Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University , Shanghai 200433, China
| | - April Z Gu
- Department of Civil and Environmental Engineering, Northeastern University , Boston, Massachusetts 02115, United States
| | - Miao He
- Environmental Simulation and Pollution Control (ESPC) State Key Joint Laboratory, School of Environment, Tsinghua University , Beijing 100084, China
| | - Dan Li
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University , Shanghai 200433, China
| | - Jianmin Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University , Shanghai 200433, China
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11
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Rajasekar KV, Lovering AL, Dancea F, Scott DJ, Harris SA, Bingle LEH, Roessle M, Thomas CM, Hyde EI, White SA. Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator. Nucleic Acids Res 2016; 44:4947-56. [PMID: 27016739 PMCID: PMC4889941 DOI: 10.1093/nar/gkw191] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 03/08/2016] [Accepted: 03/11/2016] [Indexed: 12/03/2022] Open
Abstract
The IncP (Incompatibility group P) plasmids are important carriers in the spread of antibiotic resistance across Gram-negative bacteria. Gene expression in the IncP-1 plasmids is stringently controlled by a network of four global repressors, KorA, KorB, TrbA and KorC interacting cooperatively. Intriguingly, KorA and KorB can act as co-repressors at varying distances between their operators, even when they are moved to be on opposite sides of the DNA. KorA is a homodimer with the 101-amino acid subunits, folding into an N-terminal DNA-binding domain and a C-terminal dimerization domain. In this study, we have determined the structures of the free KorA repressor and two complexes each bound to a 20-bp palindromic DNA duplex containing its consensus operator sequence. Using a combination of X-ray crystallography, nuclear magnetic resonance spectroscopy, SAXS and molecular dynamics calculations, we show that the linker between the two domains is very flexible and the protein remains highly mobile in the presence of DNA. This flexibility allows the DNA-binding domains of the dimer to straddle the operator DNA on binding and is likely to be important in cooperative binding to KorB. Unexpectedly, the C-terminal domain of KorA is structurally similar to the dimerization domain of the tumour suppressor p53.
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Affiliation(s)
- Karthik V Rajasekar
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Andrew L Lovering
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Felician Dancea
- School of Cancer Studies, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - David J Scott
- School of Biosciences, Sutton Bonington Campus, University of Nottingham, Nottingham LE12 5RD, UK
| | - Sarah A Harris
- School of Physics and Astronomy and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Lewis E H Bingle
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | - Christopher M Thomas
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Eva I Hyde
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Scott A White
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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Suvorova IA, Korostelev YD, Gelfand MS. GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution. PLoS One 2015; 10:e0132618. [PMID: 26151451 PMCID: PMC4494728 DOI: 10.1371/journal.pone.0132618] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/16/2015] [Indexed: 12/03/2022] Open
Abstract
The GntR family of transcription factors (TFs) is a large group of proteins present in diverse bacteria and regulating various biological processes. Here we use the comparative genomics approach to reconstruct regulons and identify binding motifs of regulators from three subfamilies of the GntR family, FadR, HutC, and YtrA. Using these data, we attempt to predict DNA-protein contacts by analyzing correlations between binding motifs in DNA and amino acid sequences of TFs. We identify pairs of positions with high correlation between amino acids and nucleotides for FadR, HutC, and YtrA subfamilies and show that the most predicted DNA-protein interactions are quite similar in all subfamilies and conform well to the experimentally identified contacts formed by FadR from E. coli and AraR from B. subtilis. The most frequent predicted contacts in the analyzed subfamilies are Arg-G, Asn-A, Asp-C. We also analyze the divergon structure and preferred site positions relative to regulated genes in the FadR and HutC subfamilies. A single site in a divergon usually regulates both operons and is approximately in the middle of the intergenic area. Double sites are either involved in the co-operative regulation of both operons and then are in the center of the intergenic area, or each site in the pair independently regulates its own operon and tends to be near it. We also identify additional candidate TF-binding boxes near palindromic binding sites of TFs from the FadR, HutC, and YtrA subfamilies, which may play role in the binding of additional TF-subunits.
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Affiliation(s)
- Inna A. Suvorova
- Research and Training Center on Bioinformatics, Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia
- * E-mail:
| | - Yuri D. Korostelev
- Research and Training Center on Bioinformatics, Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia
| | - Mikhail S. Gelfand
- Research and Training Center on Bioinformatics, Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
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Malhotra S, Sowdhamini R. Re-visiting protein-centric two-tier classification of existing DNA-protein complexes. BMC Bioinformatics 2012; 13:165. [PMID: 22800292 PMCID: PMC3472317 DOI: 10.1186/1471-2105-13-165] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 03/26/2012] [Indexed: 01/28/2023] Open
Abstract
Background Precise DNA-protein interactions play most important and vital role in maintaining the normal physiological functioning of the cell, as it controls many high fidelity cellular processes. Detailed study of the nature of these interactions has paved the way for understanding the mechanisms behind the biological processes in which they are involved. Earlier in 2000, a systematic classification of DNA-protein complexes based on the structural analysis of the proteins was proposed at two tiers, namely groups and families. With the advancement in the number and resolution of structures of DNA-protein complexes deposited in the Protein Data Bank, it is important to revisit the existing classification. Results On the basis of the sequence analysis of DNA binding proteins, we have built upon the protein centric, two-tier classification of DNA-protein complexes by adding new members to existing families and making new families and groups. While classifying the new complexes, we also realised the emergence of new groups and families. The new group observed was where β-propeller was seen to interact with DNA. There were 34 SCOP folds which were observed to be present in the complexes of both old and new classifications, whereas 28 folds are present exclusively in the new complexes. Some new families noticed were NarL transcription factor, Z-α DNA binding proteins, Forkhead transcription factor, AP2 protein, Methyl CpG binding protein etc. Conclusions Our results suggest that with the increasing number of availability of DNA-protein complexes in Protein Data Bank, the number of families in the classification increased by approximately three fold. The folds present exclusively in newly classified complexes is suggestive of inclusion of proteins with new function in new classification, the most populated of which are the folds responsible for DNA damage repair. The proposed re-visited classification can be used to perform genome-wide surveys in the genomes of interest for the presence of DNA-binding proteins. Further analysis of these complexes can aid in developing algorithms for identifying DNA-binding proteins and their family members from mere sequence information.
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Affiliation(s)
- Sony Malhotra
- National Centre for Biological Sciences, UAS-GKVK Campus, Bangalore 560 065, India
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Kolatka K, Kubik S, Rajewska M, Konieczny I. Replication and partitioning of the broad-host-range plasmid RK2. Plasmid 2010; 64:119-34. [DOI: 10.1016/j.plasmid.2010.06.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 06/08/2010] [Accepted: 06/21/2010] [Indexed: 11/27/2022]
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Frost LS, Koraimann G. Regulation of bacterial conjugation: balancing opportunity with adversity. Future Microbiol 2010; 5:1057-71. [PMID: 20632805 DOI: 10.2217/fmb.10.70] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Conjugative plasmids are involved in the dissemination of important traits such as antibiotic resistance, virulence determinants and metabolic pathways involved in adapting to environmental niches, a process termed horizontal or lateral gene transfer. Conjugation is the process of transferring DNA from a donor to a recipient cell with the establishment of the incoming DNA and its cargo of genetic traits within the transconjugant. Conjugation is mediated by self-transmissible plasmids as well as phage-like sequences that have been integrated into the bacterial chromosome, such as integrative and conjugative elements (ICEs) that now include conjugative transposons. Both conjugative plasmids and ICEs can mediate the transfer of mobilizable elements by sharing their conjugative machinery. Conjugation can either be induced, usually by small molecules or peptides or by excision of the ICE from the host chromosome, or it can be tightly regulated by plasmid- and host-encoded factors. The transfer potential of these transfer regions depends on the integration of many signals in response to environmental and physiological cues. This review will focus on the mechanisms that influence transfer potential in these systems, particularly those of the IncF incompatibility group.
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Affiliation(s)
- Laura S Frost
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada.
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Hultdin UW, Lindberg S, Grundström C, Huang S, Uhlin BE, Sauer-Eriksson AE. Structure of FocB - a member of a family of transcription factors regulating fimbrial adhesin expression in uropathogenic Escherichia coli. FEBS J 2010; 277:3368-81. [DOI: 10.1111/j.1742-4658.2010.07742.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS. Origins of specificity in protein-DNA recognition. Annu Rev Biochem 2010; 79:233-69. [PMID: 20334529 DOI: 10.1146/annurev-biochem-060408-091030] [Citation(s) in RCA: 656] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Specific interactions between proteins and DNA are fundamental to many biological processes. In this review, we provide a revised view of protein-DNA interactions that emphasizes the importance of the three-dimensional structures of both macromolecules. We divide protein-DNA interactions into two categories: those when the protein recognizes the unique chemical signatures of the DNA bases (base readout) and those when the protein recognizes a sequence-dependent DNA shape (shape readout). We further divide base readout into those interactions that occur in the major groove from those that occur in the minor groove. Analogously, the readout of the DNA shape is subdivided into global shape recognition (for example, when the DNA helix exhibits an overall bend) and local shape recognition (for example, when a base pair step is kinked or a region of the minor groove is narrow). Based on the >1500 structures of protein-DNA complexes now available in the Protein Data Bank, we argue that individual DNA-binding proteins combine multiple readout mechanisms to achieve DNA-binding specificity. Specificity that distinguishes between families frequently involves base readout in the major groove, whereas shape readout is often exploited for higher resolution specificity, to distinguish between members within the same DNA-binding protein family.
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Affiliation(s)
- Remo Rohs
- Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
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