1
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Chen MM, Zhang YQ, Cheng LC, Zhao FJ, Wang P. Photoaged nanoplastics with multienzyme-like activities significantly shape the horizontal transfer of antibiotic resistance genes. JOURNAL OF HAZARDOUS MATERIALS 2024; 475:134884. [PMID: 38878434 DOI: 10.1016/j.jhazmat.2024.134884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/17/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024]
Abstract
Nanoplastics (NPs), identified as emerging pollutants, pose a great risk to environment and global public health, exerting profound influences on the prevalence and dissemination of antibiotic resistance genes (ARGs). Despite evidence suggesting that nano-sized plastic particles can facilitate the horizontal gene transfer (HGT) of ARGs, it is imperative to explore strategies for inhibiting the transfer of ARGs. Currently, limited information exists regarding the characteristics of environmentally aged NPs and their impact on ARGs propagation. Herein, we investigated the impact of photo-aged NPs on the transfer of ARG-carrying plasmids into Escherichia coli (E. coli) cells. Following simulated sunlight irradiation, photo-aged nano-sized polystyrene plastics (PS NPs) exhibited multiple enzyme-like activities, including peroxidase (POD) and oxidase (OXD), leading to a burst of reactive oxygen species (ROS). At relatively low concentrations (0.1, 1 μg/mL), both pristine and aged PS NPs facilitated the transfer of pUC19 and pHSG396 plasmids within E. coli due to moderate ROS production and enhanced cell membrane permeability. Intriguingly, at relatively high concentrations (5, 10 μg/mL), aged PS NPs significantly suppressed plasmids transformation. The non-unidirectional impact of aged PS NPs involved the overproduction of ROS (•OH and •O2-) via nanozyme activity, directly degrading ARGs and damaging plasmid structure. Additionally, oxidative damage to bacteria resulted from the presence of much toxic free radicals, causing physical damage to cell membranes, reduction of the SOS response and restriction of adenosine-triphosphate (ATP) supply, ultimately leading to inactivation of recipient cells. This study unveils the intrinsic multienzyme-like activity of environmentally aged NPs, highlighting their potential to impede the transfer and dissemination of ARGs.
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Affiliation(s)
- Ming-Ming Chen
- Centre for Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan-Qing Zhang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lu-Chen Cheng
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fang-Jie Zhao
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Wang
- Centre for Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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2
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Hu Q, Zhang L, Yang R, Tang J, Dong G. Quaternary ammonium biocides promote conjugative transfer of antibiotic resistance gene in structure- and species-dependent manner. ENVIRONMENT INTERNATIONAL 2024; 189:108812. [PMID: 38878503 DOI: 10.1016/j.envint.2024.108812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 06/03/2024] [Accepted: 06/09/2024] [Indexed: 06/19/2024]
Abstract
The linkage between biocides and antibiotic resistance has been widely suggested in laboratories and various environments. However, the action mechanism of biocides on antibiotic resistance genes (ARGs) spread is still unclear. Thus, 6 quaternary ammonium biocides (QACs) with different bonded substituents or alkyl chain lengths were selected to assess their effects on the conjugation transfer of ARGs in this study. Two conjugation models with the same donor (E. coli DH5α (RP4)) into two receptors, E. coli MG1655 and pathogenic S. sonnei SE6-1, were constructed. All QACs were found to significantly promote intra- and inter-genus conjugative transfer of ARGs, and the frequency was highly impacted by their structure and receptors. At the same environmental exposure level (4 × 10-1 mg/L), didecyl dimethyl ammonium chloride (DDAC (C10)) promoted the most frequency of conjugative transfer, while benzathine chloride (BEC) promoted the least. With the same donor, the enhanced frequency of QACs of intra-transfer is higher than inter-transfer. Then, the acquisition mechanisms of two receptors were further determined using biochemical combined with transcriptome analysis. For the recipient E. coli, the promotion of the intragenus conjugative transfer may be associated with increased cell membrane permeability, reactive oxygen species (ROS) production and proton motive force (PMF)-induced enhancement of flagellar motility. Whereas, the increase of cell membrane permeability and decreased flagellar motility due to PMF disruption but encouraged biofilm formation, maybe the main reasons for promoting intergenus conjugative transfer in the recipient S. sonnei. As one pathogenic bacterium, S. sonnei was first found to acquire ARGs by biocide exposure.
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Affiliation(s)
- Qin Hu
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China
| | - Lilan Zhang
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China.
| | - Rui Yang
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Jialin Tang
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Guoliang Dong
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing 400045, China
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3
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Zhang C, Wang C, Zhao X, Hakizimana I. Effect of resistance difference on distribution of antibiotics in bacterial cell and conjugative gene transfer risks during electrochemical flow through reaction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:163142. [PMID: 36996977 DOI: 10.1016/j.scitotenv.2023.163142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/24/2023] [Accepted: 03/25/2023] [Indexed: 05/13/2023]
Abstract
The occurrences and spread of antibiotic resistance (AR) mediated by horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) in aquatic environment have been aggravated because of the abuse of antibiotics. While the pressure of different antibiotics is known to induce the spread of AR in bacteria, whether distribution of different antibiotics in cell structure could affect HGT risks is not clear. Here, a significant difference between the distribution of tetracycline hydrochloride (Tet) and sulfamethoxazole (Sul) in cell structure during electrochemical flow through reaction (EFTR) process was firstly reported. Meanwhile, EFTR treatment possessed excellent disinfection performance and consequently controlled the HGT risks. The intracellular Tet (iTet) was discharged through efflux pumps to increase the content of extracellular Tet (eTet) due to the resistance of donor E. coli DH5α under the selective pressure of Tet, declining the damage of donor and plasmid RP4. The HGT frequency was 8.18-fold increase compared with that by EFTR treatment alone. While the secretion of intracellular Sul (iSul) was inhibited by blocking the formation of efflux pumps to inactivate the donor under the Sul pressure, and the total content of iSul and adsorbed Sul (aSul) to be 1.36-fold higher than that of eSul. Therefore, the reactive oxygen species (ROS) generation and cell membrane permeability were improved to release ARGs, and •OH attacked plasmid RP4 in the EFTR process, inhibiting the HGT risks. This study advances the awareness of the interaction between distribution of different antibiotics in cell structure and the HGT risks in the EFTR process.
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Affiliation(s)
- Cong Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Can Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China.
| | - Xin Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China.
| | - Israel Hakizimana
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
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4
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Engin AB, Engin ED, Engin A. Effects of co-selection of antibiotic-resistance and metal-resistance genes on antibiotic-resistance potency of environmental bacteria and related ecological risk factors. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 98:104081. [PMID: 36805463 DOI: 10.1016/j.etap.2023.104081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 01/23/2023] [Accepted: 02/12/2023] [Indexed: 06/18/2023]
Abstract
The inadequate elimination of micropollutants in wastewater treatment plants (WWTP), cause to increase in the incidence of antibiotic resistant bacterial strains. Growth of microbial pathogens in WWTP is one of the serious public health problems. The widespread and simultaneous emergence of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment with heavy metals create persistent and selective pressure for co-selection of both genes on environmental microorganisms. Co-localization of ARGs and HMRGs on the same horizontal mobile genetic elements (MGEs) allows the spreading of numerous antibiotic-resistant strains of bacteria in aquatic and terrestrial environment. The biofilm formation and colonization potential of environmental bacteria leads to the co-selection of multi-antibiotic resistance and multi-metal tolerance. Horizontal gene transfer (HGT), co-localization of both ARGs and HMRGs on the same MGEs, and the shared resistomes are important bacteria-associated ecological risks factors, which reduce the effectiveness of antibiotics against bacterial infections.
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Affiliation(s)
- Ayse Basak Engin
- Gazi University, Faculty of Pharmacy, Department of Toxicology, Ankara, Turkey.
| | - Evren Doruk Engin
- Ankara University, Biotechnology Institute, Gumusdere Campus, Kecioren, Ankara, Turkey
| | - Atilla Engin
- Gazi University, Faculty of Medicine, Department of General Surgery, Ankara, Turkey
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5
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Cory MB, Li A, Hurley CM, Hostetler ZM, Venkatesh Y, Jones CM, Petersson EJ, Kohli RM. Engineered RecA Constructs Reveal the Minimal SOS Activation Complex. Biochemistry 2022; 61:2884-2896. [PMID: 36473084 PMCID: PMC9982712 DOI: 10.1021/acs.biochem.2c00505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The SOS response is a bacterial DNA damage response pathway that has been heavily implicated in bacteria's ability to evolve resistance to antibiotics. Activation of the SOS response is dependent on the interaction between two bacterial proteins, RecA and LexA. RecA acts as a DNA damage sensor by forming lengthy oligomeric filaments (RecA*) along single-stranded DNA (ssDNA) in an ATP-dependent manner. RecA* can then bind to LexA, the repressor of SOS response genes, triggering LexA degradation and leading to induction of the SOS response. Formation of the RecA*-LexA complex therefore serves as the key "SOS activation signal." Given the challenges associated with studying a complex involving multiple macromolecular interactions, the essential constituents of RecA* that allow LexA cleavage are not well defined. Here, we leverage head-to-tail linked and end-capped RecA constructs as tools to define the minimal RecA* filament that can engage LexA. In contrast to previously postulated models, we found that as few as three linked RecA units are capable of ssDNA binding, LexA binding, and LexA cleavage. We further demonstrate that RecA oligomerization alone is insufficient for LexA cleavage, with an obligate requirement for ATP and ssDNA binding to form a competent SOS activation signal with the linked constructs. Our minimal system for RecA* highlights the limitations of prior models for the SOS activation signal and offers a novel tool that can inform efforts to slow acquired antibiotic resistance by targeting the SOS response.
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Affiliation(s)
- Michael B. Cory
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Allen Li
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Christina M. Hurley
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zachary M. Hostetler
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yarra Venkatesh
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chloe M. Jones
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rahul M. Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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6
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Ahmed R, Forman-Kay JD. NMR insights into dynamic, multivalent interactions of intrinsically disordered regions: from discrete complexes to condensates. Essays Biochem 2022; 66:863-873. [PMID: 36416859 PMCID: PMC9760423 DOI: 10.1042/ebc20220056] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022]
Abstract
The spatial and temporal organization of interactions between proteins underlie the regulation of most cellular processes. The requirement for such interactions to be specific predisposes a view that protein-protein interactions are relatively static and are formed through the stable complementarity of the interacting partners. A growing body of reports indicate, however, that many interactions lead to fuzzy complexes with an ensemble of conformations in dynamic exchange accounting for the observed binding. Here, we discuss how NMR has facilitated the characterization of these discrete, dynamic complexes and how such characterization has aided the understanding of dynamic, condensed phases of phase-separating proteins with exchanging multivalent interactions.
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Affiliation(s)
- Rashik Ahmed
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Julie D Forman-Kay
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
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7
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Viola MG, Perdikari TM, Trebino CE, Rahmani N, Mathews KL, Pena CM, Chua XY, Xuan B, LaBreck CJ, Fawzi NL, Camberg JL. An enhancer sequence in the intrinsically disordered region of FtsZ promotes polymer-guided substrate processing by ClpXP protease. Protein Sci 2022; 31:e4306. [PMID: 35481648 PMCID: PMC8996474 DOI: 10.1002/pro.4306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 11/09/2022]
Abstract
The essential bacterial division protein in Escherichia coli, FtsZ, assembles into the FtsZ-ring at midcell and recruits other proteins to the division site to promote septation. A region of the FtsZ amino acid sequence that links the conserved polymerization domain to a C-terminal protein interaction site was predicted to be intrinsically disordered and has been implicated in modulating spacing and architectural arrangements of FtsZ filaments. While the majority of cell division proteins that directly bind to FtsZ engage either the polymerization domain or the C-terminal interaction site, ClpX, the recognition and unfolding component of the bacterial ClpXP proteasome, has a secondary interaction with the predicted intrinsically disordered region (IDR) of FtsZ when FtsZ is polymerized. Here, we use NMR spectroscopy and reconstituted degradation reactions in vitro to demonstrate that this linker region is indeed disordered in solution and, further, that amino acids in the IDR of FtsZ enhance the degradation in polymer-guided interactions.
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Affiliation(s)
- Marissa G. Viola
- Department of Cell and Molecular BiologyUniversity of Rhode IslandKingstonRhode IslandUSA
| | | | - Catherine E. Trebino
- Department of Cell and Molecular BiologyUniversity of Rhode IslandKingstonRhode IslandUSA
| | - Negar Rahmani
- Department of Cell and Molecular BiologyUniversity of Rhode IslandKingstonRhode IslandUSA
| | - Kaylee L. Mathews
- Molecular Biology, Cell Biology, & Biochemistry Graduate ProgramBrown UniversityProvidenceRhode IslandUSA
| | - Carolina Mejia Pena
- Molecular Biology, Cell Biology, & Biochemistry Graduate ProgramBrown UniversityProvidenceRhode IslandUSA
| | - Xien Yu Chua
- Department of Molecular Pharmacology, Physiology & BiotechnologyBrown UniversityProvidenceRhode IslandUSA
| | - Botai Xuan
- Department of Molecular Pharmacology, Physiology & BiotechnologyBrown UniversityProvidenceRhode IslandUSA
| | - Christopher J. LaBreck
- Department of Cell and Molecular BiologyUniversity of Rhode IslandKingstonRhode IslandUSA
| | - Nicolas L. Fawzi
- Department of Molecular Pharmacology, Physiology & BiotechnologyBrown UniversityProvidenceRhode IslandUSA
| | - Jodi L. Camberg
- Department of Cell and Molecular BiologyUniversity of Rhode IslandKingstonRhode IslandUSA
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8
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Zhang S, Sun WL, Song HL, Zhang T, Yin M, Wang Q, Zuo X. Effects of voltage on the emergence and spread of antibiotic resistance genes in microbial electrolysis cells: From mutation to horizontal gene transfer. CHEMOSPHERE 2022; 291:132703. [PMID: 34718024 DOI: 10.1016/j.chemosphere.2021.132703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/16/2021] [Accepted: 10/24/2021] [Indexed: 06/13/2023]
Abstract
Microbial electrolysis cells (MECs) are widely considered as promising alternatives for degrading antibiotics. As one of the major operating parameters in MECs, voltage might affect the spread of antibiotic resistance genes (ARGs) given it can affect the physiological characteristics of bacteria. However, little is known about the impacts of voltage on the acceleration of bacterial mutation and the promotion of ARG dissemination via horizontal transfer in MECs. In this study, two voltages (0.9 V and 1.5 V) were applied to identify if electrical stimulation could increase bacterial mutation frequency. Three voltages (0.9 V, 1.5 V, and 2.5 V) were used to evaluate the conjugative transfer frequency of plasmid-encoded the ARGs from the donor (E. coli K-12) to the recipient (E. coli HB101) in MECs. After repeating subculture in MECs for 10 days, the mutation frequency of E. coli K-12 was promoted, consequently, the generated mutants became more resistant against tetracycline. When the voltage was higher than 0.9 V, conjugative ARG transfer frequency was significantly increased in the anode chamber (p < 0.05). The over-production of reactive oxygen species (ROS) (voltage >0.9 V) and cell membrane permeability (voltage >1.5 V) were significantly enhanced under electrical stimulations (p < 0.05). Genome-wide RNA sequencing indicated that the expressions of genes related to oxidative stress and cell membrane were upregulated with exposure to electrical stimulation. Electrical stimulations induced oxidative reactions, which triggered ROS over-production, SOS response, and enhancement of cell membrane permeability for both donor and recipient in the MECs. These findings provide insights into the potential role of voltage in the generation and spread of ARGs in MECs.
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Affiliation(s)
- Shuai Zhang
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CIC-AEET), Nanjing University of Information Science &Technology, Nanjing, 210044, China
| | - Wen-Long Sun
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CIC-AEET), Nanjing University of Information Science &Technology, Nanjing, 210044, China
| | - Hai-Liang Song
- School of Environment, Nanjing Normal University, Jiangsu Engineering Lab of Water and Soil Eco-remediation, Wenyuan Road 1, Nanjing, 210023, China
| | - Ting Zhang
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CIC-AEET), Nanjing University of Information Science &Technology, Nanjing, 210044, China
| | - Minghao Yin
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CIC-AEET), Nanjing University of Information Science &Technology, Nanjing, 210044, China
| | - Qilin Wang
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - XiaoJun Zuo
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CIC-AEET), Nanjing University of Information Science &Technology, Nanjing, 210044, China.
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9
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Li Z, Gao J, Guo Y, Cui Y, Wang Y, Duan W, Wu Z. Enhancement of antibiotic resistance dissemination by artificial sweetener acesulfame potassium: Insights from cell membrane, enzyme, energy supply and transcriptomics. JOURNAL OF HAZARDOUS MATERIALS 2022; 422:126942. [PMID: 34449343 DOI: 10.1016/j.jhazmat.2021.126942] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/09/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
The abuse of antibiotics on animals could induce the development of antibiotic resistant genes (ARGs) and antibiotic resistant bacteria (ARB), and acesulfame potassium (ACE) is the widely used artificial sweetener in animal feed. Generally speaking, ACE and ARB often coexist in livestock wastewater, however, the impact of the co-occurrence of ACE and ARB on the transmission of ARGs is still unknown. In this study, the effects of ACE on vertical gene transfer (VGT) and horizontal gene transfer (HGT) were both evaluated. For VGT, ACE may hinder the spread of sul gene in Pseudomonas HLS-6 by blocking ARB growth. As for HGT (from Escherichia coli DH5α to Pseudomonas HLS-6), environmentally relevant ACE concentration could facilitate the conjugative transfer. The underlying mechanisms of HGT were characterized by enhanced cell membrane permeability, reactive oxygen species overproduction, SOS response, energy supply, which were all further verified by the changes in transcription levels of related genes. Interestingly, intracellular Mg2+ in donor strain was found for the first time as an indicator for the conjugation occurrence in ACE treated mating system. This study may provide new insights into the role of ACE on ARGs proliferation and highlight its potential environmental impacts.
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Affiliation(s)
- Ziqiao Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Jingfeng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China.
| | - Yi Guo
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Yingchao Cui
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Yuwei Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Wanjun Duan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Zejie Wu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
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10
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Chlorine disinfection facilitates natural transformation through ROS-mediated oxidative stress. THE ISME JOURNAL 2021; 15:2969-2985. [PMID: 33941886 PMCID: PMC8091644 DOI: 10.1038/s41396-021-00980-4] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 04/08/2021] [Indexed: 02/01/2023]
Abstract
The bacterial infection that involves antimicrobial resistance is a rising global threat to public health. Chlorine-based water disinfection processes can inactivate antibiotic resistant bacteria. However, at the same time, these processes may cause the release of antibiotic resistance genes into the water as free DNA, and consequently increase the risk to disseminate antibiotic resistance via natural transformation. Presently, little is known about the contribution of residual chlorine affecting the transformation of extracellular antibiotic resistance genes (ARGs). This study investigates whether chloramine and free chlorine promote the transformation of ARGs and how this may occur. We reveal that both chloramine and free chlorine, at practically relevant concentrations, significantly stimulated the transformation of plasmid-encoded ARGs by the recipient Acinetobacter baylyi ADP1, by up to a 10-fold increase. The underlying mechanisms underpinning the increased transformations were revealed. Disinfectant exposure induced a series of cell responses, including increased levels of reactive oxygen species (ROS), bacterial membrane damage, ROS-mediated DNA damage, and increased stress response. These effects thus culminated in the enhanced transformation of ARGs. This promoted transformation was observed when exposing disinfectant-pretreated A. baylyi to free plasmid. In contrast, after pretreating free plasmid with disinfectants, the transformation of ARGs decreased due to the damage of plasmid integrity. These findings provide important insight on the roles of disinfectants affecting the horizontal transfer of ARGs, which could be crucial in the management of antibiotic resistance in our water systems.
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11
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Seychell BC, Beck T. Molecular basis for protein-protein interactions. Beilstein J Org Chem 2021; 17:1-10. [PMID: 33488826 PMCID: PMC7801801 DOI: 10.3762/bjoc.17.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/07/2020] [Indexed: 01/11/2023] Open
Abstract
This minireview provides an overview on the current knowledge of protein-protein interactions, common characterisation methods to characterise them, and their role in protein complex formation with some examples. A deep understanding of protein-protein interactions and their molecular interactions is important for a number of applications, including drug design. Protein-protein interactions and their discovery are thus an interesting avenue for understanding how protein complexes, which make up the majority of proteins, work.
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Affiliation(s)
- Brandon Charles Seychell
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
| | - Tobias Beck
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
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12
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Pu Q, Fan XT, Li H, An XL, Lassen SB, Su JQ. Cadmium enhances conjugative plasmid transfer to a fresh water microbial community. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115903. [PMID: 33120155 DOI: 10.1016/j.envpol.2020.115903] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/14/2020] [Accepted: 10/18/2020] [Indexed: 05/11/2023]
Abstract
Co-selection of antibiotic resistance genes (ARGs) by heavy metals might facilitate the spread of ARGs in the environments. Cadmium contamination is ubiquitous, while, it remains unknown the extent to which cadmium (Cd2+) impact plasmid-mediated transfer of ARGs in aquatic bacterial communities. In the present study, we found that Cd2+ amendment at sub-inhibitory concentration significantly increased conjugation frequency of RP4 plasmid from Pseudomonas putida KT2442 to a fresh water microbial community by liquid mating method. Cd2+ treatment (1-100 mg/L) significantly increased the cell membrane permeability and antioxidant activities of conjugation mixtures. Amendments of 10 and 100 mg/L Cd2+ significantly enhanced the mRNA expression levels of mating pair formation gene (trbBp) and the DNA transfer and replication gene (trfAp) due to the repression of regulatory genes (korA, korB and trbA). Phylogenetic analysis of transconjugants indicated that Proteobacteria was the dominant recipients and high concentration of Cd2+ treatment resulted in expanded recipient taxa. This study suggested that sub-inhibitory Cd2+ contamination would facilitate plasmid conjugation and contributed to the maintenance and spread of plasmid associated ARGs, and highlighted the urgent need for effective remediation of Cd2+ in aquatic environments.
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Affiliation(s)
- Qiang Pu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Xiao-Ting Fan
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Xin-Li An
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Simon Bo Lassen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark; Sino-Danish Center of Education and Research, Beijing, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China.
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13
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Wang Y, Lu J, Engelstädter J, Zhang S, Ding P, Mao L, Yuan Z, Bond PL, Guo J. Non-antibiotic pharmaceuticals enhance the transmission of exogenous antibiotic resistance genes through bacterial transformation. THE ISME JOURNAL 2020; 14:2179-2196. [PMID: 32424247 PMCID: PMC7367833 DOI: 10.1038/s41396-020-0679-2] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 12/19/2022]
Abstract
Antibiotic resistance is a serious global threat for public health. Considering the high abundance of cell-free DNA encoding antibiotic resistance genes (ARGs) in both clinical and environmental settings, natural transformation is an important horizontal gene transfer pathway to transmit antibiotic resistance. It is acknowledged that antibiotics are key drivers for disseminating antibiotic resistance, yet the contributions of non-antibiotic pharmaceuticals on transformation of ARGs are overlooked. In this study, we report that some commonly consumed non-antibiotic pharmaceuticals, at clinically and environmentally relevant concentrations, significantly facilitated the spread of antibiotic resistance through the uptake of exogenous ARGs. This included nonsteroidal anti-inflammatories, ibuprofen, naproxen, diclofenac, the lipid-lowering drug, gemfibrozil, and the β-blocker propranolol. Based on the results of flow cytometry, whole-genome RNA sequencing and proteomic analysis, the enhanced transformation of ARGs was affiliated with promoted bacterial competence, enhanced stress levels, over-produced reactive oxygen species and increased cell membrane permeability. In addition, a mathematical model was proposed and calibrated to predict the dynamics of transformation during exposure to non-antibiotic pharmaceuticals. Given the high consumption of non-antibiotic pharmaceuticals, these findings reveal new concerns regarding antibiotic resistance dissemination exacerbated by non-antibiotic pharmaceuticals.
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Affiliation(s)
- Yue Wang
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ji Lu
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Shuai Zhang
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Pengbo Ding
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Likai Mao
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, 4072, Australia.
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14
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The Mammalian High Mobility Group Protein AT-Hook 2 (HMGA2): Biochemical and Biophysical Properties, and Its Association with Adipogenesis. Int J Mol Sci 2020; 21:ijms21103710. [PMID: 32466162 PMCID: PMC7279267 DOI: 10.3390/ijms21103710] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/30/2020] [Accepted: 05/12/2020] [Indexed: 12/11/2022] Open
Abstract
The mammalian high-mobility-group protein AT-hook 2 (HMGA2) is a small DNA-binding protein and consists of three “AT-hook” DNA-binding motifs and a negatively charged C-terminal motif. It is a multifunctional nuclear protein directly linked to obesity, human height, stem cell youth, human intelligence, and tumorigenesis. Biochemical and biophysical studies showed that HMGA2 is an intrinsically disordered protein (IDP) and could form homodimers in aqueous buffer solution. The “AT-hook” DNA-binding motifs specifically bind to the minor groove of AT-rich DNA sequences and induce DNA-bending. HMGA2 plays an important role in adipogenesis most likely through stimulating the proliferative expansion of preadipocytes and also through regulating the expression of transcriptional factor Peroxisome proliferator-activated receptor γ (PPARγ) at the clonal expansion step from preadipocytes to adipocytes. Current evidence suggests that a main function of HMGA2 is to maintain stemness and renewal capacity of stem cells by which HMGA2 binds to chromosome and lock chromosome into a specific state, to allow the human embryonic stem cells to maintain their stem cell potency. Due to the importance of HMGA2 in adipogenesis and tumorigenesis, HMGA2 is considered a potential therapeutic target for anticancer and anti-obesity drugs. Efforts are taken to identify inhibitors targeting HMGA2.
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15
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Sigalov AB. Letter to the Editor: No folding upon binding of intrinsically disordered proteins: Still interesting but not unique and novel. A commentary on “A novel mode of interaction between intrinsically disordered proteins. by Hibino, E. and Hoshino, M., Biophysics and Physicobiology 17, 86–93 (2020). DOI: 10.2142/biophysico.BSJ-2020012”. Biophys Physicobiol 2020; 17:156-158. [PMID: 33447498 PMCID: PMC7781792 DOI: 10.2142/biophysico.bsj-2020025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/27/2020] [Indexed: 12/01/2022] Open
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16
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Zhang S, Wang Y, Song H, Lu J, Yuan Z, Guo J. Copper nanoparticles and copper ions promote horizontal transfer of plasmid-mediated multi-antibiotic resistance genes across bacterial genera. ENVIRONMENT INTERNATIONAL 2019; 129:478-487. [PMID: 31158594 DOI: 10.1016/j.envint.2019.05.054] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/16/2019] [Accepted: 05/21/2019] [Indexed: 05/21/2023]
Abstract
The spread of antibiotic resistance has become a major concern for public health. As emerging contaminants, various metallic nanoparticles (NPs) and ionic heavy metals have been ubiquitously detected in various environments. Although previous studies have indicated NPs and ionic heavy metals could exhibit co-selection effects for antibiotic resistance, little is known about whether and how they could promote antibiotic resistance spread via horizontal gene transfer across bacterial genera. This study, we report both CuO NPs and copper ions (Cu2+) could stimulate the conjugative transfer of multiple-drug resistance genes. When exposing bacteria to CuO NPs or Cu2+ at environmental-relevant and sub-inhibitory concentrations (e.g., 1-100 μmol/L), conjugation frequencies of plasmid-encoded antibiotic resistance genes across genera (i.e., from Escherichia coli to Pseudomonas putida) were significantly enhanced (p < 0.05). The over-production of reactive oxygen species played a crucial role in promoting conjugative transfer. Genome-wide RNA and protein sequencing suggested expressional levels of genes and proteins related to oxidative stress, cell membrane permeability, and pilus generation were significantly up-regulated under CuO NPs and Cu2+ exposure (p < 0.05). This study provides insights in the contributions of NPs and heavy metals on the spread of antibiotic resistance.
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Affiliation(s)
- Shuai Zhang
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia; School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, No.219, Ningliu Road, Nanjing 210044, China
| | - Yue Wang
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Hailiang Song
- School of Environment, Nanjing Normal University, Jiangsu Engineering Lab of Water and Soil Eco-remediation, Wenyuan Road 1, Nanjing 210023, China
| | - Ji Lu
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia.
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17
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Merle DA, Witternigg A, Tam-Amersdorfer C, Hartlmüller C, Spreitzer E, Schrank E, Wagner-Lichtenegger S, Werzer O, Zangger K, Kungl AJ, Madl T, Meyer NH, Falsone SF. Increased Aggregation Tendency of Alpha-Synuclein in a Fully Disordered Protein Complex. J Mol Biol 2019; 431:2581-2598. [PMID: 31034892 DOI: 10.1016/j.jmb.2019.04.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 01/17/2023]
Abstract
The recent discovery of biologically active fully disordered, so called random fuzzy protein-protein interactions leads to the question of how the high flexibility of these protein complexes correlates to aggregation and pathologic misfolding. We identify the structural mechanism by which a random fuzzy protein complex composed of the intrinsically disordered proteins alpha-Synuclein and SERF1a is able to potentiate cytotoxic aggregation. A structural model derived from an integrated NMR/SAXS analysis of the reconstituted aSyn:SERF1a complex enabled us to observe the partial deprotection of one precise aSyn amyloid nucleation element in the fully unstructured ensemble. This minimal exposure was sufficient to increase the amyloidogenic tendency of SERF1a-bound aSyn. Our findings provide a structural explanation of the previously observed pro-amyloid activity of SERF1a. They further demonstrate that random fuzziness can trigger a structurally organized disease-associated reaction such as amyloid polymerization.
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Affiliation(s)
- David A Merle
- Institute of Chemistry, University of Graz, Heinrichstr. 28, 8010 Graz, Austria
| | - Anja Witternigg
- Institute of Chemistry, University of Graz, Heinrichstr. 28, 8010 Graz, Austria
| | - Carmen Tam-Amersdorfer
- Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Institute of Pathophysiology and Immunology, Medical University of Graz, Heinrichstr, 31, 8010 Graz, Austria
| | - Christoph Hartlmüller
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry Technische Universität München, Lichtenbergstr. 4, 87548, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Emil Spreitzer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Institute of Molecular Biology & Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Evelyne Schrank
- Institute of Chemistry, University of Graz, Heinrichstr. 28, 8010 Graz, Austria
| | - Sabine Wagner-Lichtenegger
- Diagnostic & Research Center for Molecular BioMedicine, Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Neue Stiftingtalstraße 2, 8010 Graz, Austria
| | - Oliver Werzer
- Institute of Pharmaceutical Sciences, University of Graz, Schubertstr. 1, 8010 Graz, Austria
| | - Klaus Zangger
- Institute of Chemistry, University of Graz, Heinrichstr. 28, 8010 Graz, Austria
| | - Andreas J Kungl
- Institute of Pharmaceutical Sciences, University of Graz, Schubertstr. 1, 8010 Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Institute of Molecular Biology & Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria.
| | - N Helge Meyer
- Division of Experimental Allergology and Immunodermatology, Department of Human Medicine, University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany.
| | - S Fabio Falsone
- Institute of Pharmaceutical Sciences, University of Graz, Schubertstr. 1, 8010 Graz, Austria.
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18
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Wang Y, Lu J, Mao L, Li J, Yuan Z, Bond PL, Guo J. Antiepileptic drug carbamazepine promotes horizontal transfer of plasmid-borne multi-antibiotic resistance genes within and across bacterial genera. THE ISME JOURNAL 2019; 13:509-522. [PMID: 30291330 PMCID: PMC6331567 DOI: 10.1038/s41396-018-0275-x] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/18/2018] [Accepted: 08/26/2018] [Indexed: 02/02/2023]
Abstract
Antibiotic resistance is a severe global threat for public health, causing around 700,000 deaths per year. Horizontal gene transfer (HGT) is one of the most significant pathways to disseminate antibiotic resistance. It is commonly acknowledged that sub-minimum inhibition concentrations of antibiotics are major contributors in promoting antibiotic resistance through HGT. Pharmaceuticals are occurring in our environments at increased levels, yet little is known whether non-antibiotic pharmaceuticals cause or accelerate the dissemination of antibiotic resistance. Here, we report for the first time that the antiepileptic drug, carbamazepine, promotes conjugative transfer of antibiotic resistance genes. It was seen that environmentally relevant concentrations of carbamazepine (e.g., 0.05 mg/L) significantly enhanced the conjugative transfer of multiresistance genes carried by plasmid within and across bacterial genera. The underlying mechanisms of the enhanced HGT were revealed by detecting oxidative stress and cell membrane permeability, in combination with MinION DNA sequencing, genome-wide RNA sequencing, and proteomic analysis. Carbamazepine induced a series of acute responses, including increased levels of reactive oxygen species, the SOS response; increased cell membrane permeability, and pilus generation. Expressional levels of genes related to these processes were significantly upregulated during carbamazepine exposure. Given that HGT occurs widely among different species in various environments, these findings are an early warning for a wide assessment of the roles of non-antibiotic pharmaceuticals in the spread of antibiotic resistance.
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Affiliation(s)
- Yue Wang
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Ji Lu
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Likai Mao
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Jie Li
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia.
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19
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The C Terminus of the Ribosomal-Associated Protein LrtA Is an Intrinsically Disordered Oligomer. Int J Mol Sci 2018; 19:ijms19123902. [PMID: 30563168 PMCID: PMC6321479 DOI: 10.3390/ijms19123902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 11/28/2018] [Accepted: 12/02/2018] [Indexed: 01/01/2023] Open
Abstract
The 191-residue-long LrtA protein of Synechocystis sp. PCC 6803 is involved in post-stress survival and in stabilizing 70S ribosomal particles. It belongs to the hibernating promoting factor (HPF) family, intervening in protein synthesis. The protein consists of two domains: The N-terminal region (N-LrtA, residues 1–101), which is common to all the members of the HPF, and seems to be well-folded; and the C-terminal region (C-LrtA, residues 102–191), which is hypothesized to be disordered. In this work, we studied the conformational preferences of isolated C-LrtA in solution. The protein was disordered, as shown by computational modelling, 1D-1H NMR, steady-state far-UV circular dichroism (CD) and chemical and thermal denaturations followed by fluorescence and far-UV CD. Moreover, at physiological conditions, as indicated by several biochemical and hydrodynamic techniques, isolated C-LrtA intervened in a self-association equilibrium, involving several oligomerization reactions. Thus, C-LrtA was an oligomeric disordered protein.
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20
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The chromatin nuclear protein NUPR1L is intrinsically disordered and binds to the same proteins as its paralogue. Biochem J 2018; 475:2271-2291. [DOI: 10.1042/bcj20180365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/16/2018] [Accepted: 06/19/2018] [Indexed: 12/24/2022]
Abstract
NUPR1 is a protumoral multifunctional intrinsically disordered protein (IDP), which is activated during the acute phases of pancreatitis. It interacts with other IDPs such as prothymosin α, as well as with folded proteins such as the C-terminal region of RING1-B (C-RING1B) of the Polycomb complex; in all those interactions, residues around Ala33 and Thr68 (the ‘hot-spot’ region) of NUPR1 intervene. Its paralogue, NUPR1L, is also expressed in response to DNA damage, it is p53-regulated, and its expression down-regulates that of the NUPR1 gene. In this work, we characterized the conformational preferences of isolated NUPR1L and its possible interactions with the same molecular partners of NUPR1. Our results show that NUPR1L was an oligomeric IDP from pH 2.0 to 12.0, as judged by steady-state fluorescence, circular dichroism (CD), dynamic light scattering, 1D 1H-NMR (nuclear magnetic resonance), and as indicated by structural modelling. However, in contrast with NUPR1, there was evidence of local helical- or turn-like structures; these structures were not rigid, as judged by the lack of sigmoidal behaviour in the chemical and thermal denaturation curves obtained by CD and fluorescence. Interestingly enough, NUPR1L interacted with prothymosin α and C-RING1B, and with a similar affinity to that of NUPR1 (in the low micromolar range). Moreover, NUPR1L hetero-associated with NUPR1 with an affinity of 0.4 µM and interacted with the ‘hot-spot’ region of NUPR1. Thus, we suggest that the regulation of NUPR1 gene by NUPR1L does not only happen at the DNA level, but it could also involve direct interactions with NUPR1 natural partners.
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21
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Murison DA, Timson RC, Koleva BN, Ordazzo M, Beuning PJ. Identification of the Dimer Exchange Interface of the Bacterial DNA Damage Response Protein UmuD. Biochemistry 2017; 56:4773-4785. [DOI: 10.1021/acs.biochem.7b00560] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David A. Murison
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Rebecca C. Timson
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Bilyana N. Koleva
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Michael Ordazzo
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Penny J. Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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22
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Structural biology of intrinsically disordered proteins: Revisiting unsolved mysteries. Biochimie 2016; 125:112-8. [PMID: 27004461 DOI: 10.1016/j.biochi.2016.03.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/17/2016] [Indexed: 01/30/2023]
Abstract
The emergence of intrinsically disordered proteins (IDPs) has challenged the classical protein structure-function paradigm by introducing a new paradigm of "coupled binding and folding". This paradigm suggests that IDPs fold upon binding to their partners. Further studies, however, revealed a novel and previously unrecognized phenomenon of "uncoupled binding and folding" suggesting that IDPs do not necessarily fold upon interaction with their lipid and protein partners. The complex and often unusual biophysics of IDPs makes structural characterization of these proteins and their complexes not only challenging but often resulting in opposite conclusions. For this reason, some crucial questions in this field remain unsolved for well over a decade. Considering an important role of IDPs in cellular regulation, signaling and control in health and disease, more efforts are needed to solve these mysteries. Here, I focus on two long-standing contradictions in the literature concerning dimerization and membrane-binding activities of IDPs. Molecular explanation of these discrepancies is provided. I also demonstrate how resolution of these critical issues in the field of IDPs results in our expanded understanding of cell function and has multiple applications in biology and medicine.
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23
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Fuzzy complexes: Specific binding without complete folding. FEBS Lett 2015; 589:2533-42. [PMID: 26226339 DOI: 10.1016/j.febslet.2015.07.022] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/20/2015] [Accepted: 07/21/2015] [Indexed: 12/17/2022]
Abstract
Specific molecular recognition is assumed to require a well-defined set of contacts and devoid of conformational and interaction ambiguities. Growing experimental evidence demonstrates however, that structural multiplicity or dynamic disorder can be retained in protein complexes, termed as fuzziness. Fuzzy regions establish alternative contacts between specific partners usually via transient interactions. Nature often tailors the dynamic properties of these segments via post-translational modifications or alternative splicing to fine-tune affinity. Most experimentally characterized fuzzy complexes are involved in regulation of gene-expression, signal transduction and cell-cycle regulation. Fuzziness is also characteristic to viral protein complexes, cytoskeleton structure, and surprisingly in a few metabolic enzymes. A plausible role of fuzzy complexes in increasing half-life of intrinsically disordered proteins is also discussed.
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24
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Frost L, Baez MAM, Harrilal C, Garabedian A, Fernandez-Lima F, Leng F. The Dimerization State of the Mammalian High Mobility Group Protein AT-Hook 2 (HMGA2). PLoS One 2015; 10:e0130478. [PMID: 26114780 PMCID: PMC4482583 DOI: 10.1371/journal.pone.0130478] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/20/2015] [Indexed: 01/06/2023] Open
Abstract
The mammalian high mobility group protein AT-hook 2 (HMGA2) is a chromosomal architectural transcription factor involved in cell transformation and oncogenesis. It consists of three positively charged “AT-hooks” and a negatively charged C-terminus. Sequence analyses, circular dichroism experiments, and gel-filtration studies showed that HMGA2, in the native state, does not have a defined secondary or tertiary structure. Surprisingly, using combined approaches of 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC) chemical cross-linking, analytical ultracentrifugation, fluorescence resonance energy transfer (FRET), and mass spectrometry, we discovered that HMGA2 is capable of self-associating into homodimers in aqueous buffer solution. Our results showed that electrostatic interactions between the positively charged “AT-hooks” and the negatively charged C-terminus greatly contribute to the homodimer formation.
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Affiliation(s)
- Lorraine Frost
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Maria A. M. Baez
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Christopher Harrilal
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Alyssa Garabedian
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Francisco Fernandez-Lima
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Fenfei Leng
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
- * E-mail:
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25
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Bugay AN, Krasavin EA, Parkhomenko AY, Vasilyeva MA. Modeling nucleotide excision repair and its impact on UV-induced mutagenesis during SOS-response in bacterial cells. J Theor Biol 2015; 364:7-20. [DOI: 10.1016/j.jtbi.2014.08.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/31/2014] [Accepted: 08/22/2014] [Indexed: 02/01/2023]
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26
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Sormanni P, Camilloni C, Fariselli P, Vendruscolo M. The s2D method: simultaneous sequence-based prediction of the statistical populations of ordered and disordered regions in proteins. J Mol Biol 2014; 427:982-996. [PMID: 25534081 DOI: 10.1016/j.jmb.2014.12.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/10/2014] [Accepted: 12/12/2014] [Indexed: 11/18/2022]
Abstract
Extensive amounts of information about protein sequences are becoming available, as demonstrated by the over 79 million entries in the UniProt database. Yet, it is still challenging to obtain proteome-wide experimental information on the structural properties associated with these sequences. Fast computational predictors of secondary structure and of intrinsic disorder of proteins have been developed in order to bridge this gap. These two types of predictions, however, have remained largely separated, often preventing a clear characterization of the structure and dynamics of proteins. Here, we introduce a computational method to predict secondary-structure populations from amino acid sequences, which simultaneously characterizes structure and disorder in a unified statistical mechanics framework. To develop this method, called s2D, we exploited recent advances made in the analysis of NMR chemical shifts that provide quantitative information about the probability distributions of secondary-structure elements in disordered states. The results that we discuss show that the s2D method predicts secondary-structure populations with an average error of about 14%. A validation on three datasets of mostly disordered, mostly structured and partly structured proteins, respectively, shows that its performance is comparable to or better than that of existing predictors of intrinsic disorder and of secondary structure. These results indicate that it is possible to perform rapid and quantitative sequence-based characterizations of the structure and dynamics of proteins through the predictions of the statistical distributions of their ordered and disordered regions.
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Affiliation(s)
- Pietro Sormanni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Piero Fariselli
- Department of Computer Science, University of Bologna, 40127 Bologna, Italy
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27
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Sigalov AB. Unusual biophysics of immune signaling-related intrinsically disordered proteins. SELF NONSELF 2014; 1:271-281. [PMID: 21487502 DOI: 10.4161/self.1.4.13641] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 09/15/2010] [Accepted: 09/15/2010] [Indexed: 11/19/2022]
Abstract
Intrinsically disordered (ID) regions, the regions that lack a well-defined three-dimensional structure under physiological conditions, are preferentially located in the cytoplasmic segments of plasma membrane proteins, many of which are known to be involved in cell signaling. This is in line with our studies that demonstrated that cytoplasmic domains of signaling subunits of immune receptors, including those of ζ, CD3ε, CD3δ and CD3γ chains of T cell receptor, Igα and Igβ chains of B cell receptor as well as the Fc receptor γ chain represent a novel class of ID proteins (IDPs). The domains all have one or more copies of an immunoreceptor tyrosine-based activation motif, tyrosine residues of which are phosphorylated upon receptor engagement in an early and obligatory event in the signaling cascade. Our studies of these IDPs revealed several unusual biophysical phenomena, including (1) the specific dimerization of disordered protein molecules, (2) the fast and slow dimerization equilibrium, depending on the protein, (3) no disorder-to-order transition and the lack of significant chemical shift and peak intensity changes upon dimerization or interaction with a well-folded partner protein and (4) the dual mode of binding to model membranes (with and without folding), depending on the lipid bilayer stability. Here, I highlight several of these studies that not only facilitate a rethinking process of the fundamental paradigms in protein biophysics but also open new perspectives on the molecular mechanisms involved in receptor signaling.
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Homodimerization propensity of the intrinsically disordered N-terminal domain of Ultraspiracle from Aedes aegypti. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1153-66. [PMID: 24704038 DOI: 10.1016/j.bbapap.2014.03.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 03/21/2014] [Accepted: 03/25/2014] [Indexed: 11/20/2022]
Abstract
The mosquito Aedes aegypti is the principal vector of dengue, one of the most devastating arthropod-borne viral infections in humans. The isoform specific A/B region, called the N-terminal domain (NTD), is hypervariable in sequence and length and is poorly conserved within the Ultraspiracle (Usp) family. The Usp protein together with ecdysteroid receptor (EcR) forms a heterodimeric complex. Up until now, there has been little data on the molecular properties of the isolated Usp-NTD. Here, we describe the biochemical and biophysical properties of the recombinant NTD of the Usp isoform B (aaUsp-NTD) from A. aegypti. These results, in combination with in silico bioinformatics approaches, indicate that aaUsp-NTD exhibits properties of an intrinsically disordered protein (IDP). We also present the first experimental evidence describing the dimerization propensity of the isolated NTD of Usp. These characteristics also appear for other members of the Usp family in different species, for example, in the Usp-NTD from Drosophila melanogaster and Bombyx mori. However, aaUsp-NTD exhibits the strongest homodimerization potential. We postulate that the unique dimerization of the NTD might be important for Usp function by providing an additional platform for interactions, in addition to the nuclear receptor superfamily dimerization via DNA binding domains and ligand binding domains that has already been extensively documented. Furthermore, the unique NTD-NTD interaction that was observed might contribute new insight into the dimerization propensities of nuclear receptors.
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Valéry C, Pandey R, Gerrard JA. Protein β-interfaces as a generic source of native peptide tectons. Chem Commun (Camb) 2013; 49:2825-7. [PMID: 23443967 DOI: 10.1039/c3cc39052g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Motifs of 7-8 amino acids were designed from the β-continuous interfaces of non-related homo-oligomeric proteins. These peptides intrinsically self-assembled into nanoarchitectures in water, while retaining some properties of their parent interfaces, especially reversibility of assembly. These results reveal a novel source of native peptide tectons.
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Affiliation(s)
- Céline Valéry
- Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.
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30
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Chaurasiya KR, Ruslie C, Silva MC, Voortman L, Nevin P, Lone S, Beuning PJ, Williams MC. Polymerase manager protein UmuD directly regulates Escherichia coli DNA polymerase III α binding to ssDNA. Nucleic Acids Res 2013; 41:8959-68. [PMID: 23901012 PMCID: PMC3799427 DOI: 10.1093/nar/gkt648] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Replication by Escherichia coli DNA polymerase III is disrupted on encountering DNA damage. Consequently, specialized Y-family DNA polymerases are used to bypass DNA damage. The protein UmuD is extensively involved in modulating cellular responses to DNA damage and may play a role in DNA polymerase exchange for damage tolerance. In the absence of DNA, UmuD interacts with the α subunit of DNA polymerase III at two distinct binding sites, one of which is adjacent to the single-stranded DNA-binding site of α. Here, we use single molecule DNA stretching experiments to demonstrate that UmuD specifically inhibits binding of α to ssDNA. We predict using molecular modeling that UmuD residues D91 and G92 are involved in this interaction and demonstrate that mutation of these residues disrupts the interaction. Our results suggest that competition between UmuD and ssDNA for α binding is a new mechanism for polymerase exchange.
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Affiliation(s)
- Kathy R. Chaurasiya
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Clarissa Ruslie
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Michelle C. Silva
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Lukas Voortman
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Philip Nevin
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Samer Lone
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Penny J. Beuning
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
- *To whom correspondence should be addressed. Tel: +1 617 373 7323; Fax: +1 617 373 2943;
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
- *To whom correspondence should be addressed. Tel: +1 617 373 7323; Fax: +1 617 373 2943;
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31
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Nishi H, Hashimoto K, Madej T, Panchenko AR. Evolutionary, physicochemical, and functional mechanisms of protein homooligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:3-24. [PMID: 23663963 PMCID: PMC3786560 DOI: 10.1016/b978-0-12-386931-9.00001-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Protein homooligomers afford several important benefits for the cell; they mediate and regulate gene expression, activity of many enzymes, ion channels, receptors, and cell-cell adhesion processes. The evolutionary and physical mechanisms of oligomer formation are very diverse and are not well understood. Certain homooligomeric states may be conserved within protein subfamilies and between different subfamilies, therefore providing the specificity to particular substrates while minimizing interactions with unwanted partners. In addition, transitions between different oligomeric states may regulate protein activity and support the switch between different pathways. In this chapter, we summarize the biological importance of homooligomeric assemblies, physicochemical properties of their interfaces, experimental methods for their identification, their evolution, and role in human diseases.
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Affiliation(s)
- Hafumi Nishi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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32
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Abstract
Macromolecular crowding decreases the diffusion rate, shifts the equilibrium of protein-protein and protein-substrate interactions, and changes protein conformational dynamics. Collectively, these effects contribute to enzyme catalysis. Here we describe how crowding may bias the conformational change and dynamics of enzyme populations and in this way affect catalysis. Crowding effects have been studied using artificial crowding agents and in vivo-like environments. These studies revealed a correlation between protein dynamics and function in the crowded environment. We suggest that crowded environments be classified into uniform crowding and structured crowding. Uniform crowding represents random crowding conditions created by synthetic particles with a narrow size distribution. Structured crowding refers to the highly coordinated cellular environment, where proteins and other macromolecules are clustered and organized. In structured crowded environments the perturbation of protein thermal stability may be lower; however, it may still be able to modulate functions effectively and dynamically. Dynamic, allosteric enzymes could be more sensitive to cellular perturbations if their free energy landscape is flatter around the native state; on the other hand, if their free energy landscape is rougher, with high kinetic barriers separating deep minima, they could be more robust. Above all, cells are structured; and this holds both for the cytosol and for the membrane environment. The crowded environment is organized, which limits the search, and the crowders are not necessarily inert. More likely, they too transmit allosteric effects, and as such play important functional roles. Overall, structured cellular crowding may lead to higher enzyme efficiency and specificity.
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Affiliation(s)
- Judith Klinman
- Department of Chemistry Department of Molecular and Cell Biology, University of California The california institute for Quantitativ, Berkeley, CA, USA
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33
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Dimer exchange and cleavage specificity of the DNA damage response protein UmuD. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:611-20. [PMID: 23220418 DOI: 10.1016/j.bbapap.2012.11.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 11/01/2012] [Accepted: 11/27/2012] [Indexed: 11/23/2022]
Abstract
The cellular response to DNA damage in Escherichia coli is controlled in part by the activity of the umuD gene products. The full-length dimeric UmuD(2) is the initial product that is expressed shortly after the induction of the SOS response and inhibits bacterial mutagenesis, allowing for error-free repair to occur. Over time, the slow auto-cleavage of UmuD(2) to UmuD'(2) promotes mutagenesis to ensure cell survival. The intracellular levels of UmuD(2) and UmuD'(2) are further regulated by degradation in vivo, returning the cell to a non-mutagenic state. To further understand the dynamic regulatory roles of the umuD gene products, we monitored the kinetics of exchange and cleavage of the UmuD(2) and UmuD'(2) homodimers as well as of the UmuDD' heterodimer under equilibrium conditions. We found that the heterodimer is the preferred but not exclusive protein form, and that both the heterodimer and homodimers exhibit slow exchange kinetics which is further inhibited in the presence of interacting partner DinB. In addition, the heterodimer efficiently cleaves to form UmuD'(2). Together, this work reveals an intricate UmuD lifecycle that involves dimer exchange and cleavage in the regulation of the DNA damage response.
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Abstract
Proteins are a remarkable class of molecules that exhibit wide diversity of shapes or topological features that underpin protein interactions and give rise to biological function. In addition to quantitation of abundance levels of proteins in biological systems under a variety of conditions, the field of proteome research has as a primary mission the assignment of function for proteins and if possible, illumination of factors that enable function. For many years, chemical cross-linking methods have been used to provide structural data on single purified proteins and purified protein complexes. However, these methods also offer the alluring possibility to extend capabilities to complex biological samples such as cell lysates or intact living cells where proteins may exhibit native topological features that do not exist in purified form. Recent efforts are beginning to provide glimpses of protein complexes and topologies in cells that suggest continued development will yield novel capabilities to view functional topological features of many proteins and complexes as they exist in cells, tissues, or other complex samples. This review will describe rationale, challenges, and a few success stories along the path of development of cross-linking technologies for measurement of in vivo protein interaction topologies.
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Affiliation(s)
- James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA.
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35
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Hare JM, Adhikari S, Lambert KV, Hare AE, Grice AN. The Acinetobacter regulatory UmuDAb protein cleaves in response to DNA damage with chimeric LexA/UmuD characteristics. FEMS Microbiol Lett 2012; 334:57-65. [PMID: 22697494 DOI: 10.1111/j.1574-6968.2012.02618.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 05/21/2012] [Accepted: 06/11/2012] [Indexed: 11/29/2022] Open
Abstract
In the DNA damage response of most bacteria, UmuD forms part of the error-prone (UmuD'(2) )C polymerase V and is activated for this function by self-cleavage after DNA damage. However, the umuD homolog (umuDAb) present throughout the Acinetobacter genus encodes an extra N-terminal region, and in Acinetobacter baylyi, regulates transcription of DNA damage-induced genes. UmuDAb expressed in cells was correspondingly larger (24 kDa) than the Escherichia coli UmuD (15 kDa). DNA damage from mitomycin C or UV exposure caused UmuDAb cleavage in both E. coli wild-type and ΔumuD cells on a timescale resembling UmuD, but did not require UmuD. Like the self-cleaving serine proteases LexA and UmuD, UmuDAb required RecA for cleavage. This cleavage produced a UmuDAb' fragment of a size consistent with the predicted cleavage site of Ala83-Gly84. Site-directed mutations at Ala83 abolished cleavage, as did mutations at either the Ser119 or Lys156 predicted enzymatic residues. Co-expression of the cleavage site mutant and an enzymatic mutant did not allow cleavage, demonstrating a strictly intramolecular mechanism of cleavage that more closely resembles the LexA-type repressors than UmuD. These data show that UmuDAb undergoes a post-translational, LexA-like cleavage event after DNA damage, possibly to achieve its regulatory action.
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Affiliation(s)
- Janelle M Hare
- Department of Biology and Chemistry, Morehead State University, KY, USA.
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36
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Silva MC, Nevin P, Ronayne EA, Beuning PJ. Selective disruption of the DNA polymerase III α-β complex by the umuD gene products. Nucleic Acids Res 2012; 40:5511-22. [PMID: 22406830 PMCID: PMC3384344 DOI: 10.1093/nar/gks229] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA polymerase III (DNA pol III) efficiently replicates the Escherichia coli genome, but it cannot bypass DNA damage. Instead, translesion synthesis (TLS) DNA polymerases are employed to replicate past damaged DNA; however, the exchange of replicative for TLS polymerases is not understood. The umuD gene products, which are up-regulated during the SOS response, were previously shown to bind to the α, β and ε subunits of DNA pol III. Full-length UmuD inhibits DNA replication and prevents mutagenic TLS, while the cleaved form UmuD' facilitates mutagenesis. We show that α possesses two UmuD binding sites: at the N-terminus (residues 1-280) and the C-terminus (residues 956-975). The C-terminal site favors UmuD over UmuD'. We also find that UmuD, but not UmuD', disrupts the α-β complex. We propose that the interaction between α and UmuD contributes to the transition between replicative and TLS polymerases by removing α from the β clamp.
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Affiliation(s)
- Michelle C Silva
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
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37
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Fuxreiter M, Tompa P. Fuzzy Complexes: A More Stochastic View of Protein Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 725:1-14. [DOI: 10.1007/978-1-4614-0659-4_1] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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38
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Affiliation(s)
- Monika Fuxreiter
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary.
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39
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Lee KAW. Molecular recognition by the EWS transcriptional activation domain. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 725:106-25. [PMID: 22399321 DOI: 10.1007/978-1-4614-0659-4_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Interactions between Intrinsically Disordered Protein Regions (IDRs) and their targets commonly exhibit localised contacts via target-induced disorder to order transitions. Other more complex IDR target interactions have been termed "fuzzy" because the IDR does not form a well-defined induced structure. In some remarkable cases of fuzziness IDR function is apparently sequence independent and conferred by amino acid composition. Such cases have been referred to as "random fuzziness" but the molecular features involved are poorly characterised. The transcriptional activation domain (EAD) of oncogenic Ewing's Sarcoma Fusion Proteins (EFPs) is an ≈280 residue IDR with a biased composition restricted to Ala, Gly, Gln, Pro, Ser, Thr and Tyr. Multiple aromatic side chains (exclusively from Try residues) and the particular EAD composition are crucial for molecular recognition but there appears to be no other major geometrically constrained requirement. Computational analysis of the EAD using PONDR (Molecular Kinetics, Inc. http://www.pondr. com) complements the functional data and shows, accordingly, that propensity for structural order within the EAD is conferred by Tyr residues. To conclude, molecular recognition by the EAD is extraordinarily malleable and involves multiple aromatic contacts facilitated by a flexible peptide backbone and, most likely, a limited number of weaker contributions from amenable side chains. I propose to refer to this mode of fuzzy recognition as "polyaromatic", noting that it shares some fundamental features with the "polyelectrostatic" (phosphorylation-dependent) interaction of the Sic1 Cdk inhibitor and Cdc4._I will also speculate on more detailed models for molecular recognition by the EAD and their relationship to native (non-oncogenic) EAD function.
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Affiliation(s)
- Kevin A W Lee
- Department of Biology, Hong Kong University of Science and Technology, Hong Kong, China.
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40
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Sigalov AB. Interplay Between Protein Order, Disorder and Oligomericity in Receptor Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 725:50-73. [DOI: 10.1007/978-1-4614-0659-4_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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41
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Ollivierre JN, Budil DE, Beuning PJ. Electron spin labeling reveals the highly dynamic N-terminal arms of the SOS mutagenesis protein UmuD. MOLECULAR BIOSYSTEMS 2011; 7:3183-6. [PMID: 21975937 DOI: 10.1039/c1mb05334e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy was used to probe the conformational dynamics of the N-terminal arms of the umuD gene products. We determined that the arms of UmuD(2) display a large degree of motion, are largely unbound from the globular C-terminal domain, and that the free energy of dissociation is +2.1 kJ mol(-1).
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Affiliation(s)
- Jaylene N Ollivierre
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, USA
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42
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Sigalov AB. Uncoupled binding and folding of immune signaling-related intrinsically disordered proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2011; 106:525-36. [DOI: 10.1016/j.pbiomolbio.2011.08.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 08/10/2011] [Indexed: 10/17/2022]
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43
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Hashimoto K, Nishi H, Bryant S, Panchenko AR. Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization. Phys Biol 2011; 8:035007. [PMID: 21572178 DOI: 10.1088/1478-3975/8/3/035007] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Many soluble and membrane proteins form homooligomeric complexes in a cell which are responsible for the diversity and specificity of many pathways, may mediate and regulate gene expression, activity of enzymes, ion channels, receptors, and cell adhesion processes. The evolutionary and physical mechanisms of oligomerization are very diverse and its general principles have not yet been formulated. Homooligomeric states may be conserved within certain protein subfamilies and might be important in providing specificity to certain substrates while minimizing interactions with other unwanted partners. Moreover, recent studies have led to a greater awareness that transitions between different oligomeric states may regulate protein activity and provide the switch between different pathways. In this paper we summarize the biological importance of homooligomeric assemblies, physico-chemical properties of their interfaces, experimental and computational methods for their identification and prediction. We particularly focus on homooligomer evolution and describe the mechanisms to develop new specificities through the formation of different homooligomeric complexes. Finally, we discuss the possible role of oligomeric transitions in the regulation of protein activity and compile a set of experimental examples with such regulatory mechanisms.
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Affiliation(s)
- Kosuke Hashimoto
- National Center for Biotechnology Information, National Library of Medicine, National Institutes ofHealth, Bethesda, MD 20894, USA
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44
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Shemetov AA, Seit-Nebi AS, Gusev NB. Phosphorylation of human small heat shock protein HspB8 (Hsp22) by ERK1 protein kinase. Mol Cell Biochem 2011; 355:47-55. [DOI: 10.1007/s11010-011-0837-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Accepted: 04/15/2011] [Indexed: 11/25/2022]
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45
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Ollivierre JN, Sikora JL, Beuning PJ. The dimeric SOS mutagenesis protein UmuD is active as a monomer. J Biol Chem 2010; 286:3607-17. [PMID: 21118802 DOI: 10.1074/jbc.m110.167254] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The homodimeric umuD gene products play key roles in regulating the cellular response to DNA damage in Escherichia coli. UmuD(2) is composed of 139-amino acid subunits and is up-regulated as part of the SOS response. Subsequently, damage-induced RecA·ssDNA nucleoprotein filaments mediate the slow self-cleavage of the N-terminal 24-amino acid arms yielding UmuD'(2). UmuD(2) and UmuD'(2) make a number of distinct protein-protein contacts that both prevent and facilitate mutagenic translesion synthesis. Wild-type UmuD(2) and UmuD'(2) form exceptionally tight dimers in solution; however, we show that the single amino acid change N41D generates stable, active UmuD and UmuD' monomers that functionally mimic the dimeric wild-type proteins. The UmuD N41D monomer is proficient for cleavage and interacts physically with DNA polymerase IV (DinB) and the β clamp. Furthermore, the N41D variants facilitate UV-induced mutagenesis and promote overall cell viability. Taken together, these observations show that a monomeric form of UmuD retains substantial function in vivo and in vitro.
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Affiliation(s)
- Jaylene N Ollivierre
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
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46
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Ollivierre JN, Fang J, Beuning PJ. The Roles of UmuD in Regulating Mutagenesis. J Nucleic Acids 2010; 2010. [PMID: 20936072 PMCID: PMC2948943 DOI: 10.4061/2010/947680] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Accepted: 08/01/2010] [Indexed: 11/20/2022] Open
Abstract
All organisms are subject to DNA damage from both endogenous and environmental sources. DNA damage that is not fully repaired can lead to mutations. Mutagenesis is now understood to be an active process, in part facilitated by lower-fidelity DNA polymerases that replicate DNA in an error-prone manner. Y-family DNA polymerases, found throughout all domains of life, are characterized by their lower fidelity on undamaged DNA and their specialized ability to copy damaged DNA. Two E. coli Y-family DNA polymerases are responsible for copying damaged DNA as well as for mutagenesis. These DNA polymerases interact with different forms of UmuD, a dynamic protein that regulates mutagenesis. The UmuD gene products, regulated by the SOS response, exist in two principal forms: UmuD(2), which prevents mutagenesis, and UmuD(2)', which facilitates UV-induced mutagenesis. This paper focuses on the multiple conformations of the UmuD gene products and how their protein interactions regulate mutagenesis.
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Affiliation(s)
- Jaylene N Ollivierre
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, 102 Hurtig Hall, Boston, MA 02115, USA
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47
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Woodruff RV, Bomar MG, D'Souza S, Zhou P, Walker GC. The unusual UBZ domain of Saccharomyces cerevisiae polymerase η. DNA Repair (Amst) 2010; 9:1130-41. [PMID: 20837403 DOI: 10.1016/j.dnarep.2010.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 07/19/2010] [Accepted: 08/02/2010] [Indexed: 11/25/2022]
Abstract
Recent research has revealed the presence of ubiquitin-binding domains in the Y family polymerases. The ubiquitin-binding zinc finger (UBZ) domain of human polymerase η is vital for its regulation, localization, and function. Here, we elucidate structural and functional features of the non-canonical UBZ motif of Saccharomyces cerevisiae pol η. Characterization of pol η mutants confirms the importance of the UBZ motif and implies that its function is independent of zinc binding. Intriguingly, we demonstrate that zinc does bind to and affect the structure of the purified UBZ domain, but is not required for its ubiquitin-binding activity. Our finding that this unusual zinc finger is able to interact with ubiquitin even in its apo form adds support to the model that ubiquitin binding is the primary and functionally important activity of the UBZ domain in S. cerevisiae polymerase η. Putative ubiquitin-binding domains, primarily UBZs, are identified in the majority of known pol η homologs. We discuss the implications of our observations for zinc finger structure and pol η regulation.
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Affiliation(s)
- Rachel V Woodruff
- Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, USA
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48
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Foti JJ, Delucia AM, Joyce CM, Walker GC. UmuD(2) inhibits a non-covalent step during DinB-mediated template slippage on homopolymeric nucleotide runs. J Biol Chem 2010; 285:23086-95. [PMID: 20467052 DOI: 10.1074/jbc.m110.115774] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli DinB (DNA polymerase IV) possesses an enzyme architecture resulting in specialized lesion bypass function and the potential for creating -1 frameshifts in homopolymeric nucleotide runs. We have previously shown that the mutagenic potential of DinB is regulated by the DNA damage response protein UmuD(2). In the current study, we employ a pre-steady-state fluorescence approach to gain a mechanistic understanding of DinB regulation by UmuD(2). Our results suggest that DinB, like its mammalian and archaeal orthologs, uses a template slippage mechanism to create single base deletions on homopolymeric runs. With 2-aminopurine as a fluorescent reporter in the DNA substrate, the template slippage reaction results in a prechemistry fluorescence change that is inhibited by UmuD(2). We propose a model in which DNA templates containing homopolymeric nucleotide runs, when bound to DinB, are in an equilibrium between non-slipped and slipped conformations. UmuD(2), when bound to DinB, displaces the equilibrium in favor of the non-slipped conformation, thereby preventing frameshifting and potentially enhancing DinB activity on non-slipped substrates.
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Affiliation(s)
- James J Foti
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Sigalov AB. The SCHOOL of nature: II. Protein order, disorder and oligomericity in transmembrane signaling. SELF/NONSELF 2010; 1:89-102. [PMID: 21487511 PMCID: PMC3065667 DOI: 10.4161/self.1.2.11590] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 02/20/2010] [Accepted: 02/22/2010] [Indexed: 11/19/2022]
Abstract
Recent reports have revealed that many proteins that do not adopt globular structures under native conditions, thus termed intrinsically disordered proteins (IDPs), are involved in cell signaling. Intriguingly, physiologically relevant oligomerization of IDPs has been recently observed and shown to exhibit unique biophysical characteristics, including the lack of significant changes in chemical shift and peak intensity upon binding. In this work, I summarize several distinct features of protein disorder that are especially important as related to receptor-mediated transmembrane signal transduction. I also hypothesize that interactions of IDPs with their protein or lipid partners represent a general biphasic process with the "no disorder-to-order" fast interaction which, depending on the interacting partner, may or may not be accompanied by the slow formation of a secondary structure. Further, I suggest signaling-related functional connections between protein order, disorder, and oligomericity and hypothesize that receptor oligomerization induced or tuned upon ligand binding outside the cell is translated across the membrane into protein oligomerization inside the cell, thus providing a general platform, the Signaling Chain HOmoOLigomerization (SCHOOL) platform, for receptor-mediated signaling. This structures our current multidisciplinary knowledge and views of the mechanisms governing the coupling of recognition to signal transduction and cell response. Importantly, this approach not only reveals previously unrecognized striking similarities in the basic mechanistic principles of function of numerous functionally diverse and unrelated surface membrane receptors, but also suggests the similarity between therapeutic targets, thus opening new horizons for both fundamental and clinically relevant studies.
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Fang J, Rand KD, Silva MC, Wales TE, Engen JR, Beuning PJ. Conformational dynamics of the Escherichia coli DNA polymerase manager proteins UmuD and UmuD'. J Mol Biol 2010; 398:40-53. [PMID: 20206636 DOI: 10.1016/j.jmb.2010.02.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 02/18/2010] [Accepted: 02/23/2010] [Indexed: 01/24/2023]
Abstract
The expression of Escherichia coli umuD gene products is upregulated as part of the SOS response to DNA damage. UmuD is initially produced as a 139-amino-acid protein, which subsequently cleaves off its N-terminal 24 amino acids in a reaction dependent on RecA/single-stranded DNA, giving UmuD'. The two forms of the umuD gene products play different roles in the cell. UmuD is implicated in a primitive DNA damage checkpoint and prevents DNA polymerase IV-dependent -1 frameshift mutagenesis, while the cleaved form facilitates UmuC-dependent mutagenesis via formation of DNA polymerase V (UmuD'(2)C). Thus, the cleavage of UmuD is a crucial switch that regulates replication and mutagenesis via numerous protein-protein interactions. A UmuD variant, UmuD3A, which is noncleavable but is a partial biological mimic of the cleaved form UmuD', has been identified. We used hydrogen-deuterium exchange mass spectrometry (HXMS) to probe the conformations of UmuD, UmuD', and UmuD3A. In HXMS experiments, backbone amide hydrogens that are solvent accessible or not involved in hydrogen bonding become labeled with deuterium over time. Our HXMS results reveal that the N-terminal arm of UmuD, which is truncated in the cleaved form UmuD', is dynamic. Residues that are likely to contact the N-terminal arm show more deuterium exchange in UmuD' and UmuD3A than in UmuD. These observations suggest that noncleavable UmuD3A mimics the cleaved form UmuD' because, in both cases, the arms are relatively unbound from the globular domain. Gas-phase hydrogen exchange experiments, which specifically probe the exchange of side-chain hydrogens and are carried out on shorter timescales than solution experiments, show that UmuD' incorporates more deuterium than either UmuD or UmuD3A. This work indicates that these three forms of the UmuD gene products are highly flexible, which is of critical importance for their many protein interactions.
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Affiliation(s)
- Jing Fang
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
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