1
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Wu Q, Wu GG, Pan KN, Wang XP, Li HY, Tian Z, Jin RC, Fan NS. Beta-blocker drives the conjugative transfer of multidrug resistance genes in pure and complex biological systems. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135403. [PMID: 39096644 DOI: 10.1016/j.jhazmat.2024.135403] [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: 03/19/2024] [Revised: 06/13/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Drug resistance poses a high risk to human health. Extensive use of non-antibiotic drugs contributes to antibiotic resistance genes (ARGs) transfer. However, how they affect the spread of broad-host plasmids in complex biological systems remains unknown. This study investigated the effect of metoprolol on the transfer frequency and host range of ARGs in both intrageneric and intergeneric pure culture systems, as well as in anammox microbiome. The results showed that environmental concentrations of metoprolol significantly promoted the intrageneric and intergeneric conjugative transfer. Initially, metoprolol induced excessive oxidative stress, resulting in high cell membrane permeability and bacterial SOS response. Meanwhile, more pili formation increased the adhesion and contact between bacteria, and the abundance of conjugation-related genes also increased significantly. Activation of the electron transport chain provided more ATP for this energy-consuming process. The underlying mechanism was further verified in the complex anammox conjugative system. Metoprolol induced the enrichment of ARGs and mobile genetic elements. The enhanced bacterial interaction and energy generation facilitated the high conjugative transfer frequency of ARGs. In addition, plasmid-borne ARGs tended to transfer to opportunistic pathogens. This work raises public concerns about the health and ecological risks of non-antibiotic drugs.
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Affiliation(s)
- Qian Wu
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Ge-Ge Wu
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Kai-Nan Pan
- School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
| | - Xue-Ping Wang
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Hong-Yan Li
- School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
| | - Zhe Tian
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China
| | - Ren-Cun Jin
- School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
| | - Nian-Si Fan
- School of Engineering, Hangzhou Normal University, Hangzhou 310018, China.
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2
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Wei Y, Shi D, Chen T, Zhou S, Yang Z, Li H, Yang D, Li J, Jin M. Hypervirulent Klebsiella pneumoniae with a hypermucoviscosity phenotype challenges strategies of water disinfection for its capsular polysaccharides. WATER RESEARCH 2024; 266:122416. [PMID: 39265212 DOI: 10.1016/j.watres.2024.122416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/28/2024] [Accepted: 09/07/2024] [Indexed: 09/14/2024]
Abstract
Due to the strong pathogenicity of hypervirulent Klebsiella pneumoniae (hvKP), its performance against disinfectants in water should be understood to protect public health and ecological environment. Unfortunately, the disinfectant tolerance of hvKP with a hypermucoviscosity (HMV) phenotype is a critical underexplored area. Here, the tolerance of K. pneumoniae isolates to common disinfectants was evaluated, and its underlying mechanisms were clarified. Results showed that hvKP strains with HMV exhibited remarkable tolerance to triclosan (TCS), sodium hypochlorite (NaClO), and benzalkonium bromide (BB), surpassing that of low-virulent K. pneumoniae (lvKP) and Escherichia coli, which is the microbial indicator of drinking water quality. Ct value of NaClO reached 4.41 mg/L·min to kill 4-log hvKP, while the values were 2.52 and 2.28 mg/L·min to achieve 4-log killing of lvKP and E. coli, respectively. The curing of the virulence plasmid from hvKP strain K2044 revealed that capsular polysaccharide (CPS) synthesis, driven by the virulence plasmids, helped mitigate cell membrane injury and bacterial inactivation under NaClO stress; consequently, it provided a protective advantage to hvKP. Enhancing the antioxidative stress system to reduce ROS production and mitigate oxidative stress caused by NaClO further improved the disinfectant resistance of hvKP strains with HMV. This study emphasized that hvKP strains with HMV posed a considerable challenge to disinfection procedure of water treatment. It also revealed that an improved dosage of NaClO ensures bacteria killing, indicating the optimization of the design of water treatment processes involving disinfection strategies and technical parameters should be considered.
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Affiliation(s)
- Yijun Wei
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, No1 Dali Road, Tianjin 300050, China
| | - Danyang Shi
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, No1 Dali Road, Tianjin 300050, China
| | - Tianjiao Chen
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, No1 Dali Road, Tianjin 300050, China
| | - Shuqing Zhou
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, No1 Dali Road, Tianjin 300050, China
| | - Zhongwei Yang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, No1 Dali Road, Tianjin 300050, China
| | - Haibei Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, No1 Dali Road, Tianjin 300050, China
| | - Dong Yang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, No1 Dali Road, Tianjin 300050, China
| | - Junwen Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, No1 Dali Road, Tianjin 300050, China
| | - Min Jin
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, No1 Dali Road, Tianjin 300050, China.
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3
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Zhang M, Wang X, Deng X, Zheng S, Zhang W, He JZ, Yu X, Feng M, Ye C. Viable but non-culturable state formation and resuscitation of different antibiotic-resistant Escherichia coli induced by UV/chlorine. WATER RESEARCH 2024; 261:122011. [PMID: 38959654 DOI: 10.1016/j.watres.2024.122011] [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: 04/13/2024] [Revised: 06/12/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024]
Abstract
The presence of "viable but nonculturable" (VBNC) state and bacterial antibiotic resistance (BAR) both pose significant threats to the safety of drinking water. However, limited data was available that explicitly addressed the contribution of bacterial VBNC state in the maintenance and propagation of BAR. Here, the VBNC state induction and resuscitation of two antibiotic-resistant Escherichia coli K12 strains, one carrying multidrug-resistant plasmid (RP4 E. coli) and the other with chromosomal mutation (RIF E. coli) were characterized by subjecting them to different doses of UV/chlorine. The results illustrated that the induction, resuscitation, and associated mechanisms of VBNC ARB exhibit variations based on resistance determinants. RP4 E. coli exhibited a higher susceptibility to enter VBNC state compared to the RIF E. coli., and most VBNC state and resuscitated RP4 E. coli retained original antibiotic resistance. While, reverse mutation in the rpoB gene was observed in VBNC state and recovered RIF E. coli strains induced by high doses of UV/chlorine treatment, leading to the loss of rifampicin resistance. According to RT-qPCR results, ARGs conferring efflux pumps appeared to play a more significant role in the VBNC state formation of RP4 E. coli and the down-regulation of rpoS gene enhanced the speed at which this plasmid-carrying ARB entered into the dormant state. As to RIF E. coli, the induction of VBNC state was supposed to be regulated by the combination of general stress response, SOS response, stringent response, and TA system. Above all, this study highlights that ARB could become VBNC state during UV/chlorine treatments and retain, in some cases, their ability to spread ARGs. Importantly, compared with chromosomal mutation-mediated ARB, both VBNC and resuscitated state ARB that carries multidrug-resistant plasmids poses more serious health risks. Our study provides insights into the relationship between the VBNC state and the propagation of BAR in drinking water systems.
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Affiliation(s)
- Menglu Zhang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, China; Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou 350007, China; Fujian Sanming Forest Ecosystem National Observation and Research Station, Fujian Normal University, Sanming 365002, China; Fujian Key Laboratory of Pollution Control & Resource Reuse, Fuzhou 350117, China
| | - Xuansen Wang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, China; Fujian Key Laboratory of Pollution Control & Resource Reuse, Fuzhou 350117, China
| | - Xiaofeng Deng
- Fujian Minhuan Testing and Inspection Co., Fuzhou 350000, China
| | - Suxia Zheng
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, China
| | - Weifang Zhang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, China; Fujian Key Laboratory of Pollution Control & Resource Reuse, Fuzhou 350117, China
| | - Ji-Zheng He
- Fujian Sanming Forest Ecosystem National Observation and Research Station, Fujian Normal University, Sanming 365002, China; Fujian Key Laboratory of Pollution Control & Resource Reuse, Fuzhou 350117, China
| | - Xin Yu
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment & Ecology, Xiamen University, Xiamen, 361102, China
| | - Mingbao Feng
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment & Ecology, Xiamen University, Xiamen, 361102, China
| | - Chengsong Ye
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment & Ecology, Xiamen University, Xiamen, 361102, China.
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4
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Long S, Liu X, Xiao J, Ren D, Liu Z, Fu Q, He D, Wang D. Mitigation of Triclocarban Inhibition in Microbial Electrolysis Cell-Assisted Anaerobic Digestion. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:9272-9282. [PMID: 38749055 DOI: 10.1021/acs.est.3c10604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Triclocarban (TCC), as a widely used antimicrobial agent, is accumulated in waste activated sludge at a high level and inhibits the subsequent anaerobic digestion of sludge. This study, for the first time, investigated the effectiveness of microbial electrolysis cell-assisted anaerobic digestion (MEC-AD) in mitigating the inhibition of TCC to methane production. Experimental results showed that 20 mg/L TCC inhibited sludge disintegration, hydrolysis, acidogenesis, and methanogenesis processes and finally reduced methane production from traditional sludge anaerobic digestion by 19.1%. Molecular docking revealed the potential inactivation of binding of TCC to key enzymes in these processes. However, MEC-AD with 0.6 and 0.8 V external voltages achieved much higher methane production and controlled the TCC inhibition to less than 5.8%. TCC in the MEC-AD systems was adsorbed by humic substances and degraded to dichlorocarbanilide, leading to a certain detoxification effect. Methanogenic activities were increased in MEC-AD systems, accompanied by complete VFA consumption. Moreover, the applied voltage promoted cell apoptosis and sludge disintegration to release biodegradable organics. Metagenomic analysis revealed that the applied voltage increased the resistance of electrode biofilms to TCC by enriching functional microorganisms (syntrophic VFA-oxidizing and electroactive bacteria and hydrogenotrophic methanogens), acidification and methanogenesis pathways, multidrug efflux pumps, and SOS response.
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Affiliation(s)
- Sha Long
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, P. R. China
| | - Xuran Liu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, P. R. China
| | - Jun Xiao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, P. R. China
| | - Dejiang Ren
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, P. R. China
| | - Zewei Liu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, P. R. China
| | - Qizi Fu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, P. R. China
| | - Dandan He
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, P. R. China
| | - Dongbo Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, P. R. China
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5
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Cory MB, Li A, Hurley CM, Carman PJ, Pumroy RA, Hostetler ZM, Perez RM, Venkatesh Y, Li X, Gupta K, Petersson EJ, Kohli RM. The LexA-RecA* structure reveals a cryptic lock-and-key mechanism for SOS activation. Nat Struct Mol Biol 2024:10.1038/s41594-024-01317-3. [PMID: 38755298 DOI: 10.1038/s41594-024-01317-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 04/15/2024] [Indexed: 05/18/2024]
Abstract
The bacterial SOS response plays a key role in adaptation to DNA damage, including genomic stress caused by antibiotics. SOS induction begins when activated RecA*, an oligomeric nucleoprotein filament that forms on single-stranded DNA, binds to and stimulates autoproteolysis of the repressor LexA. Here, we present the structure of the complete Escherichia coli SOS signal complex, constituting full-length LexA bound to RecA*. We uncover an extensive interface unexpectedly including the LexA DNA-binding domain, providing a new molecular rationale for ordered SOS gene induction. We further find that the interface involves three RecA subunits, with a single residue in the central engaged subunit acting as a molecular key, inserting into an allosteric binding pocket to induce LexA cleavage. Given the pro-mutagenic nature of SOS activation, our structural and mechanistic insights provide a foundation for developing new therapeutics to slow the evolution of antibiotic resistance.
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Affiliation(s)
- Michael B Cory
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Allen Li
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Christina M Hurley
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter J Carman
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ruth A Pumroy
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Ryann M Perez
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Yarra Venkatesh
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Xinning Li
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Rahul M Kohli
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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6
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Fang Y, Chen C, Cui B, Zhou D. Nanoscale zero-valent iron alleviate antibiotic resistance risk during managed aquifer recharge (MAR) by regulating denitrifying bacterial network. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133238. [PMID: 38134694 DOI: 10.1016/j.jhazmat.2023.133238] [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: 09/15/2023] [Revised: 11/05/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023]
Abstract
The frequent occurrence of antibiotics in reclaimed water is concerning, in the case of managed aquifer recharge (MAR), it inevitably hinders further water purification and accelerates the evolutionary resistance in indigenous bacteria. In this study, we constructed two column reactors and nanoscale zero-valent iron (nZVI) amendment was applied for its effects on water quality variation, microbial community succession, and antibiotic resistance genes (ARGs) dissemination, deciphered the underlying mechanism of resistance risk reduction. Results showed that nZVI was oxidized to iron oxides in the sediment column, and total effluent iron concentration was within permissible limits. nZVI enhanced NO3--N removal by 15.5% through enriching denitrifying bacteria and genes, whereas made no effects on oxacillin (OXA) removal. In addition, nZVI exhibited a pivotal impact on ARGs and plasmids decreasing. Network analysis elucidated that the diversity and richness of ARG host declined with nZVI amendment. Denitrifying bacteria play a key role in suppressing horizontal gene transfer (HGT). The underlying mechanisms of inhibited HGT included the downregulated SOS response, the inhibited Type-Ⅳ secretion system and the weakened driving force. This study afforded vital insights into ARG spread control, providing a reference for future applications of nZVI in MAR.
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Affiliation(s)
- Yuanping Fang
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China
| | - Congli Chen
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China
| | - Bin Cui
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China.
| | - Dandan Zhou
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China.
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7
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Aseev LV, Koledinskaya LS, Boni IV. Extraribosomal Functions of Bacterial Ribosomal Proteins-An Update, 2023. Int J Mol Sci 2024; 25:2957. [PMID: 38474204 DOI: 10.3390/ijms25052957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Ribosomal proteins (r-proteins) are abundant, highly conserved, and multifaceted cellular proteins in all domains of life. Most r-proteins have RNA-binding properties and can form protein-protein contacts. Bacterial r-proteins govern the co-transcriptional rRNA folding during ribosome assembly and participate in the formation of the ribosome functional sites, such as the mRNA-binding site, tRNA-binding sites, the peptidyl transferase center, and the protein exit tunnel. In addition to their primary role in a cell as integral components of the protein synthesis machinery, many r-proteins can function beyond the ribosome (the phenomenon known as moonlighting), acting either as individual regulatory proteins or in complexes with various cellular components. The extraribosomal activities of r-proteins have been studied over the decades. In the past decade, our understanding of r-protein functions has advanced significantly due to intensive studies on ribosomes and gene expression mechanisms not only in model bacteria like Escherichia coli or Bacillus subtilis but also in little-explored bacterial species from various phyla. The aim of this review is to update information on the multiple functions of r-proteins in bacteria.
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Affiliation(s)
- Leonid V Aseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
| | | | - Irina V Boni
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
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8
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Lu H, Chen Z, Xie T, Zhong S, Suo S, Song S, Wang L, Xu H, Tian B, Zhao Y, Zhou R, Hua Y. The Deinococcus protease PprI senses DNA damage by directly interacting with single-stranded DNA. Nat Commun 2024; 15:1892. [PMID: 38424107 PMCID: PMC10904395 DOI: 10.1038/s41467-024-46208-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
Bacteria have evolved various response systems to adapt to environmental stress. A protease-based derepression mechanism in response to DNA damage was characterized in Deinococcus, which is controlled by the specific cleavage of repressor DdrO by metallopeptidase PprI (also called IrrE). Despite the efforts to document the biochemical, physiological, and downstream regulation of PprI-DdrO, the upstream regulatory signal activating this system remains unclear. Here, we show that single-stranded DNA physically interacts with PprI protease, which enhances the PprI-DdrO interactions as well as the DdrO cleavage in a length-dependent manner both in vivo and in vitro. Structures of PprI, in its apo and complexed forms with single-stranded DNA, reveal two DNA-binding interfaces shaping the cleavage site. Moreover, we show that the dynamic monomer-dimer equilibrium of PprI is also important for its cleavage activity. Our data provide evidence that single-stranded DNA could serve as the signal for DNA damage sensing in the metalloprotease/repressor system in bacteria. These results also shed light on the survival and acquired drug resistance of certain bacteria under antimicrobial stress through a SOS-independent pathway.
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Affiliation(s)
- Huizhi Lu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zijing Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Teng Xie
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China
| | - Shitong Zhong
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shasha Suo
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shuang Song
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Bing Tian
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Ruhong Zhou
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.
- Department of Chemistry, Columbia University, New York, NY, USA.
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.
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9
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Ruhland E, Siemers M, Gerst R, Späth F, Vogt LN, Figge MT, Papenfort K, Fröhlich KS. The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division. Proc Natl Acad Sci U S A 2024; 121:e2317322121. [PMID: 38377209 PMCID: PMC10907235 DOI: 10.1073/pnas.2317322121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/18/2024] [Indexed: 02/22/2024] Open
Abstract
The ubiquitous RNA chaperone Hfq is involved in the regulation of key biological processes in many species across the bacterial kingdom. In the opportunistic human pathogen Klebsiella pneumoniae, deletion of the hfq gene affects the global transcriptome, virulence, and stress resistance; however, the ligands of the major RNA-binding protein in this species have remained elusive. In this study, we have combined transcriptomic, co-immunoprecipitation, and global RNA interactome analyses to compile an inventory of conserved and species-specific RNAs bound by Hfq and to monitor Hfq-mediated RNA-RNA interactions. In addition to dozens of RNA-RNA pairs, our study revealed an Hfq-dependent small regulatory RNA (sRNA), DinR, which is processed from the 3' terminal portion of dinI mRNA. Transcription of dinI is controlled by the master regulator of the SOS response, LexA. As DinR accumulates in K. pneumoniae in response to DNA damage, the sRNA represses translation of the ftsZ transcript by occupation of the ribosome binding site. Ectopic overexpression of DinR causes depletion of ftsZ mRNA and inhibition of cell division, while deletion of dinR antagonizes cell elongation in the presence of DNA damage. Collectively, our work highlights the important role of RNA-based gene regulation in K. pneumoniae and uncovers the central role of DinR in LexA-controlled division inhibition during the SOS response.
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Affiliation(s)
- Eric Ruhland
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
| | - Malte Siemers
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
| | - Ruman Gerst
- Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology–Hans Knöll Institute, Jena07745, Germany
| | - Felix Späth
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
| | - Laura Nicole Vogt
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
| | - Marc Thilo Figge
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology–Hans Knöll Institute, Jena07745, Germany
| | - Kai Papenfort
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
| | - Kathrin Sophie Fröhlich
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
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10
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Sabei A, Prentiss M, Prévost C. Modeling the Homologous Recombination Process: Methods, Successes and Challenges. Int J Mol Sci 2023; 24:14896. [PMID: 37834348 PMCID: PMC10573387 DOI: 10.3390/ijms241914896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Homologous recombination (HR) is a fundamental process common to all species. HR aims to faithfully repair DNA double strand breaks. HR involves the formation of nucleoprotein filaments on DNA single strands (ssDNA) resected from the break. The nucleoprotein filaments search for homologous regions in the genome and promote strand exchange with the ssDNA homologous region in an unbroken copy of the genome. HR has been the object of intensive studies for decades. Because multi-scale dynamics is a fundamental aspect of this process, studying HR is highly challenging, both experimentally and using computational approaches. Nevertheless, knowledge has built up over the years and has recently progressed at an accelerated pace, borne by increasingly focused investigations using new techniques such as single molecule approaches. Linking this knowledge to the atomic structure of the nucleoprotein filament systems and the succession of unstable, transient intermediate steps that takes place during the HR process remains a challenge; modeling retains a very strong role in bridging the gap between structures that are stable enough to be observed and in exploring transition paths between these structures. However, working on ever-changing long filament systems submitted to kinetic processes is full of pitfalls. This review presents the modeling tools that are used in such studies, their possibilities and limitations, and reviews the advances in the knowledge of the HR process that have been obtained through modeling. Notably, we will emphasize how cooperative behavior in the HR nucleoprotein filament enables modeling to produce reliable information.
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Affiliation(s)
- Afra Sabei
- CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Université de Paris, 13 Rue Pierre et Marie Curie, F-75005 Paris, France;
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, F-75005 Paris, France
| | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA02138, USA;
| | - Chantal Prévost
- CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Université de Paris, 13 Rue Pierre et Marie Curie, F-75005 Paris, France;
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, F-75005 Paris, France
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Cory MB, Jones CM, Shaffer KD, Venkatesh Y, Giannakoulias S, Perez RM, Lougee MG, Hummingbird E, Pagar VV, Hurley CM, Li A, Mach RH, Kohli RM, Petersson EJ. FRETing about the details: Case studies in the use of a genetically encoded fluorescent amino acid for distance-dependent energy transfer. Protein Sci 2023; 32:e4633. [PMID: 36974585 PMCID: PMC10108435 DOI: 10.1002/pro.4633] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
Abstract
Förster resonance energy transfer (FRET) is a valuable method for monitoring protein conformation and biomolecular interactions. Intrinsically fluorescent amino acids that can be genetically encoded, such as acridonylalanine (Acd), are particularly useful for FRET studies. However, quantitative interpretation of FRET data to derive distance information requires careful use of controls and consideration of photophysical effects. Here we present two case studies illustrating how Acd can be used in FRET experiments to study small molecule induced conformational changes and multicomponent biomolecular complexes.
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Affiliation(s)
- Michael B. Cory
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Chloe M. Jones
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Kyle D. Shaffer
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Yarra Venkatesh
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Sam Giannakoulias
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Ryann M. Perez
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Marshall G. Lougee
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Eshe Hummingbird
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Vinayak V. Pagar
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Christina M. Hurley
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Allen Li
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Robert H. Mach
- Department of RadiologyPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Rahul M. Kohli
- Department of Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
- Department of MedicinePerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - E. James Petersson
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
- Department of Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
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Mutate or die: Atomic structures explain bacterial SOS induction. Proc Natl Acad Sci U S A 2023; 120:e2221605120. [PMID: 36693092 PMCID: PMC9945995 DOI: 10.1073/pnas.2221605120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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