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Yin M, Wu Y, Li D, Zhang Y, Bian X, Li J, Pei Y, Cui Y, Li J. Non-filamentous bulking of activated sludge induced by graphene oxide: Insights from extracellular polymeric substances. BIORESOURCE TECHNOLOGY 2024; 399:130574. [PMID: 38471631 DOI: 10.1016/j.biortech.2024.130574] [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: 01/05/2024] [Revised: 03/03/2024] [Accepted: 03/09/2024] [Indexed: 03/14/2024]
Abstract
Widespread use of nanomaterials raises concerns. The underlying mechanism by which graphene oxide (GO) nanoparticles causes poor settleability of activated sludge remains unclear. To explore this mechanism, three reactors with different GO concentrations were established. Extended Derjaguin-Landau-Verwey-Overbeek theory indicated that GO destroyed the property of extracellular polymeric substances (EPS), increasing the energy barrier between bacteria. Low levels of uronic acid and hydrogen bonding in exopolysaccharide weakened the EPS gelation increasing aggregation repulsion. Lager amounts of hydrophilic amino acid and looser structure of extracellular proteins for exposing inner hydrophilic groups significantly contributed to the hydrophilicity of EPS. Both changes implied deterioration in EPS structure under GO stress. Metagenome demonstrated a decrease in genes responsible for capsular polysaccharide colonization and genes regulated the translocation of loose proteins were increased, which increased repulsion between bacteria. This study elucidated that changes in EPS secretion under GO exposure are the underlying causes of poor settleability.
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Affiliation(s)
- Muchen Yin
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Yaodong Wu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Dongyue Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Yanzhuo Zhang
- School of Environment, Henan Key Laboratory for Environmental Pollution Control, Key Laboratory for Yellow River and Huai River Water Environmental Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, China
| | - Xueying Bian
- BGI Engineering Consultants Ltd., Beijing 100038, China
| | - Jiarui Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Yanxue Pei
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Yanan Cui
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Jun Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China.
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2
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Lyu Z, Ling Y, van Hoof A, Ling J. Inactivation of the ribosome assembly factor RimP causes streptomycin resistance and impairs motility in Salmonella. Antimicrob Agents Chemother 2024:e0000224. [PMID: 38629858 DOI: 10.1128/aac.00002-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/27/2024] [Indexed: 05/02/2024] Open
Abstract
The ribosome is the central hub for protein synthesis and the target of many antibiotics. Although the majority of ribosome-targeting antibiotics inhibit protein synthesis and are bacteriostatic, aminoglycosides promote protein mistranslation and are bactericidal. Understanding the resistance mechanisms of bacteria against aminoglycosides is not only vital for improving the efficacy of this critically important group of antibiotics but also crucial for studying the molecular basis of translational fidelity. In this work, we analyzed Salmonella mutants evolved in the presence of the aminoglycoside streptomycin (Str) and identified a novel gene rimP to be involved in Str resistance. RimP is a ribosome assembly factor critical for the maturation of the 30S small subunit that binds Str. Deficiency in RimP increases resistance against Str and facilitates the development of even higher resistance. Deleting rimP decreases mistranslation and cellular uptake of Str and further impairs flagellar motility. Our work thus highlights a previously unknown mechanism of aminoglycoside resistance via defective ribosome assembly.
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Affiliation(s)
- Zhihui Lyu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, Maryland, USA
| | - Yunyi Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, Maryland, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, Maryland, USA
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Veisi R, Nazarian S, Fathi J, Hadi N. Expression and purification of TolC as a recombinant protein vaccine against Shigella flexneri and evaluation of immunogenic response in mice. Microb Pathog 2024; 188:106539. [PMID: 38211835 DOI: 10.1016/j.micpath.2024.106539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/30/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024]
Abstract
BACKGROUND Shigella is one of the major causes of dysenteric diarrhea, which is known shigelosis. Shigelosis causes 160,000 deaths annually of diarrheal disease in the global scale especially children less than 5 years old. No licensed vaccine is available against shigelosis, therefore, efforts for develop an effective and safe vaccine against Shigella as before needed. The reverse vaccinology (RV) is a novel strategy that evaluate genome or proteome of the organism to find a new promising vaccine candidate. In this study, immunogenicity of a designed-recombinant antigen is evaluated through the in silico studies and animal experiments to predict a new immunogenic candidate against Shigella. METHODS In the first step, proteome of Shigella flexneri was obtained from UniProtKB and then the outer membrane and extracellular proteins were predicted. In this study TolC as an outer membrane protein was selected and confirmed among candidates. In next steps, pre-selected protein was evaluated for transmembrane domains, homology, conservation, antigenicity, solubility, and B- and T-cell prediction by different online servers. RESULT TolC as a conserved outer membrane protein, using different immune-informatics tools had acceptable scores and was selected as the immunogenic antigen for animal experiment studies. Recombinant TolC protein after expression and purification, was administered to BALB/c mice over three intraperitoneal routes. The sera of mice was used to evaluate the IgG1 production assay by indirect-ELISA. The immunized mice depicted effective protection against 2LD50 of Shigella. Flexneri ATCC12022 (challenge study). CONCLUSION Therefore, the reverse vaccinology approach and experimental test results demonstrated that TolC as a novel effective and immunogenic antigen is capable for protection against shigellosis.
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Affiliation(s)
- Razieh Veisi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shahram Nazarian
- Department of Biological Sciences, Faculty of Science, Imam Hossein University, Tehran, Iran
| | - Javad Fathi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nahal Hadi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
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4
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Ren J, Wang M, Zhou W, Liu Z. Efflux pumps as potential targets for biofilm inhibition. Front Microbiol 2024; 15:1315238. [PMID: 38596384 PMCID: PMC11002903 DOI: 10.3389/fmicb.2024.1315238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/26/2024] [Indexed: 04/11/2024] Open
Abstract
Biofilms account for a great deal of infectious diseases and contribute significantly to antimicrobial resistance. Efflux pumps confer antimicrobial resistance to microorganisms and involve multiple processes of biofilm formation. Efflux pump inhibitors (EPIs) are attracting considerable attention as a biofilm inhibition strategy. The regulatory functions of efflux pumps in biofilm formation such as mediating adherence, quorum sensing (QS) systems, and the expression of biofilm-associated genes have been increasingly identified. The versatile properties confer efflux pumps both positive and negative effects on biofilm formation. Furthermore, the expression and function of efflux pumps in biofilm formation are species-specific. Therefore, this review aims to detail the double-edged sword role of efflux pumps in biofilm formation to provide potential inhibition targets and give an overview of the effects of EPIs on biofilm formation.
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Affiliation(s)
| | | | - Wenjuan Zhou
- Department of Implantology, Yantai Stomatological Hospital Affiliated to Binzhou Medical University, Yantai, China
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5
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Lyu Z, Ling Y, van Hoof A, Ling J. Deficiency in ribosome biogenesis causes streptomycin resistance and impairs motility in Salmonella. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574728. [PMID: 38260697 PMCID: PMC10802465 DOI: 10.1101/2024.01.08.574728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The ribosome is the central hub for protein synthesis and the target of many antibiotics. Whereas the majority of ribosome-targeting antibiotics inhibit protein synthesis and are bacteriostatic, aminoglycosides promote protein mistranslation and are bactericidal. Understanding the resistance mechanisms of bacteria against aminoglycosides is not only vital for improving the efficacy of this critically important group of antibiotics but also crucial for studying the molecular basis of translational fidelity. In this work, we analyzed Salmonella mutants evolved in the presence of the aminoglycoside streptomycin (Str) and identified a novel gene rimP to be involved in Str resistance. RimP is a ribosome assembly factor critical for the maturation of the 30S small subunit that binds Str. Deficiency in RimP increases resistance against Str and facilitates the development of even higher resistance. Deleting rimP decreases mistranslation and cellular uptake of Str, and further impairs flagellar motility. Our work thus highlights a previously unknown mechanism of aminoglycoside resistance via defective ribosome assembly.
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Affiliation(s)
- Zhihui Lyu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Yunyi Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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Zhang T, Zhang M, Xu Z, He Y, Zhao X, Cheng H, Chen X, Xu J, Ding Z. The Screening of the Protective Antigens of Aeromonas hydrophila Using the Reverse Vaccinology Approach: Potential Candidates for Subunit Vaccine Development. Vaccines (Basel) 2023; 11:1266. [PMID: 37515081 PMCID: PMC10383140 DOI: 10.3390/vaccines11071266] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
The threat of bacterial septicemia caused by Aeromonas hydrophila infection to aquaculture growth can be prevented through vaccination, but differences among A. hydrophila strains may affect the effectiveness of non-conserved subunit vaccines or non-inactivated A. hydrophila vaccines, making the identification and development of conserved antigens crucial. In this study, a bioinformatics analysis of 4268 protein sequences encoded by the A. hydrophila J-1 strain whole genome was performed based on reverse vaccinology. The specific analysis included signal peptide prediction, transmembrane helical structure prediction, subcellular localization prediction, and antigenicity and adhesion evaluation, as well as interspecific and intraspecific homology comparison, thereby screening the 39 conserved proteins as candidate antigens for A. hydrophila vaccine. The 9 isolated A. hydrophila strains from diseased fish were categorized into 6 different molecular subtypes via enterobacterial repetitive intergenic consensus (ERIC)-PCR technology, and the coding regions of 39 identified candidate proteins were amplified via PCR and sequenced to verify their conservation in different subtypes of A. hydrophila and other Aeromonas species. In this way, conserved proteins were screened out according to the comparison results. Briefly, 16 proteins were highly conserved in different A. hydrophila subtypes, of which 2 proteins were highly conserved in Aeromonas species, which could be selected as candidate antigens for vaccines development, including type IV pilus secretin PilQ (AJE35401.1) and TolC family outer membrane protein (AJE35877.1). The present study screened the conserved antigens of A. hydrophila by using reverse vaccinology, which provided basic foundations for developing broad-spectrum protective vaccines of A. hydrophila.
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Affiliation(s)
- Ting Zhang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Key Laboratory of Marine Biotechnology, School of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China
| | - Minying Zhang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Key Laboratory of Marine Biotechnology, School of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China
| | - Zehua Xu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Key Laboratory of Marine Biotechnology, School of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yang He
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang Normal University, Neijiang 641000, China
| | - Xiaoheng Zhao
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Key Laboratory of Marine Biotechnology, School of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China
| | - Hanliang Cheng
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Key Laboratory of Marine Biotechnology, School of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xiangning Chen
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Key Laboratory of Marine Biotechnology, School of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China
| | - Jianhe Xu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Key Laboratory of Marine Biotechnology, School of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China
| | - Zhujin Ding
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Key Laboratory of Marine Biotechnology, School of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Institute of Marine Resources Development, Lianyungang 222005, China
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7
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Yi X, Yang D, Xu X, Wang Y, Guo Y, Zhang M, Wang Y, He Y, Zhu J. Cold plasma pretreatment reinforces the lignocellulose-derived aldehyde inhibitors tolerance and bioethanol fermentability for Zymomonas mobilis. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:102. [PMID: 37322470 DOI: 10.1186/s13068-023-02354-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/29/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Lignocellulose-derived aldehyde inhibitors seriously blocked the biorefinery of biofuels and biochemicals. To date, the economic production of lignocellulose-based products heavily relied on high productivities of fermenting strains. However, it was expensive and time-consuming for the achievable rational modification to strengthen stress tolerance robustness of aldehyde inhibitors. Here, it aimed to improve aldehyde inhibitors tolerance and cellulosic bioethanol fermentability for the chassis Zymomonas mobilis ZM4 pretreated using energy-efficient and eco-friendly cold plasma. RESULTS It was found that bioethanol fermentability was weaker in CSH (corn stover hydrolysates) than that in synthetic medium for Z. mobilis, and thus was attributed to the inhibition of the lignocellulose-derived aldehyde inhibitors in CSH. Convincingly, it further confirmed that the mixed aldehydes severely decreased bioethanol accumulation through additional aldehydes supplementary assays in synthetic medium. After assayed under different processing time (10-30 s), discharge power (80-160 W), and working pressure (120-180 Pa) using cold atmosphere plasma (CAP), it achieved the increased bioethanol fermentability for Z. mobilis after pretreated at the optimized parameters (20 s, 140 W and 165 Pa). It showed that cold plasma brought about three mutation sites including ZMO0694 (E220V), ZMO0843 (L471L) and ZMO0843 (P505H) via Genome resequencing-based SNPs (single nucleotide polymorphisms). A serial of differentially expressed genes (DEGs) were further identified as the potential contributors for stress tolerance via RNA-Seq sequencing, including ZMO0253 and ZMO_RS09265 (type I secretion outer membrane protein), ZMO1941 (Type IV secretory pathway protease TraF-like protein), ZMOr003 and ZMOr006 (16S ribosomal RNA), ZMO0375 and ZMO0374 (levansucrase) and ZMO1705 (thioredoxins). It enriched cellular process, followed by metabolic process and single-organism process for biological process. For KEGG analysis, the mutant was also referred to starch and sucrose metabolism, galactose metabolism and two-component system. Finally, but interestingly, it simultaneously achieved the enhanced stress tolerance capacity of aldehyde inhibitors and bioethanol fermentability in CSH for the mutant Z. mobilis. CONCLUSIONS Of several candidate genetic changes, the mutant Z. mobilis treated with cold plasma was conferred upon the facilitated aldehyde inhibitors tolerance and bioethanol production. This work would provide a strain biocatalyst for the efficient production of lignocellulosic biofuels and biochemicals.
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Affiliation(s)
- Xia Yi
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, Changzhou, 213164, China.
- Institute of Urban and Rural Mining, Changzhou University, Changzhou, 213164, China.
- Changzhou Key Laboratory of Biomass Green, Safe & High Value Utilization Technology, Changzhou University, Changzhou, 213164, Jiangsu, China.
| | - Dong Yang
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Xiaoyan Xu
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Youjun Wang
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Yan Guo
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Meng Zhang
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Yilong Wang
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Yucai He
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, Changzhou, 213164, China.
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China.
| | - Jie Zhu
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, Changzhou, 213164, China.
- Institute of Urban and Rural Mining, Changzhou University, Changzhou, 213164, China.
- Changzhou Key Laboratory of Biomass Green, Safe & High Value Utilization Technology, Changzhou University, Changzhou, 213164, Jiangsu, China.
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China.
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Hajiagha MN, Kafil HS. Efflux pumps and microbial biofilm formation. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023:105459. [PMID: 37271271 DOI: 10.1016/j.meegid.2023.105459] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/06/2023]
Abstract
Biofilm-related infections are resistant forms of pathogens that are regarded as a medical problem, particularly due to the spread of multiple drug resistance. One of the factors associated with biofilm drug resistance is the presence of various types of efflux pumps in bacteria. Efflux pumps also play a role in biofilm formation by influencing Physical-chemical interactions, mobility, gene regulation, quorum sensing (QS), extracellular polymeric substances (EPS), and toxic compound extrusion. According to the findings of studies based on efflux pump expression analysis, their role in the anatomical position within the biofilm will differ depending on the biofilm formation stage, encoding gene expression level, the type and concentration of substrate. In some cases, the function of the efflux pumps can overlap with each other, so it seems necessary to accurate identify the efflux pumps of biofilm-forming bacteria along with their function in this process. Such studies will help to choose treatment strategy, at least in combination with antibiotics. Furthermore, if the goal of treatment is an efflux pump manipulation, we should not limit it to inhibition.
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Affiliation(s)
- Mahdyeh Neghabi Hajiagha
- Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Tumskiy R, Khlebtsov B, Tumskaia A, Evstigneeva S, Antoshkina E, Zakharevich A, Khlebtsov NG. Enhanced Antibacterial Activity of Novel Fluorescent Glutathione-Capped Ag Nanoclusters. Int J Mol Sci 2023; 24:ijms24098306. [PMID: 37176012 PMCID: PMC10179335 DOI: 10.3390/ijms24098306] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Ag nanomaterials are promising candidates for the discovery of next-generation antibiotics with a high antibacterial effect against multi-drug resistant strains. This paper reports a simple synthesis of novel water-soluble glutathione-capped silver nanoclusters (GSH-Ag NCs) with an enhanced antibacterial activity. According to thin layer chromatography (TLC), the synthesized GSH-Ag NCs are an individual fraction of the same composition without any impurities. According to matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) and energy dispersive X-ray (EDX) analyses, the silver core of the GSH-Ag NCs contains approximately 35 silver atoms, and the molecular weight of these nanoclusters is about 11 kDa. The fabricated silver nanoclusters have a reddish fluorescence (λex/λem = 509/645 nm), with a large Stokes shift (>130 nm), and ultra-small size (less than 2 nm) according to transmission electron microscopy (TEM) data and dynamic light scattering (DLS) analysis. The antibacterial activity and minimal inhibitory concentrations of the silver nanoclusters towards Escherichia coli, Staphylococcus aureus, Bacillus cereus and Enterobacter cloacae were evaluated using the agar well-diffusion method and resazurin metabolism assay. The antibacterial activity of chelated silver in the nanoclusters was found to be significantly higher compared to the activity of free silver ions. To explain the possible mechanisms underlying the antibacterial actions of the GSH-Ag nanoclusters, molecular docking was performed, and prospective bacterial targets were identified using AutoDock.
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Affiliation(s)
- Roman Tumskiy
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | - Boris Khlebtsov
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | | | - Stella Evstigneeva
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | - Evgeniya Antoshkina
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences (INEOS RAS), 28 Vavilova Str, Bld.1, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 9 Institutskiy per., 141700 Dolgoprudny, Russia
| | | | - Nikolai G Khlebtsov
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
- Institute of Physics, Saratov State University, 410012 Saratov, Russia
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Fathi J, Amani J, Nazarian S, Hadi N, Mirhosseini SA, Ranjbar R, Abianeh HS. Investigate the immunogenic and protective effect of trivalent chimeric protein containing IpaD-StxB-TolC antigens as a vaccine candidate against S. dysenteri and S. flexneri. Microb Pathog 2023; 178:106066. [PMID: 36924900 DOI: 10.1016/j.micpath.2023.106066] [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: 12/07/2022] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023]
Abstract
BACKGROUND s: Shigella spp. causes bloody diarrhea and leads to death, especially in children. Chimeric proteins containing virulence factors can prevent Shigella infection. The purpose of this study is to investigate the immunogenic and protective effect of trivalent chimeric protein containing IpaD-StxB-TolC antigens against shiga toxin, S. dysenteri and S. flexneri in vitro and in vivo conditions. METHODS Recombinant vector was transferred to E. coli BL21. The expression of the chimeric protein was confirmed by SDS PAGE and purified using the Ni-NTA column. Mice were immunized with recombinant protein and antibody titer was evaluated by ELISA. 10, 25 and 50 LD50 of Shiga toxin neutralization was evaluated in vitro (Vero cell line) and in vivo conditions. Also, the challenge of immunized mice with 10, 25 and 50 LD50 of S. dysentery and S. flexneri was done. RESULTS The expression and purification of the recombinant protein with 60.6 kDa was done. ELISA showed increased antibody titer against the chimeric protein. MTT assay indicated that 1/8000 dilution of the sera had a 51% of cell viability against the toxin in Vero cell line. The challenge of mice immunized with toxin showed that the mice had complete protection against 10 and 25 LD50 of toxin and had 40% survival against 50 LD50. Mice receiving 10 and 25 LD50 of S. dysenteri and S. flexneri had 100% protection and in 50 LD50 the survival rate was 60 and 50%, respectively. Organ burden showed that the amount of bacterial colonization in immunized mice was 1 × 104 CFU/mL, which was significantly different from the control group. CONCLUSION This study showed that chimeric proteins can create favorable immunogenicity in the host as vaccine candidates.
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Affiliation(s)
- Javad Fathi
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Jafar Amani
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Shahram Nazarian
- Department of Biological Sciences, Faculty of Science, Imam Hossein University, Tehran, Iran.
| | - Nahal Hadi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Ali Mirhosseini
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Hossein Samiei Abianeh
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Fang X, Allison KR. Resuscitation dynamics reveal persister partitioning after antibiotic treatment. Mol Syst Biol 2023; 19:e11320. [PMID: 36866643 PMCID: PMC10090945 DOI: 10.15252/msb.202211320] [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: 08/26/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/04/2023] Open
Abstract
Bacteria can survive antibiotics by forming dormant, drug-tolerant persisters. Persisters can resuscitate from dormancy after treatment and prolong infections. Resuscitation is thought to occur stochastically, but its transient, single-cell nature makes it difficult to investigate. We tracked the resuscitation of individual persisters by microscopy after ampicillin treatment and, by characterizing their dynamics, discovered that Escherichia coli and Salmonella enterica persisters resuscitate exponentially rather than stochastically. We demonstrated that the key parameters controlling resuscitation map to the ampicillin concentration during treatment and efflux during resuscitation. Consistently, we observed many persister progeny have structural defects and transcriptional responses indicative of cellular damage, for both β-lactam and quinolone antibiotics. During resuscitation, damaged persisters partition unevenly, generating both healthy daughter cells and defective ones. This persister partitioning phenomenon was observed in S. enterica, Klebsiella pneumoniae, Pseudomonas aeruginosa, and an E. coli urinary tract infection (UTI) isolate. It was also observed in the standard persister assay and after in situ treatment of a clinical UTI sample. This study reveals novel properties of resuscitation and indicates that persister partitioning may be a survival strategy in bacteria that lack genetic resistance.
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Affiliation(s)
- Xin Fang
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA.,Department of Medicine/Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Kyle R Allison
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA.,Department of Medicine/Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
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12
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Sun Z, Heacock-Kang Y, McMillan IA, Cabanas D, Zarzycki-Siek J, Hoang TT. A virulence activator of a surface attachment protein in Burkholderia pseudomallei acts as a global regulator of other membrane-associated virulence factors. Front Microbiol 2023; 13:1063287. [PMID: 36726566 PMCID: PMC9884982 DOI: 10.3389/fmicb.2022.1063287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/30/2022] [Indexed: 01/19/2023] Open
Abstract
Burkholderia pseudomallei (Bp), causing a highly fatal disease called melioidosis, is a facultative intracellular pathogen that attaches and invades a variety of cell types. We previously identified BP1026B_I0091 as a surface attachment protein (Sap1) and an essential virulence factor, contributing to Bp pathogenesis in vitro and in vivo. The expression of sap1 is regulated at different stages of Bp intracellular lifecycle by unidentified regulator(s). Here, we identified SapR (BP1026B_II1046) as a transcriptional regulator that activates sap1, using a high-throughput transposon mutagenesis screen in combination with Tn-Seq. Consistent with phenotypes of the Δsap1 mutant, the ΔsapR activator mutant exhibited a significant reduction in Bp attachment to the host cell, leading to subsequent decreased intracellular replication. RNA-Seq analysis further revealed that SapR regulates sap1. The regulation of sap1 by SapR was confirmed quantitatively by qRT-PCR, which also validated the RNA-Seq data. SapR globally regulates genes associated with the bacterial membrane in response to diverse environments, and some of the genes regulated by SapR are virulence factors that are required for Bp intracellular infection (e.g., type III and type VI secretion systems). This study has identified the complex SapR regulatory network and its importance as an activator of an essential Sap1 attachment factor.
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Affiliation(s)
- Zhenxin Sun
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Yun Heacock-Kang
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Ian A McMillan
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Darlene Cabanas
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Jan Zarzycki-Siek
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Tung T Hoang
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, United States
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13
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Zhou G, Wang YS, Peng H, Li SJ, Sun TL, Shi QS, Garcia-Ojalvo J, Xie XB. Proteomic signatures of synergistic interactions in antimicrobials. J Proteomics 2023; 270:104743. [PMID: 36210012 DOI: 10.1016/j.jprot.2022.104743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/12/2022] [Accepted: 10/01/2022] [Indexed: 11/06/2022]
Abstract
Mounting evidence has shown that antimicrobial agents can interfere synergistically with bacterial viability and proliferation when acting together at both the planktonic and biofilm levels without clear underlying molecular mechanisms. Here, multiplexed proteomics by iTRAQ was used to study the interplay between two biocides, the isothiazolone 1,2-benzisothiazolin-3-one (BIT) and the chelating agent disodium ethylenediaminetetraacetic acid (EDTA-2Na), employing the Citrobacter werkmanii as a model system. We first confirmed that these two biocides act synergistically on this bacterial species and then extracted the proteomic profiles of C. werkmanii cells in the presence of BIT, EDTA-2Na, and their combinations. In particular, we identified 43 core proteins that are differentially expressed in all three conditions simultaneously. Meanwhile, we found that these core proteins are consistently up-regulated when these two biocides are present, but not for single biocides, where we found a balanced mix of up- and down-regulation. Meanwhile, most of the deletion mutants of the core DEPs exhibited biofilm growth inhibition under joint biocide action, while their response was very heterogenous, with respect to the wild-type strain. Together, our results show that while BIT and EDTA-2Na act on multiple protein targets, they interact synergistically at the protein level in a very consistent manner. SIGNIFICANCE: Our preliminary experiments have demonstrated that a combination of 1,2-benzisothiazolin-3-one (BIT) and EDTA-2Na shows higher inhibitory effects on planktonic growth and biofilm formation in both C. werkmanii and Staphylococcus aureus than when these two biocides act alone. However, the mechanistic basis of such synergistic interaction is still unknown. Therefore, the key proteins involved in the above-mentioned enhanced antimicrobial synergy were elucidated using multiplexed proteomics analysis by isobaric tags for relative and absolute quantification (iTRAQ). Our results reveal that the joint action of BIT and EDTA-2Na induces consistent protein expression alteration in a set of core proteins of C. werkmanii, which underlies a strong synergistic antimicrobial effect, which increase our understanding of the action modes of BIT and EDTA-2Na as well as their combinations.
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Affiliation(s)
- Gang Zhou
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510070, People's Republic of China; Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Dr. Aiguader 88, Barcelona, 08003, Spain.
| | - Ying-Si Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510070, People's Republic of China
| | - Hong Peng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510070, People's Republic of China
| | - Su-Juan Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510070, People's Republic of China
| | - Ting-Li Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510070, People's Republic of China
| | - Qing-Shan Shi
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510070, People's Republic of China.
| | - Jordi Garcia-Ojalvo
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Dr. Aiguader 88, Barcelona, 08003, Spain.
| | - Xiao-Bao Xie
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510070, People's Republic of China.
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14
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An in silico reverse vaccinology study of Brachyspira pilosicoli, the causative organism of intestinal spirochaetosis, to identify putative vaccine candidates. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Identification of Key Functions Required for Production and Utilization of the Siderophore Piscibactin Encoded by the High-Pathogenicity Island irp-HPI in Vibrionaceae. Int J Mol Sci 2022; 23:ijms23168865. [PMID: 36012135 PMCID: PMC9408133 DOI: 10.3390/ijms23168865] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/27/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022] Open
Abstract
Piscibactin is a widespread siderophore system present in many different bacteria, especially within the Vibrionaceae family. Previous works showed that most functions required for biosynthesis and transport of this siderophore are encoded by the high-pathogenicity island irp-HPI. In the present work, using Vibrio anguillarum as a model, we could identify additional key functions encoded by irp-HPI that are necessary for piscibactin production and transport and that have remained unknown. Allelic exchange mutagenesis, combined with cross-feeding bioassays and LC-MS analysis, were used to demonstrate that Irp4 protein is an essential component for piscibactin synthesis since it is the thioesterase required for nascent piscibactin be released from the NRPS Irp1. We also show that Irp8 is a MFS-type protein essential for piscibactin secretion. In addition, after passage through the outer membrane transporter FrpA, the completion of ferri-piscibactin internalization through the inner membrane would be achieved by the ABC-type transporter FrpBC. The expression of this transporter is coordinated with the expression of FrpA and with the genes encoding biosynthetic functions. Since piscibactin is a major virulence factor of some pathogenic vibrios, the elements of biosynthesis and transport described here could be additional interesting targets for the design of novel antimicrobials against these bacterial pathogens.
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16
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Fanti RC, Vasconcelos SNS, Catta-Preta CMC, Sullivan JR, Riboldi GP, Dos Reis CV, Ramos PZ, Edwards AM, Behr MA, Couñago RM. A Target Engagement Assay to Assess Uptake, Potency, and Retention of Antibiotics in Living Bacteria. ACS Infect Dis 2022; 8:1449-1467. [PMID: 35815896 DOI: 10.1021/acsinfecdis.2c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New antibiotics are urgently needed to counter the emergence of antimicrobial-resistant pathogenic bacteria. A major challenge in antibiotic drug discovery is to turn potent biochemical inhibitors of essential bacterial components into effective antimicrobials. This difficulty is underpinned by a lack of methods to investigate the physicochemical properties needed for candidate antibiotics to permeate the bacterial cell envelope and avoid clearance by the action of bacterial efflux pumps. To address these issues, here we used a target engagement assay to measure the equilibrium and kinetic binding parameters of antibiotics targeting dihydrofolate reductase (DHFR) in live bacteria. We also used this assay to identify novel DHFR ligands having antimicrobial activity. We validated this approach using the Gram-negative bacteria Escherichia coli and the emerging human pathogen Mycobacterium abscessus. We expect the use of target engagement assays in bacteria to expedite the discovery and progression of novel, cell-permeable antibiotics with on-target activity.
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Affiliation(s)
- Rebeka C Fanti
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil.,Post-Graduate Program in Genetics and Molecular Biology (PGBM), UNICAMP, Campinas 13083-970, Brazil
| | - Stanley N S Vasconcelos
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Carolina M C Catta-Preta
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Jaryd R Sullivan
- Department of Microbiology & Immunology, McGill University, Montréal H3A 2B4, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal H4A 3J1, Canada.,McGill International TB Centre, Montréal H4A 3S5, Canada
| | - Gustavo P Riboldi
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Caio V Dos Reis
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Priscila Z Ramos
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Aled M Edwards
- Structural Genomics Consortium, 101 College Street, Toronto M5G 1L7, Canada
| | - Marcel A Behr
- Department of Microbiology & Immunology, McGill University, Montréal H3A 2B4, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal H4A 3J1, Canada.,McGill International TB Centre, Montréal H4A 3S5, Canada.,Department of Medicine, McGill University Health Centre, Montréal H4A 3J1, Canada
| | - Rafael M Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil.,Post-Graduate Program in Genetics and Molecular Biology (PGBM), UNICAMP, Campinas 13083-970, Brazil
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17
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Niebling S, Veith K, Vollmer B, Lizarrondo J, Burastero O, Schiller J, Struve García A, Lewe P, Seuring C, Witt S, García-Alai M. Biophysical Screening Pipeline for Cryo-EM Grid Preparation of Membrane Proteins. Front Mol Biosci 2022; 9:882288. [PMID: 35813810 PMCID: PMC9259969 DOI: 10.3389/fmolb.2022.882288] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Successful sample preparation is the foundation to any structural biology technique. Membrane proteins are of particular interest as these are important targets for drug design, but also notoriously difficult to work with. For electron cryo-microscopy (cryo-EM), the biophysical characterization of sample purity, homogeneity, and integrity as well as biochemical activity is the prerequisite for the preparation of good quality cryo-EM grids as these factors impact the result of the computational reconstruction. Here, we present a quality control pipeline prior to single particle cryo-EM grid preparation using a combination of biophysical techniques to address the integrity, purity, and oligomeric states of membrane proteins and its complexes to enable reproducible conditions for sample vitrification. Differential scanning fluorimetry following the intrinsic protein fluorescence (nDSF) is used for optimizing buffer and detergent conditions, whereas mass photometry and dynamic light scattering are used to assess aggregation behavior, reconstitution efficiency, and oligomerization. The data collected on nDSF and mass photometry instruments can be analyzed with web servers publicly available at spc.embl-hamburg.de. Case studies to optimize conditions prior to cryo-EM sample preparation of membrane proteins present an example quality assessment to corroborate the usefulness of our pipeline.
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Affiliation(s)
- Stephan Niebling
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Katharina Veith
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Benjamin Vollmer
- Centre for Structural Systems Biology (CSSB), Leibniz Institute of Virology (LIV), Hamburg, Germany
| | | | - Osvaldo Burastero
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Janina Schiller
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Angelica Struve García
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Philipp Lewe
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carolin Seuring
- Centre for Structural Systems Biology (CSSB), Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Susanne Witt
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - María García-Alai
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- *Correspondence: María García-Alai,
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18
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Baas-Thomas MS, Oehm SB, Ostrov N, Church GM. Characterization of ColE1 Production for Robust tolC Plate Dual-Selection in E. coli. ACS Synth Biol 2022; 11:2009-2014. [PMID: 35666547 PMCID: PMC9208019 DOI: 10.1021/acssynbio.2c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Bacterial selection
is an indispensable tool for E. coli genetic
engineering. Marker genes allow for mutant isolation even
at low editing efficiencies. TolC is an especially
useful E. coli marker: its presence can be selected
for with sodium dodecyl sulfate, while its absence can be selected
for with the bactericidal protein ColE1. However, utilization of this
selection system is greatly limited by the lack of commercially available
ColE1 protein. Here, we provide a simple, plate-based, ColE1 negative-selection
protocol that does not require purification of ColE1. Using agar plates
containing a nonpurified lysate from a ColE1-production strain, we
achieved a stringent negative selection with an escape rate of 10–7. Using this powerful negative-selection assay, we
then performed the scarless deletion of multiple, large genomic loci
(>10 kb), screening only 12 colonies each. We hope this accessible
protocol for ColE1 production will lower the barrier of entry for
any lab that wishes to harness tolC’s dual
selection for genetic engineering.
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Affiliation(s)
| | - Sebastian B Oehm
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Nili Ostrov
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States.,Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
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19
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Wan X, Li Q, Olsen RH, Meng H, Zhang Z, Wang J, Zheng H, Li L, Shi L. Engineering a CRISPR interference system targeting AcrAB-TolC efflux pump to prevent multidrug resistance development in Escherichia coli. J Antimicrob Chemother 2022; 77:2158-2166. [PMID: 35642356 DOI: 10.1093/jac/dkac166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/06/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES We engineered a CRISPR interference (CRISPRi) system targeting the AcrAB-TolC efflux pump to prevent MDR development in Escherichia coli. METHODS Nine specific single-guide RNAs (sgRNAs) were designed to target the components of the AcrAB-TolC efflux pump, namely AcrA, AcrB and TolC. A total of thirteen CRISPRi recombinant plasmids were constructed with single or clustered sgRNAs. The transcriptional levels of the target genes, MICs of multiple antibiotics and biofilm formation in each CRISPRi strain were tested. RESULTS The CRISPRi system expressing sgRNA clusters targeting acrB and tolC simultaneously exhibited the highest inhibitory effect on AcrAB-TolC efflux pump activity in E. coli HB101, with 78.3%, 90.0% and 65.4% inhibition rates on the transcriptional levels of acrA, acrB and tolC, respectively. The CRISPRi system resulted in ∼2-, ∼8- and 16-fold increased susceptibility to rifampicin, erythromycin and tetracycline, respectively. In addition, the constructed CRISPRi system reduced biofilm formation with inhibition rates in the range of 11.2% to 58.2%. CONCLUSIONS To the best of our knowledge, this is the first report on the construction of an inducible CRISPRi system targeting the AcrAB-TolC efflux pump to prevent MDR development in E. coli. This study provides insights for future regulation and manipulation of AcrAB-TolC activity and bacterial MDR by a CRISPRi system.
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Affiliation(s)
- Xiulin Wan
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Qingyang Li
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Rikke Heidemann Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Hecheng Meng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Zhigang Zhang
- State Key Laboratory of Food Safety Technology for Meat Products, Xiamen Yinxiang Group, Xiamen, China
| | - Junlin Wang
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Hanyu Zheng
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Lili Li
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China.,State Key Laboratory of Food Safety Technology for Meat Products, Xiamen Yinxiang Group, Xiamen, China
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20
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Sun Z, Zhou N, Zhang W, Xu Y, Yao YF. Dual role of CsrA in regulating the hemolytic activity of Escherichia coli O157:H7. Virulence 2022; 13:859-874. [PMID: 35609307 PMCID: PMC9132389 DOI: 10.1080/21505594.2022.2073023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Post-transcriptional global carbon storage regulator A (CsrA) is a sequence-specific RNA-binding protein involved in the regulation of multiple bacterial processes. Hemolysin is an important virulence factor in the enterohemorrhagic Escherichia coli O157:H7 (EHEC). Here, we show that CsrA plays a dual role in the regulation of hemolysis in EHEC. CsrA significantly represses plasmid-borne enterohemolysin (EhxA)-mediated hemolysis and activates chromosome-borne hemolysin E (HlyE)-mediated hemolysis through different mechanisms. RNA structure prediction revealed a well-matched stem-loop structure with two potential CsrA binding sites located on the 5' untranslated region (UTR) of ehxB, which encodes a translocator required for EhxA secretion. CsrA inhibits EhxA secretion by directly binding to the RNA leader sequence of ehxB to repress its expression in two different ways: CsrA either binds to the Shine–Dalgarno sequence of ehxB to block ribosome access or to ehxB transcript to promote its mRNA decay. The predicted CsrA-binding site 1 of ehxB is essential for its regulation. There is a single potential CsrA-binding site at the 5'-end of the hlyE transcript, and its mutation completely abolishes CsrA-dependent activation. CsrA can also stabilize hlyE mRNA by directly binding to its 5' UTR. Overall, our results indicate that CsrA acts as a hemolysis modulator to regulate pathogenicity under certain conditions.
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Affiliation(s)
- Zhibin Sun
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ning Zhou
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenting Zhang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Xu
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
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21
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Darnowski MG, Lanosky TD, Labana P, Brazeau-Henrie JT, Calvert ND, Dornan MH, Natola C, Paquette AR, Shuhendler AJ, Boddy CN. Armeniaspirol analogues with more potent Gram-positive antibiotic activity show enhanced inhibition of the ATP-dependent proteases ClpXP and ClpYQ. RSC Med Chem 2022; 13:436-444. [PMID: 35647545 PMCID: PMC9020616 DOI: 10.1039/d1md00355k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/07/2022] [Indexed: 11/21/2022] Open
Abstract
Antibiotics with fundamentally new mechanisms of action such as the armeniaspirols, which target the ATP-dependent proteases ClpXP and ClpYQ, must be developed to combat antimicrobial resistance. While the mechanism of action of armeniaspirol against Gram-positive bacteria is understood, little is known about the structure-activity relationship for its antibiotic activity. Based on the preliminary data showing that modifications of armeniaspirol's N-methyl group increased antibiotic potency, we probed the structure-activity relationship of N-alkyl armeniaspirol derivatives. A series of focused derivatives were synthesized and evaluated for antibiotic activity against clinically relevant pathogens including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus. Replacement of the N-methyl with N-hexyl, various N-benzyl, and N-phenethyl substituents led to substantial increases in antibiotic activity and potency for inhibition of both ClpYQ and ClpXP. Docking studies identified binding models for ClpXP and ClpYQ that were consistent with the inhibition data. This work confirms the role of ClpXP and ClpYQ in the mechanism of action of armeniaspirol and provides important lead compounds for further antibiotic development.
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Affiliation(s)
- Michael G. Darnowski
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Taylor D. Lanosky
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Puneet Labana
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Jordan T. Brazeau-Henrie
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Nicholas D. Calvert
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Mark H. Dornan
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Claudia Natola
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - André R. Paquette
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Adam J. Shuhendler
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
| | - Christopher N. Boddy
- Department of Chemistry and Biomolecular Sciences, University of OttawaOttawaONK1N 6N5 Canadacboddy!uottawa.ca
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22
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Hermansen S, Linke D, Leo JC. Transmembrane β-barrel proteins of bacteria: From structure to function. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 128:113-161. [PMID: 35034717 DOI: 10.1016/bs.apcsb.2021.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The outer membrane of Gram-negative bacteria is a specialized organelle conferring protection to the cell against various environmental stresses and resistance to many harmful compounds. The outer membrane has a number of unique features, including an asymmetric lipid bilayer, the presence of lipopolysaccharides and an individual proteome. The vast majority of the integral transmembrane proteins in the outer membrane belongs to the family of β-barrel proteins. These evolutionarily related proteins share a cylindrical, anti-parallel β-sheet core fold spanning the outer membrane. The loops and accessory domains attached to the β-barrel allow for a remarkable versatility in function for these proteins, ranging from diffusion pores and transporters to enzymes and adhesins. We summarize the current knowledge on β-barrel structure and folding and give an overview of their functions, evolution, and potential as drug targets.
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Affiliation(s)
- Simen Hermansen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Jack C Leo
- Antimicrobial resistance, Omics and Microbiota Group, Department of Biosciences, Nottingham Trent University, Nottingham, United Kingdom.
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23
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Singh P, Verma RK, Chatterjee S. The diffusible signal factor synthase, RpfF, in Xanthomonas oryzae pv. oryzae is required for the maintenance of membrane integrity and virulence. MOLECULAR PLANT PATHOLOGY 2022; 23:118-132. [PMID: 34704368 PMCID: PMC8659556 DOI: 10.1111/mpp.13148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/03/2021] [Accepted: 09/24/2021] [Indexed: 05/12/2023]
Abstract
The Xanthomonas group of phytopathogens communicate with a fatty acid-like cell-cell signalling molecule, cis-11-2-methyl-dodecenoic acid, also known as diffusible signal factor (DSF). In the pathogen of rice, Xanthomonas oryzae pv. oryzae, DSF is involved in the regulation of several virulence-associated functions, including production and secretion of several cell wall hydrolysing type II secretion effectors. To understand the role of DSF in the secretion of type II effectors, we characterized DSF synthase-deficient (rpfF) and DSF-deficient, type II secretion (xpsE) double mutants. Mutant analysis by expression analysis, secretion assay, fatty acid analysis, and physiological studies indicated that rpfF mutants exhibit hypersecretion of several type II effectors due to a perturbed membrane and DSF is required for maintaining membrane integrity. The rpfF mutants exhibited significantly higher uptake of 1-N-phenylnapthylamine and ethidium bromide, and up-regulation of rpoE (σE ). Increasing the osmolarity of the medium could rescue the hypersecretion phenotype of the rpfF mutant. The rpfF mutant exhibited highly reduced virulence. We report for the first time that in X. oryzae pv. oryzae RpfF is involved in the maintenance of membrane integrity by playing a regulatory role in the fatty acid synthesis pathway.
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Affiliation(s)
- Prashantee Singh
- Laboratory of Plant Microbe InteractionsCentre for DNA Fingerprinting and DiagnosticsUppalIndia
- Graduate StudiesManipal Academy of Higher EducationMangaluruIndia
| | - Raj Kumar Verma
- Laboratory of Plant Microbe InteractionsCentre for DNA Fingerprinting and DiagnosticsUppalIndia
| | - Subhadeep Chatterjee
- Laboratory of Plant Microbe InteractionsCentre for DNA Fingerprinting and DiagnosticsUppalIndia
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24
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Tamrakar A, Singh R, Kumar A, Makde RD, Ashish, Kodgire P. Biophysical characterization of the homodimers of HomA and HomB, outer membrane proteins of Helicobacter pylori. Sci Rep 2021; 11:24471. [PMID: 34963695 PMCID: PMC8714817 DOI: 10.1038/s41598-021-04039-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 11/24/2021] [Indexed: 12/16/2022] Open
Abstract
Helicobacter pylori is a Gram-negative bacterium that causes chronic inflammations in the stomach area and is involved in ulcers, which can develop into gastric malignancies. H. pylori attaches and colonizes to the human epithelium using some of their outer membrane proteins (OMPs). HomB and HomA are the most studied OMPs from H. pylori as they play a crucial role in adherence, hyper biofilm formation, antibiotic resistance and are also associated with severe gastric malignancies. The role of HomA and HomB in pathogenesis concerning their structure and function has not been evaluated yet. In the present study, we explored the structural aspect of HomA and HomB proteins using various computational, biophysical and small-angle X-ray scattering (SAXS) techniques. Interestingly, the in-silico analysis revealed that HomA/B consists of 8 discontinuous N and C terminal β-strands forming a small β-barrel, along with a large surface-exposed globular domain. Further, biophysical experiments suggested that HomA and HomB are dimeric and most likely the cysteine residues present on surface-exposed loops participate in protein-protein interactions. Our study provides essential structural information of unexplored proteins of the Hom family that can help in a better understanding of H. pylori pathogenesis.
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Affiliation(s)
- Anubhav Tamrakar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453 552, India
| | - Rahul Singh
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453 552, India
| | - Ravindra D Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - Ashish
- Protein Science and Engineering Division, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Prashant Kodgire
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453 552, India.
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25
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Hu B, Rao MJ, Deng X, Pandey SS, Hendrich C, Ding F, Wang N, Xu Q. Molecular signatures between citrus and Candidatus Liberibacter asiaticus. PLoS Pathog 2021; 17:e1010071. [PMID: 34882744 PMCID: PMC8659345 DOI: 10.1371/journal.ppat.1010071] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Citrus Huanglongbing (HLB), also known as citrus greening, is one of the most devastating citrus diseases worldwide. Candidatus Liberibacter asiaticus (CLas) is the most prevalent strain associated with HLB, which is yet to be cultured in vitro. None of the commercial citrus cultivars are resistant to HLB. The pathosystem of Ca. Liberibacter is complex and remains a mystery. In this review, we focus on the recent progress in genomic research on the pathogen, the interaction of host and CLas, and the influence of CLas infection on the transcripts, proteins, and metabolism of the host. We have also focused on the identification of candidate genes for CLas pathogenicity or the improvements of HLB tolerance in citrus. In the end, we propose potentially promising areas for mechanistic studies of CLas pathogenicity, defense regulators, and genetic improvement for HLB tolerance/resistance in the future.
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Affiliation(s)
- Bin Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Ministry of Agriculture), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Muhammad Junaid Rao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Ministry of Agriculture), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Ministry of Agriculture), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Sheo Shankar Pandey
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, Florida, United States of America
| | - Connor Hendrich
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, Florida, United States of America
| | - Fang Ding
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, Florida, United States of America
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Ministry of Agriculture), Huazhong Agricultural University, Wuhan, Hubei, China
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26
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Quantification and surface localization of the hemolysin A type 1 secretion system at the endogenous level and under conditions of overexpression. Appl Environ Microbiol 2021; 88:e0189621. [PMID: 34851699 DOI: 10.1128/aem.01896-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Secretion systems are essential for Gram-negative bacteria as these nanomachineries allow a communication with the outside world by exporting proteins into the extracellular space or directly into the cytosol of a host cell. For example, type one secretion systems (T1SS) secrete a broad range of substrates across both membranes into the extracellular space. One well-known example is the hemolysin A (HlyA) T1SS from Escherichia coli (E. coli), which consists of an ABC transporter (HlyB), a membrane fusion protein (HlyD), the outer membrane protein TolC and the substrate HlyA, a member of the family of RTX (repeats in toxins) toxins. Here, we determined the amount of TolC at the endogenous level (parental strain, UTI89) and under conditions of overexpression (T7 expression system, BL21(DE3)-BD). The overall amount of TolC was not influenced by the overexpression of the HlyBD complex. Moving one step further, we determined the localization of the HlyA T1SS by super-resolution microscopy. In contrast to other bacterial secretion systems, no polarization was observed with respect to endogenous or overexpression levels. Additionally, the cell growth and division cycle did not influence the polarization. Most importantly, the size of the observed T1SS clusters did not correlate with the recently proposed outer membrane islands. These data indicate that T1SS cluster at the outer membrane generating domains of so far not described identity. Importance Uropathogenic Escherichia coli (UPEC) strains cause about 110 million urinary tract infections each year worldwide representing a global burden to the healthcare system. UPEC secrete many virulence factors among these the TX toxin hemolysin A via a cognate T1SS into the extracellular space. In this study, we determined the endogenous copy number of the HlyA T1SS in UTI89 and analyzed the surface localization in BL21(DE3)-BD and UTI89, respectively. With approximately 800 copies of the T1SS in UTI89, this is one of the highest expressed bacterial secretion systems. Furthermore and in clear contrast to other secretion systems, no polarized surface localization was detected. Finally, quantitative analysis of the super-resolution data revealed that clusters of the HlyA T1SS are not related to the recently identified outer membrane protein islands. These data provide insights into the quantitative molecular architecture of the HlyA T1SS.
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27
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Adrien V, Rayan G, Astafyeva K, Broutin I, Picard M, Fuchs P, Urbach W, Taulier N. How to best estimate the viscosity of lipid bilayers. Biophys Chem 2021; 281:106732. [PMID: 34844029 DOI: 10.1016/j.bpc.2021.106732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/19/2021] [Accepted: 11/19/2021] [Indexed: 11/02/2022]
Abstract
The viscosity of lipid bilayers is a property relevant to biological function, as it affects the diffusion of membrane macromolecules. To determine its value, and hence portray the membrane, various literature-reported techniques lead to significantly different results. Herein we compare the results issuing from two widely used techniques to determine the viscosity of membranes: the Fluorescence Lifetime Imaging Microscopy (FLIM), and Fluorescence Recovery After Photobleaching (FRAP). FLIM relates the time of rotation of a molecular rotor inserted into the membrane to the macroscopic viscosity of a fluid. Whereas FRAP measures molecular diffusion coefficients. This approach is based on a hydrodynamic model connecting the mobility of a membrane inclusion to the viscosity of the membrane. We show that: This article emphasizes the pitfalls to be avoided and the rules to be observed in order to obtain a value of the bilayer viscosity that characterizes the bilayer instead of interactions between the bilayer and the embedded probe.
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Affiliation(s)
- Vladimir Adrien
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France; Université de Paris, CNRS, Laboratoire CiTCoM, 75006 Paris, France; Sorbonne Université, AP-HP Department of Psychiatry, Hôpital Saint-Antoine, Paris, France
| | - Gamal Rayan
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France.
| | - Ksenia Astafyeva
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France
| | - Isabelle Broutin
- Université de Paris, CNRS, Laboratoire CiTCoM, 75006 Paris, France
| | - Martin Picard
- Université de Paris, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS UMR 7099, F-75005 Paris, France; Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le développement de la recherche Scientifique, F-75005 Paris, France
| | - Patrick Fuchs
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), 75005 Paris, France; Université de Paris, UFR Sciences du Vivant, 75013 Paris, France
| | - Wladimir Urbach
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France; Sorbonne Université, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, LIB, F-75006 Paris, France
| | - Nicolas Taulier
- Sorbonne Université, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, LIB, F-75006 Paris, France
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28
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Abstract
Bacteria often secrete diffusible protein toxins (bacteriocins) to kill bystander cells during interbacterial competition. Here, we use biochemical, biophysical and structural analyses to show how a bacteriocin exploits TolC, a major outer-membrane antibiotic efflux channel in Gram-negative bacteria, to transport itself across the outer membrane of target cells. Klebicin C (KlebC), a rRNase toxin produced by Klebsiella pneumoniae, binds TolC of a related species (K. quasipneumoniae) with high affinity through an N-terminal, elongated helical hairpin domain common amongst bacteriocins. The KlebC helical hairpin opens like a switchblade to bind TolC. A cryo-EM structure of this partially translocated state, at 3.1 Å resolution, reveals that KlebC associates along the length of the TolC channel. Thereafter, the unstructured N-terminus of KlebC protrudes beyond the TolC iris, presenting a TonB-box sequence to the periplasm. Association with proton-motive force-linked TonB in the inner membrane drives toxin import through the channel. Finally, we demonstrate that KlebC binding to TolC blocks drug efflux from bacteria. Our results indicate that TolC, in addition to its known role in antibiotic export, can function as a protein import channel for bacteriocins. Bacteria can secrete diffusible protein toxins that kill competing bacteria. Here, the authors use biochemical, biophysical and structural analyses to show how one of these toxins exploits TolC (a major antibiotic efflux channel) to transport itself across the outer membrane of target cells.
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29
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Duang-Nkern J, Nontaleerak B, Udomkanarat T, Saninjuk K, Sukchawalit R, Mongkolsuk S. NieR is the repressor of a NaOCl-inducible efflux system in Agrobacterium tumefaciens C58. Microbiol Res 2021; 251:126816. [PMID: 34273784 DOI: 10.1016/j.micres.2021.126816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 05/15/2021] [Accepted: 07/08/2021] [Indexed: 11/24/2022]
Abstract
The Agrobacterium tumefaciens atu4217 gene, which encodes a TetR family transcription regulator, is a repressor of the atu4218-atu4219-atu4220 operon. The Atu4218 and Atu4219 proteins belong to the HlyD family (membrane fusion protein) and the AcrB/AcrD/AcrF family (inner membrane transporter), respectively, and may form an efflux pump. The atu4220 gene encodes a short-chain dehydrogenase. Quantitative real-time PCR analysis showed induction of atu4217 and atu4218 by NaOCl but not by N-ethylmaleimide or reactive oxygen species (ROS) including H2O2, menadione and cumene hydroperoxide; therefore, the atu4218 and atu4219 were named NaOCl-inducible efflux genes nieA and nieB, respectively. The atu4217 gene, which was named nieR, serves as a repressor of nieA and nieB. DNase I footprinting assays identified 20-bp imperfect inverted repeat (IR, underlined) motifs 5'-TAGATTTAGGATGCAATCTA-3' (box A) and 5'-TAGATTTCACTTGACATCTA-3' (box R) in the intergenic region of the divergent nieA and nieR genes; these motifs were recognized by the NieR protein. Electrophoretic mobility shift assays demonstrated that NieR specifically binds to the 20-bp IR motifs and that NaOCl prevents this NieR-DNA interaction. Promoter-lacZ fusions and mutagenesis of the NieR boxes (A and R) showed a more dominant role for box A than for box R in the repression of the nieA and nieR promoters. However, full repression of either promoter required both operators. The nieR mutant strain exhibited a small colony phenotype and was more sensitive than the wild-type to NaOCl and antibiotics, including ciprofloxacin, nalidixic acid, novobiocin, and tetracycline. By contrast, the nieAB mutant strain showed no phenotype changes under the tested conditions.
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Affiliation(s)
- Jintana Duang-Nkern
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand
| | - Benya Nontaleerak
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand
| | - Tham Udomkanarat
- Environmental Toxicology, Chulabhorn Graduate Institute, Lak Si, Bangkok, 10210, Thailand
| | - Kritsakorn Saninjuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand
| | - Rojana Sukchawalit
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand; Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok, 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand.
| | - Skorn Mongkolsuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand
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30
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Tamer YT, Gaszek I, Rodrigues M, Coskun FS, Farid M, Koh AY, Russ W, Toprak E. The antibiotic efflux protein TolC is a highly evolvable target under colicin E1 or TLS phage selection. Mol Biol Evol 2021; 38:4493-4504. [PMID: 34175926 PMCID: PMC8476145 DOI: 10.1093/molbev/msab190] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Bacteriophages and bacterial toxins are promising antibacterial agents to treat infections caused by multidrug-resistant (MDR) bacteria. In fact, bacteriophages have recently been successfully used to treat life-threatening infections caused by MDR bacteria (Schooley RT, Biswas B, Gill JJ, Hernandez-Morales A, Lancaster J, Lessor L, Barr JJ, Reed SL, Rohwer F, Benler S, et al. 2017. Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection. Antimicrob Agents Chemother. 61(10); Chan BK, Turner PE, Kim S, Mojibian HR, Elefteriades JA, Narayan D. 2018. Phage treatment of an aortic graft infected with Pseudomonas aeruginosa. Evol Med Public Health. 2018(1):60–66; Petrovic Fabijan A, Lin RCY, Ho J, Maddocks S, Ben Zakour NL, Iredell JR, Westmead Bacteriophage Therapy Team. 2020. Safety of bacteriophage therapy in severe Staphylococcus aureus infection. Nat Microbiol. 5(3):465–472). One potential problem with using these antibacterial agents is the evolution of resistance against them in the long term. Here, we studied the fitness landscape of the Escherichia coli TolC protein, an outer membrane efflux protein that is exploited by a pore forming toxin called colicin E1 and by TLS phage (Pagie L, Hogeweg P. 1999. Colicin diversity: a result of eco-evolutionary dynamics. J Theor Biol. 196(2):251–261; Andersen C, Hughes C, Koronakis V. 2000. Chunnel vision. Export and efflux through bacterial channel-tunnels. EMBO Rep. 1(4):313–318; Koronakis V, Andersen C, Hughes C. 2001. Channel-tunnels. Curr Opin Struct Biol. 11(4):403–407; Czaran TL, Hoekstra RF, Pagie L. 2002. Chemical warfare between microbes promotes biodiversity. Proc Natl Acad Sci U S A. 99(2):786–790; Cascales E, Buchanan SK, Duché D, Kleanthous C, Lloubès R, Postle K, Riley M, Slatin S, Cavard D. 2007. Colicin biology. Microbiol Mol Biol Rev. 71(1):158–229). By systematically assessing the distribution of fitness effects of ∼9,000 single amino acid replacements in TolC using either positive (antibiotics and bile salts) or negative (colicin E1 and TLS phage) selection pressures, we quantified evolvability of the TolC. We demonstrated that the TolC is highly optimized for the efflux of antibiotics and bile salts. In contrast, under colicin E1 and TLS phage selection, TolC sequence is very sensitive to mutations. Finally, we have identified a large set of mutations in TolC that increase resistance of E. coli against colicin E1 or TLS phage without changing antibiotic susceptibility of bacterial cells. Our findings suggest that TolC is a highly evolvable target under negative selection which may limit the potential clinical use of bacteriophages and bacterial toxins if evolutionary aspects are not taken into account.
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Affiliation(s)
- Yusuf Talha Tamer
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ilona Gaszek
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Marinelle Rodrigues
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Fatma Sevde Coskun
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Michael Farid
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Andrew Y Koh
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.,Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - William Russ
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Erdal Toprak
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Matuszewska M, Maciąg T, Rajewska M, Wierzbicka A, Jafra S. The carbon source-dependent pattern of antimicrobial activity and gene expression in Pseudomonas donghuensis P482. Sci Rep 2021; 11:10994. [PMID: 34040089 PMCID: PMC8154892 DOI: 10.1038/s41598-021-90488-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/12/2021] [Indexed: 02/04/2023] Open
Abstract
Pseudomonas donghuensis P482 is a tomato rhizosphere isolate with the ability to inhibit growth of bacterial and fungal plant pathogens. Herein, we analysed the impact of the carbon source on the antibacterial activity of P482 and expression of the selected genes of three genomic regions in the P482 genome. These regions are involved in the synthesis of pyoverdine, 7-hydroxytropolone (7-HT) and an unknown compound ("cluster 17") and are responsible for the antimicrobial activity of P482. We showed that the P482 mutants, defective in these regions, show variations and contrasting patterns of growth inhibition of the target pathogen under given nutritional conditions (with glucose or glycerol as a carbon source). We also selected and validated the reference genes for gene expression studies in P. donghuensis P482. Amongst ten candidate genes, we found gyrB, rpoD and mrdA the most stably expressed. Using selected reference genes in RT-qPCR, we assessed the expression of the genes of interest under minimal medium conditions with glucose or glycerol as carbon sources. Glycerol was shown to negatively affect the expression of genes necessary for 7-HT synthesis. The significance of this finding in the light of the role of nutrient (carbon) availability in biological plant protection is discussed.
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Affiliation(s)
- Marta Matuszewska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Tomasz Maciąg
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Magdalena Rajewska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Aldona Wierzbicka
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Sylwia Jafra
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland.
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Alav I, Kobylka J, Kuth MS, Pos KM, Picard M, Blair JMA, Bavro VN. Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Chem Rev 2021; 121:5479-5596. [PMID: 33909410 PMCID: PMC8277102 DOI: 10.1021/acs.chemrev.1c00055] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Tripartite efflux pumps and the related type 1 secretion systems (T1SSs) in Gram-negative organisms are diverse in function, energization, and structural organization. They form continuous conduits spanning both the inner and the outer membrane and are composed of three principal components-the energized inner membrane transporters (belonging to ABC, RND, and MFS families), the outer membrane factor channel-like proteins, and linking the two, the periplasmic adaptor proteins (PAPs), also known as the membrane fusion proteins (MFPs). In this review we summarize the recent advances in understanding of structural biology, function, and regulation of these systems, highlighting the previously undescribed role of PAPs in providing a common architectural scaffold across diverse families of transporters. Despite being built from a limited number of basic structural domains, these complexes present a staggering variety of architectures. While key insights have been derived from the RND transporter systems, a closer inspection of the operation and structural organization of different tripartite systems reveals unexpected analogies between them, including those formed around MFS- and ATP-driven transporters, suggesting that they operate around basic common principles. Based on that we are proposing a new integrated model of PAP-mediated communication within the conformational cycling of tripartite systems, which could be expanded to other types of assemblies.
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Affiliation(s)
- Ilyas Alav
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jessica Kobylka
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Miriam S. Kuth
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Klaas M. Pos
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Martin Picard
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS
UMR 7099, Université de Paris, 75005 Paris, France
- Fondation
Edmond de Rothschild pour le développement de la recherche
Scientifique, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jessica M. A. Blair
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Vassiliy N. Bavro
- School
of Life Sciences, University of Essex, Colchester, CO4 3SQ United Kingdom
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33
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Watanabe M, Chiba Y, Hirai MY. Metabolism and Regulatory Functions of O-Acetylserine, S-Adenosylmethionine, Homocysteine, and Serine in Plant Development and Environmental Responses. FRONTIERS IN PLANT SCIENCE 2021; 12:643403. [PMID: 34025692 PMCID: PMC8137854 DOI: 10.3389/fpls.2021.643403] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/17/2021] [Indexed: 05/19/2023]
Abstract
The metabolism of an organism is closely related to both its internal and external environments. Metabolites can act as signal molecules that regulate the functions of genes and proteins, reflecting the status of these environments. This review discusses the metabolism and regulatory functions of O-acetylserine (OAS), S-adenosylmethionine (AdoMet), homocysteine (Hcy), and serine (Ser), which are key metabolites related to sulfur (S)-containing amino acids in plant metabolic networks, in comparison to microbial and animal metabolism. Plants are photosynthetic auxotrophs that have evolved a specific metabolic network different from those in other living organisms. Although amino acids are the building blocks of proteins and common metabolites in all living organisms, their metabolism and regulation in plants have specific features that differ from those in animals and bacteria. In plants, cysteine (Cys), an S-containing amino acid, is synthesized from sulfide and OAS derived from Ser. Methionine (Met), another S-containing amino acid, is also closely related to Ser metabolism because of its thiomethyl moiety. Its S atom is derived from Cys and its methyl group from folates, which are involved in one-carbon metabolism with Ser. One-carbon metabolism is also involved in the biosynthesis of AdoMet, which serves as a methyl donor in the methylation reactions of various biomolecules. Ser is synthesized in three pathways: the phosphorylated pathway found in all organisms and the glycolate and the glycerate pathways, which are specific to plants. Ser metabolism is not only important in Ser supply but also involved in many other functions. Among the metabolites in this network, OAS is known to function as a signal molecule to regulate the expression of OAS gene clusters in response to environmental factors. AdoMet regulates amino acid metabolism at enzymatic and translational levels and regulates gene expression as methyl donor in the DNA and histone methylation or after conversion into bioactive molecules such as polyamine and ethylene. Hcy is involved in Met-AdoMet metabolism and can regulate Ser biosynthesis at an enzymatic level. Ser metabolism is involved in development and stress responses. This review aims to summarize the metabolism and regulatory functions of OAS, AdoMet, Hcy, and Ser and compare the available knowledge for plants with that for animals and bacteria and propose a future perspective on plant research.
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Affiliation(s)
- Mutsumi Watanabe
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yukako Chiba
- Graduate School of Life Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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34
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Liu J, Wu P, Guo Q, Lai X, Ruan B, Wang H, Rehman S, Chen M. Kaolinite weakens the co-stress of ampicillin and tetracycline on Escherichia coli through multiple pathways. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:25228-25240. [PMID: 33453031 DOI: 10.1007/s11356-021-12356-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 01/02/2021] [Indexed: 06/12/2023]
Abstract
Ampicillin and tetracycline are common antibiotics and can threaten humans by inducing antibiotic resistance in bacteria. Microorganisms are usually exposed to a mixed antibiotic system in the environment. However, there are few researches on the specific regulatory mechanisms of clay on microorganisms under the stress of complex antibiotics. In this study, tandem mass tag-based coupled with two-dimensional liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) was employed to recognize and quantify changes in protein expression of Escherichia coli (E. coli) after culture for 15 days, with or without kaolinite in the co-stress of ampicillin and tetracycline. The results indicated that kaolinite could activate metabolic pathways of E. coli such as the energy metabolism, the biosynthesis of other secondary metabolites, and the metabolism of cofactors and vitamins. Particularly, the fatty acid degradation pathway has also been promoted, indicating that in the same unfavorable environment, kaolinite might influence the composition of E. coli cell membranes. This might be due to the change in membrane composition that was a kind of adaptive strategy of bacterial evolution. Moreover, kaolinite could promote multidrug efflux system to export the bacterial intracellular toxic substances, making E. coli survive better in an adverse environment. Consequently, this study not only disclosed the regulation of kaolinite on E. coli in a complex antibiotic environment but also provided new insights into the environmental process of antibiotic resistance.
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Affiliation(s)
- Juan Liu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Pingxiao Wu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China.
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou, 510006, People's Republic of China.
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, South China University of Technology, Guangzhou, 510006, People's Republic of China.
- Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, Guangzhou, 510006, People's Republic of China.
- Guangdong Engineering and Technology Research Center for Environmental Nanomaterials, Guangzhou, 510006, People's Republic of China.
| | - Qing Guo
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Xiaolin Lai
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Bo Ruan
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Huimin Wang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Saeed Rehman
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Meiqing Chen
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, People's Republic of China
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35
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Liu D, Wang Y, Wang X, Ou D, Ling N, Zhang J, Wu Q, Ye Y. Role of the multiple efflux pump protein TolC on growth, morphology, and biofilm formation under nitric oxide stress in Cronobacter malonaticus. JDS COMMUNICATIONS 2021; 2:98-103. [PMID: 36339506 PMCID: PMC9623651 DOI: 10.3168/jdsc.2020-0040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/19/2021] [Indexed: 06/13/2023]
Abstract
Nitric oxide (NO) is a biological signal molecule that can control and prevent the growth of most pathogens. Cronobacter species are a group of gram-negative foodborne pathogens that cause severe diseases, including neonatal meningitis, septicemia, and necrotizing enterocolitis, especially among newborns and infants consuming contaminated powdered infant formula. Cronobacter species might be tolerant to NO, resulting in severe infections. However, the specific mechanism of tolerance to NO in Cronobacter species is unclear. Here, we explore the effects of a key component, the protein TolC, of a multiple efflux pump on the growth, morphological changes, and biofilm formation of Cronobacter malonaticus under NO stress. We found that deletion of tolC resulted in a decreased growth rate under 100 mM sodium nitroprusside (NO donor) and led to more disruptive morphological injury to the bacterial cells. Furthermore, C. malonaticus lacking the TolC protein (ΔtolC mutant) showed weaker biofilm formation than the wild-type strain under normal or NO stress conditions. We have proved that TolC plays an important role in cell growth and biofilm formation of C. malonaticus. Therefore, our results may provide valuable theoretical basis for formulating clinical guidelines for treatment of disease caused by C. malonaticus and ensuring food safety.
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Affiliation(s)
- Dengyu Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Yaping Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Xin Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Dexin Ou
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Na Ling
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Yingwang Ye
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
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36
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Pattanayak BS, Dehury B, Priyadarshinee M, Jha S, Beuria TK, Soren D, Mallick BC. Kanamycin-Mediated Conformational Dynamics of Escherichia coli Outer Membrane Protein TolC. Front Mol Biosci 2021; 8:636286. [PMID: 33937327 PMCID: PMC8083960 DOI: 10.3389/fmolb.2021.636286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/17/2021] [Indexed: 11/13/2022] Open
Abstract
TolC is a member of the outer membrane efflux proteins (OEPs) family and acts as an exit duct to export proteins, antibiotics, and substrate molecules across the Escherichia coli cell membrane. Export of these molecules is evidenced to be brought about through the reversible interactions and binding of substrate-specific drug molecules or antibiotics with TolC and by being open for transport, which afterward leads to cross-resistance. Hence, the binding of kanamycin with TolC was monitored through molecular docking (MD), the structural fluctuations and conformational changes to the atomic level. The results were further supported from the steady-state fluorescence binding and isothermal titration calorimetry (ITC) studies. Binding of kanamycin with TolC resulted in a concentration dependent fluorescence intensity quenching with 7 nm blue shift. ITC binding data maintains a single binding site endothermic energetic curve with binding parameters indicating an entropy driven binding process. The confirmational changes resulting from this binding were monitored by a circular dichroism (CD) study, and the results showed insignificant changes in the α-helix and β-sheets secondary structure contents, but the tertiary structure shows inclusive changes in the presence of kanamycin. The experimental data substaintially correlates the RMSD, R g, and RMSF results. The resulting conformational changes of the TolC-kanamycin complexation was stabilized through H-bonding and other interactions.
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Affiliation(s)
| | - Budheswar Dehury
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Suman Jha
- Department of Life Sciences, National Institute of Technology, Rourkela, India
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37
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Hinzke T, Kleiner M, Meister M, Schlüter R, Hentschker C, Pané-Farré J, Hildebrandt P, Felbeck H, Sievert SM, Bonn F, Völker U, Becher D, Schweder T, Markert S. Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis. eLife 2021; 10:58371. [PMID: 33404502 PMCID: PMC7787665 DOI: 10.7554/elife.58371] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 12/05/2020] [Indexed: 12/13/2022] Open
Abstract
The hydrothermal vent tubeworm Riftia pachyptila hosts a single 16S rRNA phylotype of intracellular sulfur-oxidizing symbionts, which vary considerably in cell morphology and exhibit a remarkable degree of physiological diversity and redundancy, even in the same host. To elucidate whether multiple metabolic routes are employed in the same cells or rather in distinct symbiont subpopulations, we enriched symbionts according to cell size by density gradient centrifugation. Metaproteomic analysis, microscopy, and flow cytometry strongly suggest that Riftia symbiont cells of different sizes represent metabolically dissimilar stages of a physiological differentiation process: While small symbionts actively divide and may establish cellular symbiont-host interaction, large symbionts apparently do not divide, but still replicate DNA, leading to DNA endoreduplication. Moreover, in large symbionts, carbon fixation and biomass production seem to be metabolic priorities. We propose that this division of labor between smaller and larger symbionts benefits the productivity of the symbiosis as a whole.
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Affiliation(s)
- Tjorven Hinzke
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany.,Energy Bioengineering Group, University of Calgary, Calgary, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
| | - Mareike Meister
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.,Leibniz Institute for Plasma Science and Technology, Greifswald, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, Greifswald, Germany
| | - Christian Hentschker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jan Pané-Farré
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Petra Hildebrandt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Horst Felbeck
- Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, United States
| | - Florian Bonn
- Institute of Biochemistry, University Hospital, Goethe University School of Medicine Frankfurt, Frankfurt, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Stephanie Markert
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
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38
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Huang L, Feng Y, Zong Z. Heterogeneous resistance to colistin in Enterobacter cloacae complex due to a new small transmembrane protein. J Antimicrob Chemother 2020; 74:2551-2558. [PMID: 31169899 DOI: 10.1093/jac/dkz236] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/28/2019] [Accepted: 05/05/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Enterobacter strains can display heterogeneous resistance (heteroresistance) to colistin but the mechanisms remain largely unknown. We investigated potential mechanisms of colistin heteroresistance in an Enterobacter clinical strain, WCHECl-1060, and found a new mechanism. METHODS Strain WCHECl-1060 was subjected to WGS to identify known colistin resistance mechanisms. Tn5 insertional mutagenesis, gene knockout and complementation and shotgun cloning were employed to investigate unknown colistin heteroresistance mechanisms. RNA sequencing was performed to link the newly identified mechanism with known ones. RESULTS We showed that the phoP gene [encoding part of the PhoP-PhoQ two-component system (TCS)], the dedA(Ecl) gene (encoding an inner membrane protein of the DedA family) and the tolC gene (encoding part of the AcrAB-TolC efflux pump) are required for colistin heteroresistance. We identified a new gene, ecr, encoding a 72 amino acid transmembrane protein, which was able to mediate colistin heteroresistance. We then performed RNA sequencing and transcriptome analysis and found that in the presence of ecr the expression of phoP and the arnBCADTEF operon, which synthesizes and transfers l-Ara4N to lipid A, was increased significantly. CONCLUSIONS The small protein encoded by ecr represents a new colistin heteroresistance mechanism and is likely to mediate colistin heteroresistance via the PhoP-PhoQ TCS to act on the arnBCADTEF operon.
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Affiliation(s)
- Liang Huang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Public Health Clinical Center of Chengdu, Chengdu, China
| | - Yu Feng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.,Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China
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39
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Rivas ZP, Talbot KM, Merselis LC, McCormack RM, Adkins B, Munson GP. CexE Is a Coat Protein and Virulence Factor of Diarrheagenic Pathogens. Front Microbiol 2020; 11:1374. [PMID: 32714302 PMCID: PMC7344145 DOI: 10.3389/fmicb.2020.01374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/28/2020] [Indexed: 12/27/2022] Open
Abstract
CexE is a 12 kDa protein that was originally reported to be present in just three strains of enterotoxigenic Escherichia coli (ETEC); a frequent cause of diarrheal illnesses worldwide. However, an examination of sequenced genomes has revealed that CexE is actually present in a majority of ETEC strains. In addition, homologs of CexE are present in enteroaggregative E. coli (EAEC), Yersinia enterocolitica, Providencia alcalifaciens, and Citrobacter rodentium. Although it has been hypothesized that CexE and its homologs are virulence factors, this has yet to be tested. Thus the primary aim of this study was to determine if these proteins contribute to pathogenicity. Our secondary aim was determine if they are secreted coat proteins. Here we report that all neonatal mice infected with a wild-type strain of C. rodentium perished. In contrast a cexE mutant was significantly attenuated with 45% neonate survival. In adult mice the wild-type strain reached significantly higher loads in the large intestines and were shed in greater numbers than cexE mutants. Secretion of the CexE homolog in EAEC is dependent upon an atypical Type I secretion system that accepts its client from the periplasm rather than the cytoplasm. Insertion mutants of cexC, the putative ATPase of the CexE secretion system, were attenuated in our murine model. In vitro we found that CexC is required for the secretion of CexE to the outer membranes of both ETEC and C. rodentium. Secretion is not constitutive because CexE accumulates in the periplasm when the two pathogens are cultured under noninducing conditions. Although secretion conditions differ between ETEC and C. rodentium, secreted CexE remains predominantly associated with the outer membranes of both species. In aggregate these findings demonstrate that CexE is a secreted coat protein and virulence factor that promotes colonization of host intestinal tissues by enteric pathogens.
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Affiliation(s)
| | | | | | | | | | - George P. Munson
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
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40
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Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance. Nat Commun 2020; 11:3105. [PMID: 32561723 PMCID: PMC7305214 DOI: 10.1038/s41467-020-16932-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022] Open
Abstract
Genetic perturbations that affect bacterial resistance to antibiotics have been characterized genome-wide, but how do such perturbations interact with subsequent evolutionary adaptation to the drug? Here, we show that strong epistasis between resistance mutations and systematically identified genes can be exploited to control spontaneous resistance evolution. We evolved hundreds of Escherichia coli K-12 mutant populations in parallel, using a robotic platform that tightly controls population size and selection pressure. We find a global diminishing-returns epistasis pattern: strains that are initially more sensitive generally undergo larger resistance gains. However, some gene deletion strains deviate from this general trend and curtail the evolvability of resistance, including deletions of genes for membrane transport, LPS biosynthesis, and chaperones. Deletions of efflux pump genes force evolution on inferior mutational paths, not explored in the wild type, and some of these essentially block resistance evolution. This effect is due to strong negative epistasis with resistance mutations. The identified genes and cellular functions provide potential targets for development of adjuvants that may block spontaneous resistance evolution when combined with antibiotics. The antibiotic resistance crisis calls for new ways of restricting the ability of bacteria to evolve resistance. Here, Lukačišinová et al. perform highly controlled evolution experiments in E. coli strains to identify genetic perturbations that strongly limit the evolution of antibiotic resistance through epistasis.
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41
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Subhadra B, Surendran S, Lim BR, Yim JS, Kim DH, Woo K, Kim HJ, Oh MH, Choi CH. Regulation of the AcrAB efflux system by the quorum-sensing regulator AnoR in Acinetobacter nosocomialis. J Microbiol 2020; 58:507-518. [PMID: 32462488 DOI: 10.1007/s12275-020-0185-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/11/2020] [Accepted: 05/11/2020] [Indexed: 10/24/2022]
Abstract
Multidrug efflux pumps play an important role in antimicrobial resistance and pathogenicity in bacteria. Here, we report the functional characterization of the RND (resistance-nodulation- division) efflux pump, AcrAB, in Acinetobacter nosocomialis. An in silico analysis revealed that homologues of the AcrAB efflux pump, comprising AcrA and AcrB, are widely distributed among different bacterial species. Deletion of acrA and/or acrB genes led to decreased biofilm/pellicle formation and reduced antimicrobial resistance in A. nosocomialis. RNA sequencing and mRNA expression analyses showed that expression of acrA/B was downregulated in a quorum sensing (QS) regulator (anoR)-deletion mutant, indicating transcriptional activation of the acrAB operon by AnoR in A. nosocomialis. Bioassays showed that secretion of N-acyl homoserine lactones (AHLs) was unaffected in acrA and acrB deletion mutants; however, AHL secretion was limited in a deletion mutant of acrR, encoding the acrAB regulator, AcrR. An in silico analysis indicated the presence of AcrR-binding motifs in promoter regions of anoI (encoding AHL synthase) and anoR. Specific binding of AcrR was confirmed by electrophoretic mobility shift assays, which revealed that AcrR binds to positions -214 and -217 bp upstream of the translational start sites of anoI and anoR, respectively, demonstrating transcriptional regulation of these QS genes by AcrR. The current study further addresses the possibility that AcrAB is controlled by the osmotic stress regulator, OmpR, in A. nosocomialis. Our data demonstrate that the AcrAB efflux pump plays a crucial role in biofilm/pellicle formation and antimicrobial resistance in A. nosocomialis, and is under the transcriptional control of a number of regulators. In addition, the study emphasizes the interrelationship of QS and AcrAB efflux systems in A. nosocomialis.
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Affiliation(s)
- Bindu Subhadra
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, 35015, Republic of Korea.,Department of Medical Science, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Surya Surendran
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, 35015, Republic of Korea.,Department of Medical Science, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Bo Ra Lim
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, 35015, Republic of Korea.,Department of Medical Science, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jong Sung Yim
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, 35015, Republic of Korea.,Department of Medical Science, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Dong Ho Kim
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, 35015, Republic of Korea.,Department of Medical Science, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Kyungho Woo
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, 35015, Republic of Korea.,Department of Medical Science, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hwa-Jung Kim
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, 35015, Republic of Korea.,Department of Medical Science, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Man Hwan Oh
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea.
| | - Chul Hee Choi
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, 35015, Republic of Korea. .,Department of Medical Science, Chungnam National University, Daejeon, 34134, Republic of Korea.
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42
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RNase E-dependent degradation of tnaA mRNA encoding tryptophanase is prerequisite for the induction of acid resistance in Escherichia coli. Sci Rep 2020; 10:7128. [PMID: 32346014 PMCID: PMC7188888 DOI: 10.1038/s41598-020-63981-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/09/2020] [Indexed: 01/25/2023] Open
Abstract
Acid-resistance systems are essential for pathogenic Escherichia coli to survive in the strongly acidic environment of the human stomach (pH < 2.5). Among these, the glutamic acid decarboxylase (GAD) system is the most effective. However, the precise mechanism of GAD induction is unknown. We previously reported that a tolC mutant lacking the TolC outer membrane channel was defective in GAD induction. Here, we show that indole, a substrate of TolC-dependent efflux pumps and produced by the tryptophanase encoded by the tnaA gene, negatively regulates GAD expression. GAD expression was restored by deleting tnaA in the tolC mutant; in wild-type E. coli, it was suppressed by adding indole to the growth medium. RNA-sequencing revealed that tnaA mRNA levels drastically decreased upon exposure to moderately acidic conditions (pH 5.5). This decrease was suppressed by RNase E deficiency. Collectively, our results demonstrate that the RNase E-dependent degradation of tnaA mRNA is accelerated upon acid exposure, which decreases intracellular indole concentrations and triggers GAD induction.
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43
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Feng Z, Liu D, Wang L, Wang Y, Zang Z, Liu Z, Song B, Gu L, Fan Z, Yang S, Chen J, Cui Y. A Putative Efflux Transporter of the ABC Family, YbhFSR, in Escherichia coli Functions in Tetracycline Efflux and Na +(Li +)/H + Transport. Front Microbiol 2020; 11:556. [PMID: 32390957 PMCID: PMC7190983 DOI: 10.3389/fmicb.2020.00556] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/16/2020] [Indexed: 12/20/2022] Open
Abstract
ATP-binding cassette transporters are ubiquitous in almost all organisms. The Escherichia coli genome is predicted to encode 69 ABC transporters. Eleven of the ABC transporters are presumed to be exporters, of which seven are possible drug export transporters. There has been minimal research on the function of YbhFSR, which is one of the putative drug resistance exporters. In this study, the ybhF gene of this transporter was characterized. Overexpression and knockout strains of ybhF were constructed. The ATPase activity of YbhF was studied using the malachite green assay, and the efflux abilities of knockout strains were demonstrated by using ethidium bromide (EB) as a substrate. The substrates of YbhFSR efflux, examined with the minimum inhibitory concentration (MIC), were determined to be tetracycline, oxytetracycline, chlortetracycline, doxycycline, EB, and Hoechst33342. Furthermore, tetracycline and EB efflux and accumulation experiments confirmed that the substrates of YbhFSR were tetracyclines and EB. The MIC assay and the fluorescence test results showed that tetracyclines are likely to be the major antibiotic substrate of YbhFSR. The existence of the signature NatA motif suggested that YbhFSR may also function as a Na+/H+ transporter. Overexpression of YbhF in E. coli KNabc lacking crucial Na+/H+ transporters conferred tolerance to NaCl, LiCl, and an alkaline pH. Together, the results showed that YbhFSR exhibited dual functions as a drug efflux pump and a Na+ (Li+)/H+ antiporter.
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Affiliation(s)
- Zhenyue Feng
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Defu Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Lizi Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yanhong Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhongjing Zang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhenhua Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Baifen Song
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Liwei Gu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhaowei Fan
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Siyu Yang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jing Chen
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yudong Cui
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
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Suppression of β-Lactam Resistance by Aspergillomarasmine A Is Influenced by both the Metallo-β-Lactamase Target and the Antibiotic Partner. Antimicrob Agents Chemother 2020; 64:AAC.01386-19. [PMID: 31932375 DOI: 10.1128/aac.01386-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 01/08/2020] [Indexed: 11/20/2022] Open
Abstract
The rise of Gram-negative pathogens expressing metallo-β-lactamases (MBLs) is a growing concern, threatening the efficacy of β-lactam antibiotics, in particular, the carbapenems. There are no inhibitors of MBLs in current clinical use. Aspergillomarasmine A (AMA) is an MBL inhibitor isolated from Aspergillus versicolor with the ability to rescue meropenem activity in MBL-producing bacteria both in vitro and in vivo Here, we systematically explored the pairing of AMA with six β-lactam antibiotic partners against 19 MBLs from three subclasses (B1, B2, and B3). Cell-based assays performed with Escherichia coli and Klebsiella pneumoniae showed that bacteria producing NDM-1 and VIM-2 of subclass B1 were the most susceptible to AMA inhibition, whereas bacteria producing CphA2 and AIM-1 of subclasses B2 and B3, respectively, were the least sensitive. Intracellular antibiotic accumulation assays and in vitro enzyme assays demonstrated that the efficacy of AMA/β-lactam combinations did not correlate with outer membrane permeability or drug efflux. We determined that the optimal β-lactam partners for AMA are the carbapenem antibiotics and that the efficacy of AMA is linked to the Zn2+ affinity of specific MBLs.
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Bunpa S, Chaichana N, Teng JLL, Lee HH, Woo PCY, Sermwittayawong D, Sawangjaroen N, Sermwittayawong N. Outer membrane protein A (OmpA) is a potential virulence factor of Vibrio alginolyticus strains isolated from diseased fish. JOURNAL OF FISH DISEASES 2020; 43:275-284. [PMID: 31779054 DOI: 10.1111/jfd.13120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 11/01/2019] [Accepted: 11/03/2019] [Indexed: 06/10/2023]
Abstract
Vibrio alginolyticus is one of the most serious causative agents of diseases in cultured marine fish and shellfish. However, the characteristics of virulence factors in pathogenic V. alginolyticus are poorly known. To gain insight into fish diseases caused by V. alginolyticus, we carried out two-dimensional gel electrophoresis (2-DE) combined with MALDI-TOF mass spectrometry to identify uniquely expressed proteins in the disease-causing V. alginolyticus. V. alginolyticus strains were isolated from marine environments and diseased fish obtained from southern Thailand. We identified seven unique proteins in the disease-causing V. alginolyticus strain. Among those, the outer membrane protein A (OmpA) had the strongest expression. Therefore, the function of this protein was further analysed. To investigate the role of OmpA protein, an in-frame deletion mutant of ompA was constructed using the homologous recombination method. Although the ompA mutant V. alginolyticus strain (ΔompA) grew normally, the mutant exhibited a significant defect in the swarming ability and the biofilm formation. Furthermore, Galleria mellonella larvae injected with the mutant bacteria had a significantly greater survival percentage than those injected with the wild-type strain, demonstrating that OmpA protein is required for the pathogenicity of V. alginolyticus. Together, this study suggests a potential target for vaccine development against pathogenic V. alginolyticus strain.
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Affiliation(s)
- Supansa Bunpa
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Nattarika Chaichana
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Jade L L Teng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hwei Huih Lee
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Patrick C Y Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Decha Sermwittayawong
- Department of Biochemistry, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Nongyao Sawangjaroen
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
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46
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Whole genome sequence analysis reveals the broad distribution of the RtxA type 1 secretion system and four novel putative type 1 secretion systems throughout the Legionella genus. PLoS One 2020; 15:e0223033. [PMID: 31935215 PMCID: PMC6959600 DOI: 10.1371/journal.pone.0223033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/17/2019] [Indexed: 01/18/2023] Open
Abstract
Type 1 secretion systems (T1SSs) are broadly distributed among bacteria and translocate effectors with diverse function across the bacterial cell membrane. Legionella pneumophila, the species most commonly associated with Legionellosis, encodes a T1SS at the lssXYZABD locus which is responsible for the secretion of the virulence factor RtxA. Many investigations have failed to detect lssD, the gene encoding the membrane fusion protein of the RtxA T1SS, in non-pneumophila Legionella, which has led to the assumption that this system is a virulence factor exclusively possessed by L. pneumophila. Here we discovered RtxA and its associated T1SS in a novel Legionella taurinensis strain, leading us to question whether this system may be more widespread than previously thought. Through a bioinformatic analysis of publicly available data, we classified and determined the distribution of four T1SSs including the RtxA T1SS and four novel T1SSs among diverse Legionella spp. The ABC transporter of the novel Legionella T1SS Legionella repeat protein secretion system shares structural similarity to those of diverse T1SS families, including the alkaline protease T1SS in Pseudomonas aeruginosa. The Legionella bacteriocin (1-3) secretion systems T1SSs are novel putative bacteriocin transporting T1SSs as their ABC transporters include C-39 peptidase domains in their N-terminal regions, with LB2SS and LB3SS likely constituting a nitrile hydratase leader peptide transport T1SSs. The LB1SS is more closely related to the colicin V T1SS in Escherichia coli. Of 45 Legionella spp. whole genomes examined, 19 (42%) were determined to possess lssB and lssD homologs. Of these 19, only 7 (37%) are known pathogens. There was no difference in the proportions of disease associated and non-disease associated species that possessed the RtxA T1SS (p = 0.4), contrary to the current consensus regarding the RtxA T1SS. These results draw into question the nature of RtxA and its T1SS as a singular virulence factor. Future studies should investigate mechanistic explanations for the association of RtxA with virulence.
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47
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Interplay of antibiotic resistance and food-associated stress tolerance in foodborne pathogens. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2019.11.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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48
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Frey J. RTX Toxins of Animal Pathogens and Their Role as Antigens in Vaccines and Diagnostics. Toxins (Basel) 2019; 11:toxins11120719. [PMID: 31835534 PMCID: PMC6950323 DOI: 10.3390/toxins11120719] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 01/19/2023] Open
Abstract
Exotoxins play a central role in the pathologies caused by most major bacterial animal pathogens. The large variety of vertebrate and invertebrate hosts in the animal kingdom is reflected by a large variety of bacterial pathogens and toxins. The group of repeats in the structural toxin (RTX) toxins is particularly abundant among bacterial pathogens of animals. Many of these toxins are described as hemolysins due to their capacity to lyse erythrocytes in vitro. Hemolysis by RTX toxins is due to the formation of cation-selective pores in the cell membrane and serves as an important marker for virulence in bacterial diagnostics. However, their physiologic relevant targets are leukocytes expressing β2 integrins, which act as specific receptors for RTX toxins. For various RTX toxins, the binding to the CD18 moiety of β2 integrins has been shown to be host specific, reflecting the molecular basis of the host range of RTX toxins expressed by bacterial pathogens. Due to the key role of RTX toxins in the pathogenesis of many bacteria, antibodies directed against specific RTX toxins protect against disease, hence, making RTX toxins valuable targets in vaccine research and development. Due to their specificity, several structural genes encoding for RTX toxins have proven to be essential in modern diagnostic applications in veterinary medicine.
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Affiliation(s)
- Joachim Frey
- Vetsuisse Facutly, University of Bern, 3012 Bern, Switzerland
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49
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Fonseca NP, Patané JSL, Varani AM, Felestrino ÉB, Caneschi WL, Sanchez AB, Cordeiro IF, Lemes CGDC, Assis RDAB, Garcia CCM, Belasque J, Martins J, Facincani AP, Ferreira RM, Jaciani FJ, de Almeida NF, Ferro JA, Moreira LM, Setubal JC. Analyses of Seven New Genomes of Xanthomonas citri pv. aurantifolii Strains, Causative Agents of Citrus Canker B and C, Show a Reduced Repertoire of Pathogenicity-Related Genes. Front Microbiol 2019; 10:2361. [PMID: 31681223 PMCID: PMC6797930 DOI: 10.3389/fmicb.2019.02361] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 09/27/2019] [Indexed: 11/21/2022] Open
Abstract
Xanthomonas citri pv. aurantifolii pathotype B (XauB) and pathotype C (XauC) are the causative agents respectively of citrus canker B and C, diseases of citrus plants related to the better-known citrus canker A, caused by Xanthomonas citri pv. citri. The study of the genomes of strains of these related bacterial species has the potential to bring new understanding to the molecular basis of citrus canker as well as their evolutionary history. Up to now only one genome sequence of XauB and only one genome sequence of XauC have been available, both in draft status. Here we present two new genome sequences of XauB (both complete) and five new genome sequences of XauC (two complete). A phylogenomic analysis of these seven genome sequences along with 24 other related Xanthomonas genomes showed that there are two distinct and well-supported major clades, the XauB and XauC clade and the Xanthomonas citri pv. citri clade. An analysis of 62 Type III Secretion System effector genes showed that there are 42 effectors with variable presence/absence or pseudogene status among the 31 genomes analyzed. A comparative analysis of secretion-system and surface-structure genes showed that the XauB and XauC genomes lack several key genes in pathogenicity-related subsystems. These subsystems, the Types I and IV Secretion Systems, and the Type IV pilus, therefore emerge as important ones in helping explain the aggressiveness of the A type of citrus canker and the apparent dominance in the field of the corresponding strain over the B and C strains.
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Affiliation(s)
- Natasha Peixoto Fonseca
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - José S L Patané
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
| | - Alessandro M Varani
- Departamento de Tecnologia, Universidade Estadual Paulista, UNESP, Campus de Jaboticabal, Jaboticabal, Brazil
| | - Érica Barbosa Felestrino
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Washington Luiz Caneschi
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Angélica Bianchini Sanchez
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Isabella Ferreira Cordeiro
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Camila Gracyelle de Carvalho Lemes
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Renata de Almeida Barbosa Assis
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Camila Carrião Machado Garcia
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - José Belasque
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, Brazil
| | - Joaquim Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Agda Paula Facincani
- Departamento de Tecnologia, Universidade Estadual Paulista, UNESP, Campus de Jaboticabal, Jaboticabal, Brazil
| | - Rafael Marini Ferreira
- Departamento de Tecnologia, Universidade Estadual Paulista, UNESP, Campus de Jaboticabal, Jaboticabal, Brazil
| | | | | | - Jesus Aparecido Ferro
- Departamento de Tecnologia, Universidade Estadual Paulista, UNESP, Campus de Jaboticabal, Jaboticabal, Brazil
| | - Leandro Marcio Moreira
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil.,Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - João C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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50
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Hews CL, Cho T, Rowley G, Raivio TL. Maintaining Integrity Under Stress: Envelope Stress Response Regulation of Pathogenesis in Gram-Negative Bacteria. Front Cell Infect Microbiol 2019; 9:313. [PMID: 31552196 PMCID: PMC6737893 DOI: 10.3389/fcimb.2019.00313] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/19/2019] [Indexed: 12/20/2022] Open
Abstract
The Gram-negative bacterial envelope is an essential interface between the intracellular and harsh extracellular environment. Envelope stress responses (ESRs) are crucial to the maintenance of this barrier and function to detect and respond to perturbations in the envelope, caused by environmental stresses. Pathogenic bacteria are exposed to an array of challenging and stressful conditions during their lifecycle and, in particular, during infection of a host. As such, maintenance of envelope homeostasis is essential to their ability to successfully cause infection. This review will discuss our current understanding of the σE- and Cpx-regulated ESRs, with a specific focus on their role in the virulence of a number of model pathogens.
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Affiliation(s)
- Claire L Hews
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Timothy Cho
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Gary Rowley
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Tracy L Raivio
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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