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Wang F, Sun H, Kang C, Yan J, Chen J, Feng X, Yang B. Genomic island-encoded regulatory proteins in enterohemorrhagic Escherichia coli O157:H7. Virulence 2024; 15:2313407. [PMID: 38357901 PMCID: PMC10877973 DOI: 10.1080/21505594.2024.2313407] [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: 10/24/2023] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) is an important zoonotic pathogen that is a major cause of foodborne diseases in most developed and developing countries and can cause uncomplicated diarrhoea, haemorrhagic colitis, and haemolytic uraemic syndrome. O islands (OIs), which are unique genomic islands in EHEC O157:H7, are composed of 177 isolated genomic features and harbour 26% of the total genes that are absent in the non-pathogenic E. coli K-12 genome. In the last twenty years, many OI-encoded proteins have been characterized, including proteins regulating virulence, motility, and acid resistance. Given the critical role of regulatory proteins in the systematic and hierarchical regulation of bacterial biological processes, this review summarizes the OI-encoded regulatory proteins in EHEC O157:H7 characterized to date, emphasizing OI-encoded regulatory proteins for bacterial virulence, motility, and acid resistance. This summary will be significant for further exploration and understanding of the virulence and pathogenesis of EHEC O157:H7.
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Affiliation(s)
- Fang Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- Intensive Care Unit, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Hongmin Sun
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Chenbo Kang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Jun Yan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Jingnan Chen
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Xuequan Feng
- Tianjin First Central Hospital, Nankai University, Tianjin, China
| | - Bin Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
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2
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Young MG, Straub TJ, Worby CJ, Metsky HC, Gnirke A, Bronson RA, van Dijk LR, Desjardins CA, Matranga C, Qu J, Villicana JB, Azimzadeh P, Kau A, Dodson KW, Schreiber HL, Manson AL, Hultgren SJ, Earl AM. Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582780. [PMID: 38463963 PMCID: PMC10925322 DOI: 10.1101/2024.02.29.582780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Low-abundance members of microbial communities are difficult to study in their native habitats. This includes Escherichia coli, a minor, but common inhabitant of the gastrointestinal tract and opportunistic pathogen, including of the urinary tract, where it is the primary pathogen. While multi-omic analyses have detailed critical interactions between uropathogenic Escherichia coli (UPEC) and the bladder that mediate UTI outcome, comparatively little is known about UPEC in its pre-infection reservoir, partly due to its low abundance there (<1% relative abundance). To accurately and sensitively explore the genomes and transcriptomes of diverse E. coli in gastrointestinal communities, we developed E. coli PanSelect which uses a set of probes designed to specifically recognize and capture E. coli's broad pangenome from sequencing libraries. We demonstrated the ability of E. coli PanSelect to enrich, by orders of magnitude, sequencing data from diverse E. coli using a mock community and a set of human stool samples collected as part of a cohort study investigating drivers of recurrent urinary tract infections (rUTI). Comparisons of genomes and transcriptomes between E. coli residing in the gastrointestinal tracts of women with and without a history of rUTI suggest that rUTI gut E. coli are responding to increased levels of oxygen and nitrate, suggestive of mucosal inflammation, which may have implications for recurrent disease. E. coli PanSelect is well suited for investigations of native in vivo biology of E. coli in other environments where it is at low relative abundance, and the framework described here has broad applicability to other highly diverse, low abundance organisms.
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Affiliation(s)
- Mark G Young
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Timothy J Straub
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Colin J Worby
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Hayden C Metsky
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Andreas Gnirke
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Ryan A Bronson
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Lucas R van Dijk
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands
| | | | - Christian Matranga
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - James Qu
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Jesús Bazan Villicana
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Philippe Azimzadeh
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrew Kau
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
- Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Karen W Dodson
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Henry L Schreiber
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Abigail L Manson
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Scott J Hultgren
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Ashlee M Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
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3
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Li J, Ma Q, Huang J, Liu Y, Zhou J, Yu S, Zhang Q, Lin Y, Wang L, Zou J, Li Y. Small RNA SmsR1 modulates acidogenicity and cariogenic virulence by affecting protein acetylation in Streptococcus mutans. PLoS Pathog 2024; 20:e1012147. [PMID: 38620039 PMCID: PMC11045139 DOI: 10.1371/journal.ppat.1012147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/25/2024] [Accepted: 03/25/2024] [Indexed: 04/17/2024] Open
Abstract
Post-transcriptional regulation by small RNAs and post-translational modifications (PTM) such as lysine acetylation play fundamental roles in physiological circuits, offering rapid responses to environmental signals with low energy consumption. Yet, the interplay between these regulatory systems remains underexplored. Here, we unveil the cross-talk between sRNAs and lysine acetylation in Streptococcus mutans, a primary cariogenic pathogen known for its potent acidogenic virulence. Through systematic overexpression of sRNAs in S. mutans, we identified sRNA SmsR1 as a critical player in modulating acidogenicity, a key cariogenic virulence feature in S. mutans. Furthermore, combined with the analysis of predicted target mRNA and transcriptome results, potential target genes were identified and experimentally verified. A direct interaction between SmsR1 and 5'-UTR region of pdhC gene was determined by in vitro binding assays. Importantly, we found that overexpression of SmsR1 reduced the expression of pdhC mRNA and increased the intracellular concentration of acetyl-CoA, resulting in global changes in protein acetylation levels. This was verified by acetyl-proteomics in S. mutans, along with an increase in acetylation level and decreased activity of LDH. Our study unravels a novel regulatory paradigm where sRNA bridges post-transcriptional regulation with post-translational modification, underscoring bacterial adeptness in fine-tuning responses to environmental stress.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qizhao Ma
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jun Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yaqi Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jing Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shuxing Yu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qiong Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yongwang Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Lingyun Wang
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Jing Zou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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4
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Martinez GS, Perez-Rueda E, Kumar A, Dutt M, Maya CR, Ledesma-Dominguez L, Casa PL, Kumar A, de Avila e Silva S, Kelvin DJ. CDBProm: the Comprehensive Directory of Bacterial Promoters. NAR Genom Bioinform 2024; 6:lqae018. [PMID: 38385146 PMCID: PMC10880602 DOI: 10.1093/nargab/lqae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/12/2024] [Accepted: 01/29/2024] [Indexed: 02/23/2024] Open
Abstract
The decreasing cost of whole genome sequencing has produced high volumes of genomic information that require annotation. The experimental identification of promoter sequences, pivotal for regulating gene expression, is a laborious and cost-prohibitive task. To expedite this, we introduce the Comprehensive Directory of Bacterial Promoters (CDBProm), a directory of in-silico predicted bacterial promoter sequences. We first identified that an Extreme Gradient Boosting (XGBoost) algorithm would distinguish promoters from random downstream regions with an accuracy of 87%. To capture distinctive promoter signals, we generated a second XGBoost classifier trained on the instances misclassified in our first classifier. The predictor of CDBProm is then fed with over 55 million upstream regions from more than 6000 bacterial genomes. Upon finding potential promoter sequences in upstream regions, each promoter is mapped to the genomic data of the organism, linking the predicted promoter with its coding DNA sequence, and identifying the function of the gene regulated by the promoter. The collection of bacterial promoters available in CDBProm enables the quantitative analysis of a plethora of bacterial promoters. Our collection with over 24 million promoters is publicly available at https://aw.iimas.unam.mx/cdbprom/.
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Affiliation(s)
- Gustavo Sganzerla Martinez
- Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
- Pediatrics, Izaak Walton Killam (IWK) Health Center. Canadian Center for Vaccinology (CCfV), Halifax, Nova Scotia B3H 4H7, Canada
- BioForge Canada Limited, Halifax, Nova Scotia B3N 3B9, Canada
| | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autonóma de México, Unidad Académica del Estado de Yucatán, Mérida 97302, Yucatán, Mexico
| | - Anuj Kumar
- Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
- Pediatrics, Izaak Walton Killam (IWK) Health Center. Canadian Center for Vaccinology (CCfV), Halifax, Nova Scotia B3H 4H7, Canada
- BioForge Canada Limited, Halifax, Nova Scotia B3N 3B9, Canada
| | - Mansi Dutt
- Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
- Pediatrics, Izaak Walton Killam (IWK) Health Center. Canadian Center for Vaccinology (CCfV), Halifax, Nova Scotia B3H 4H7, Canada
- BioForge Canada Limited, Halifax, Nova Scotia B3N 3B9, Canada
| | - Cinthia Rodríguez Maya
- Facultad de Ciencias e Ingeniería, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico
| | - Leonardo Ledesma-Dominguez
- Instituto de Investigaciones en Matematicas Aplicadas y en Sistemas, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico
| | - Pedro Lenz Casa
- Biotechnology Institute, Universidade de Caxias do Sul, Caxias do Sul, Rio Grande do Sul 95070-560, Brazil
| | - Aditya Kumar
- Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam 784028, India
| | - Scheila de Avila e Silva
- Biotechnology Institute, Universidade de Caxias do Sul, Caxias do Sul, Rio Grande do Sul 95070-560, Brazil
| | - David J Kelvin
- Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
- Pediatrics, Izaak Walton Killam (IWK) Health Center. Canadian Center for Vaccinology (CCfV), Halifax, Nova Scotia B3H 4H7, Canada
- BioForge Canada Limited, Halifax, Nova Scotia B3N 3B9, Canada
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5
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David L, Shpigel E, Levin I, Moshe S, Zimmerman L, Dadon-Simanowitz S, Shemer B, Levkovich SA, Larush L, Magdassi S, Belkin S. Performance upgrade of a microbial explosives' sensor strain by screening a high throughput saturation library of a transcriptional regulator. Comput Struct Biotechnol J 2023; 21:4252-4260. [PMID: 37701016 PMCID: PMC10493890 DOI: 10.1016/j.csbj.2023.08.017] [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: 05/31/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/14/2023] Open
Abstract
We present a methodology for a high-throughput screening (HTS) of transcription factor libraries, based on bacterial cells and GFP fluorescence. The method is demonstrated on the Escherichia coli LysR-type transcriptional regulator YhaJ, a key element in 2,4-dinitrotuluene (DNT) detection by bacterial explosives' sensor strains. Enhancing the performance characteristics of the YhaJ transcription factor is essential for future standoff detection of buried landmines. However, conventional directed evolution methods for modifying YhaJ are limited in scope, due to the vast sequence space and the absence of efficient screening methods to select optimal transcription factor mutants. To overcome this limitation, we have constructed a focused saturation library of ca. 6.4 × 107 yhaJ variants, and have screened over 70 % of its sequence space using fluorescence-activated cell sorting (FACS). Through this screening process, we have identified YhaJ mutants exhibiting superior fluorescence responses to DNT, which were then effectively transformed into a bioluminescence-based DNT detection system. The best modified DNT reporter strain demonstrated a 7-fold lower DNT detection threshold, a 45-fold increased signal intensity, and a 40 % shorter response time compared to the parental bioreporter. The FACS-based HTS approach presented here may hold a potential for future molecular enhancement of other sensing and catalytic bioreactions.
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Affiliation(s)
- Lidor David
- Enzymit Ltd. 3 Pinhas Sapir St., Ness Ziona 7403626, Israel
| | - Etai Shpigel
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Itay Levin
- Enzymit Ltd. 3 Pinhas Sapir St., Ness Ziona 7403626, Israel
| | - Shaked Moshe
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Lior Zimmerman
- Enzymit Ltd. 3 Pinhas Sapir St., Ness Ziona 7403626, Israel
| | | | - Benjamin Shemer
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Shon A. Levkovich
- George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Liraz Larush
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Shlomo Magdassi
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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6
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O’Boyle N, Douce GR, Farrell G, Rattray NJW, Schembri MA, Roe AJ, Connolly JPR. Distinct ecological fitness factors coordinated by a conserved Escherichia coli regulator during systemic bloodstream infection. Proc Natl Acad Sci U S A 2023; 120:e2212175120. [PMID: 36574699 PMCID: PMC9910484 DOI: 10.1073/pnas.2212175120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/11/2022] [Indexed: 12/28/2022] Open
Abstract
The ability of bacterial pathogens to adapt to host niches is driven by the carriage and regulation of genes that benefit pathogenic lifestyles. Genes that encode virulence or fitness-enhancing factors must be regulated in response to changing host environments to allow rapid response to challenges presented by the host. Furthermore, this process can be controlled by preexisting transcription factors (TFs) that acquire new roles in tailoring regulatory networks, specifically in pathogens. However, the mechanisms underlying this process are poorly understood. The highly conserved Escherichia coli TF YhaJ exhibits distinct genome-binding dynamics and transcriptome control in pathotypes that occupy different host niches, such as uropathogenic E. coli (UPEC). Here, we report that this important regulator is required for UPEC systemic survival during murine bloodstream infection (BSI). This advantage is gained through the coordinated regulation of a small regulon comprised of both virulence and metabolic genes. YhaJ coordinates activation of both Type 1 and F1C fimbriae, as well as biosynthesis of the amino acid tryptophan, by both direct and indirect mechanisms. Deletion of yhaJ or the individual genes under its control leads to attenuated survival during BSI. Furthermore, all three systems are up-regulated in response to signals derived from serum or systemic host tissue, but not urine, suggesting a niche-specific regulatory trigger that enhances UPEC fitness via pleiotropic mechanisms. Collectively, our results identify YhaJ as a pathotype-specific regulatory aide, enhancing the expression of key genes that are collectively required for UPEC bloodstream pathogenesis.
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Affiliation(s)
- Nicky O’Boyle
- School of Microbiology, University College Cork, National University of Ireland, CorkT12 K8AF, Ireland
| | - Gillian R. Douce
- Institute of Infection, Immunity and Inflammation, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Gillian Farrell
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, GlasgowG4 0RE, United Kingdom
| | - Nicholas J. W. Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, GlasgowG4 0RE, United Kingdom
| | - Mark A. Schembri
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Andrew J. Roe
- Institute of Infection, Immunity and Inflammation, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - James P. R. Connolly
- Newcastle University Biosciences Institute, Newcastle University, Newcastle-upon-TyneNE2 4HH, United Kingdom
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7
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Roussel C, Chabaud S, Lessard-Lord J, Cattero V, Pellerin FA, Feutry P, Bochard V, Bolduc S, Desjardins Y. UPEC Colonic-Virulence and Urovirulence Are Blunted by Proanthocyanidins-Rich Cranberry Extract Microbial Metabolites in a Gut Model and a 3D Tissue-Engineered Urothelium. Microbiol Spectr 2022; 10:e0243221. [PMID: 35972287 PMCID: PMC9603664 DOI: 10.1128/spectrum.02432-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 07/27/2022] [Indexed: 01/04/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) ecology-pathophysiology from the gut reservoir to its urothelium infection site is poorly understood, resulting in equivocal benefits in the use of cranberry as prophylaxis against urinary tract infections. To add further understanding from the previous findings on PAC antiadhesive properties against UPEC, we assessed in this study the effects of proanthocyanidins (PAC) rich cranberry extract microbial metabolites on UTI89 virulence and fitness in contrasting ecological UPEC's environments. For this purpose, we developed an original model combining a colonic fermentation system (SHIME) with a dialysis cassette device enclosing UPEC and a 3D tissue-engineered urothelium. Two healthy fecal donors inoculated the colons. Dialysis cassettes containing 7log10 CFU/mL UTI89 were immersed for 2h in the SHIME colons to assess the effect of untreated (7-day control diet)/treated (14-day PAC-rich extract) metabolomes on UPEC behavior. Engineered urothelium were then infected with dialysates containing UPEC for 6 h. This work demonstrated for the first time that in the control fecal microbiota condition without added PAC, the UPEC virulence genes were activated upstream the infection site, in the gut. However, PAC microbial-derived cranberry metabolites displayed a remarkable propensity to blunt activation of genes encoding toxin, adhesin/invasins in the gut and on the urothelium, in a donor-dependent manner. Variability in subjects' gut microbiota and ensuing contrasting cranberry PAC metabolism affects UPEC virulence and should be taken into consideration when designing cranberry efficacy clinical trials. IMPORTANCE Uropathogenic Escherichia coli (UPEC) are the primary cause of recurrent urinary tract infections (UTI). The poor understanding of UPEC ecology-pathophysiology from its reservoir-the gut, to its infection site-the urothelium, partly explains the inadequate and abusive use of antibiotics to treat UTI, which leads to a dramatic upsurge in antibiotic-resistance cases. In this context, we evaluated the effect of a cranberry proanthocyanidins (PAC)-rich extract on the UPEC survival and virulence in a bipartite model of a gut microbial environment and a 3D urothelium model. We demonstrated that PAC-rich cranberry extract microbial metabolites significantly blunt activation of UPEC virulence genes at an early stage in the gut reservoir. We also showed that altered virulence in the gut affects infectivity on the urothelium in a microbiota-dependent manner. Among the possible mechanisms, we surmise that specific microbial PAC metabolites may attenuate UPEC virulence, thereby explaining the preventative, yet contentious properties of cranberry against UTI.
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Affiliation(s)
- Charlène Roussel
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Québec, Quebec, Canada
| | - Stéphane Chabaud
- Centre de Recherche en Organogenèse Expérimentale de l Université Laval/LOEX, Centre de Recherche du CHU de Québec‐Université Laval, Axe Médecine Régénératrice, Québec, Quebec, Canada
| | - Jacob Lessard-Lord
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Québec, Quebec, Canada
| | - Valentina Cattero
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Québec, Quebec, Canada
| | - Félix-Antoine Pellerin
- Centre de Recherche en Organogenèse Expérimentale de l Université Laval/LOEX, Centre de Recherche du CHU de Québec‐Université Laval, Axe Médecine Régénératrice, Québec, Quebec, Canada
| | - Perrine Feutry
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Québec, Quebec, Canada
| | | | - Stéphane Bolduc
- Centre de Recherche en Organogenèse Expérimentale de l Université Laval/LOEX, Centre de Recherche du CHU de Québec‐Université Laval, Axe Médecine Régénératrice, Québec, Quebec, Canada
| | - Yves Desjardins
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Québec, Quebec, Canada
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8
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Elad T, Shemer B, Simanowitz S, Kabessa Y, Mizrachi Y, Gold A, Shpigel E, Agranat AJ, Belkin S. Enhancing DNT Detection by a Bacterial Bioreporter: Directed Evolution of the Transcriptional Activator YhaJ. Front Bioeng Biotechnol 2022; 10:821835. [PMID: 35237579 PMCID: PMC8882911 DOI: 10.3389/fbioe.2022.821835] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/17/2022] [Indexed: 12/20/2022] Open
Abstract
Detection of buried landmines is a dangerous and complicated task that consumes large financial resources and poses significant risks to the personnel involved. A potential alternative to conventional detection methodologies is the use of microbial bioreporters, capable of emitting an optical signal upon exposure to explosives, thus revealing to a remote detector the location of buried explosive devices. We have previously reported the design, construction, and optimization of an Escherichia coli-based bioreporter for the detection of 2,4,6-trinitrotoluene (TNT) and its accompanying impurity 2,4-dinitrotoluene (DNT). Here we describe the further enhancement of this bioreporter by the directed evolution of YhaJ, the transcriptional activator of the yqjF gene promoter, the sensing element of the bioreporter's molecular circuit. This process resulted in a 37-fold reduction of the detection threshold, as well as significant enhancements to signal intensity and response time, rendering this sensor strain more suitable for detecting the minute concentrations of DNT in the soil above buried landmines. The capability of this enhanced bioreporter to detect DNT buried in sand is demonstrated.
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Affiliation(s)
- Tal Elad
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Benjamin Shemer
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shilat Simanowitz
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yossef Kabessa
- Department of Applied Physics and the Brojde Center for Innovative Engineering and Computer Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yosef Mizrachi
- Department of Applied Physics and the Brojde Center for Innovative Engineering and Computer Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Azriel Gold
- Department of Applied Physics and the Brojde Center for Innovative Engineering and Computer Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Etai Shpigel
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Aharon J. Agranat
- Department of Applied Physics and the Brojde Center for Innovative Engineering and Computer Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shimshon Belkin
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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9
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Affiliation(s)
- Gavin H. Thomas
- Department of Biology, University of York, York, PO Box 373, UK,*Correspondence: Gavin H. Thomas,
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10
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Thomas GH. Microbial Musings – March 2021. Microbiology (Reading) 2021; 167. [DOI: 10.1099/mic.0.001053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Gavin H. Thomas
- Department of Biology, University of York, York YO10 5YW, UK
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Sy BM, Tree JJ. Small RNA Regulation of Virulence in Pathogenic Escherichia coli. Front Cell Infect Microbiol 2021; 10:622202. [PMID: 33585289 PMCID: PMC7873438 DOI: 10.3389/fcimb.2020.622202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/10/2020] [Indexed: 11/17/2022] Open
Abstract
Enteric and extraintestinal pathotypes of Escherichia coli utilize a wide range of virulence factors to colonize niches within the human body. During infection, virulence factors such as adhesins, secretions systems, or toxins require precise regulation and coordination to ensure appropriate expression. Additionally, the bacteria navigate rapidly changing environments with fluctuations in pH, temperature, and nutrient levels. Enteric pathogens utilize sophisticated, interleaved systems of transcriptional and post-transcriptional regulation to sense and respond to these changes and modulate virulence gene expression. Regulatory small RNAs and RNA-binding proteins play critical roles in the post-transcriptional regulation of virulence. In this review we discuss how the mosaic genomes of Escherichia coli pathotypes utilize small RNA regulation to adapt to their niche and become successful human pathogens.
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Affiliation(s)
- Brandon M Sy
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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12
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Khan F, Tabassum N, Pham DTN, Oloketuyi SF, Kim YM. Molecules involved in motility regulation in Escherichia coli cells: a review. BIOFOULING 2020; 36:889-908. [PMID: 33028083 DOI: 10.1080/08927014.2020.1826939] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
The initial colonization of the host organism by commensal, probiotic, and pathogenic Escherichia coli strains is an important step in the development of infections and biofilms. Sensing and colonization of host cell surfaces are governed by flagellar and fimbriae/pili appendages, respectively. Biofilm formation confers great advantages on pathogenic E. coli cells such as protection against the host immune system, antimicrobial agents, and several environmental stress factors. The transition from planktonic to sessile physiological states involves several signaling cascades and factors responsible for the regulation of flagellar motility in E. coli cells. These regulatory factors have thus become important targets to control pathogenicity. Hence, attenuation of flagellar motility is considered a potential therapy against pathogenic E. coli. The present review describes signaling pathways and proteins involved in direct or indirect regulation of flagellar motility. Furthermore, application strategies for antimotility natural or synthetic compounds are discussed also.
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Affiliation(s)
- Fazlurrahman Khan
- Institute of Food Science, Pukyong National University, Busan, Republic of Korea
| | - Nazia Tabassum
- Industrial Convergence Bionix Engineering, Pukyong National University, Busan, Republic of Korea
| | - Dung Thuy Nguyen Pham
- Department of Food Science and Technology, Pukyong National University, Busan, Republic of Korea
| | | | - Young-Mog Kim
- Institute of Food Science, Pukyong National University, Busan, Republic of Korea
- Department of Food Science and Technology, Pukyong National University, Busan, Republic of Korea
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13
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Widespread Strain-Specific Distinctions in Chromosomal Binding Dynamics of a Highly Conserved Escherichia coli Transcription Factor. mBio 2020; 11:mBio.01058-20. [PMID: 32576674 PMCID: PMC7315121 DOI: 10.1128/mbio.01058-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial gene regulation is governed by often hundreds of transcription factors (TFs) that bind directly to targets on the chromosome. Global studies of TFs usually make assumptions that regulatory targets within model strains will be conserved between members of the same species harboring common genetic targets. We recently discovered that YhaJ of Escherichia coli is crucial for virulence in two different pathotypes but binds to distinct regions of their genomes and regulates no common genes. This surprising result leads to strain-specific mechanisms of virulence regulation, but the implications for other E. coli pathotypes or commensals were unclear. Here, we report that heterogenous binding of YhaJ is widespread within the E. coli species. We analyzed the global YhaJ binding dynamics of four evolutionarily distinct E. coli isolates under two conditions, revealing 78 significant sites on the core genome as well as horizontally acquired loci. Condition-dependent dosage of YhaJ correlated with the number of occupied sites in vivo but did not significantly alter its enrichment at regions bound in both conditions, explaining the availability of this TF to occupy accessory sites in response to the environment. Strikingly, only ∼15% of YhaJ binding sites were common to all strains. Furthermore, differences in enrichment of uncommon sites were observed largely in chromosomal regions found in all strains and not explained exclusively by binding to strain-specific horizontally acquired elements or mutations in the DNA binding sequence. This observation suggests that intraspecies distinctions in TF binding dynamics are a widespread phenomenon and represent strain-specific gene regulatory potential.IMPORTANCE In bacterial cells, hundreds of transcription factors coordinate gene regulation and thus are a major driver of cellular processes. However, the immense diversity in bacterial genome structure and content makes deciphering regulatory networks challenging. This is particularly apparent for the model organism Escherichia coli as evolution has driven the emergence of species members with highly distinct genomes, which occupy extremely different niches in nature. While it is well-known that transcription factors must integrate horizontally acquired DNA into the regulatory network of the cell, the extent of regulatory diversity beyond single model strains is unclear. We have explored this concept in four evolutionarily distinct E. coli strains and show that a highly conserved transcription factor displays unprecedented diversity in chromosomal binding sites. Importantly, this diversity is not restricted to strain-specific DNA or mutation in binding sites. This observation suggests that strain-specific regulatory networks are potentially widespread within individual bacterial species.
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Cen S, Yin R, Mao B, Zhao J, Zhang H, Zhai Q, Chen W. Comparative genomics shows niche-specific variations of Lactobacillus plantarum strains isolated from human, Drosophila melanogaster, vegetable and dairy sources. FOOD BIOSCI 2020. [DOI: 10.1016/j.fbio.2020.100581] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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O'Boyle N, Turner NCA, Roe AJ, Connolly JPR. Plastic Circuits: Regulatory Flexibility in Fine Tuning Pathogen Success. Trends Microbiol 2020; 28:360-371. [PMID: 32298614 DOI: 10.1016/j.tim.2020.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/07/2020] [Accepted: 01/16/2020] [Indexed: 12/30/2022]
Abstract
Bacterial pathogens employ diverse fitness and virulence mechanisms to gain an advantage in competitive niches. These lifestyle-specific traits require integration into the regulatory network of the cell and are often controlled by pre-existing transcription factors. In this review, we highlight recent advances that have been made in characterizing this regulatory flexibility in prominent members of the Enterobacteriaceae. We focus on the direct global interactions between transcription factors and their target genes in pathogenic Escherichia coli and Salmonella revealed using chromatin immunoprecipitation coupled with next-generation sequencing. Furthermore, the implications and advantages of such regulatory adaptations in benefiting distinct pathogenic lifestyles are discussed.
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Affiliation(s)
- Nicky O'Boyle
- Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Natasha C A Turner
- Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Andrew J Roe
- Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK.
| | - James P R Connolly
- Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK; Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK.
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