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Ching C, Brychcy M, Nguyen B, Muller P, Pearson AR, Downs M, Regan S, Isley B, Fowle W, Chai Y, Godoy VG. RecA levels modulate biofilm development in Acinetobacter baumannii. Mol Microbiol 2024; 121:196-212. [PMID: 37918886 DOI: 10.1111/mmi.15188] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/06/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
Infections caused by Acinetobacter baumannii, a Gram-negative opportunistic pathogen, are difficult to eradicate due to the bacterium's propensity to quickly gain antibiotic resistances and form biofilms, a protective bacterial multicellular community. The A. baumannii DNA damage response (DDR) mediates the antibiotic resistance acquisition and regulates RecA in an atypical fashion; both RecALow and RecAHigh cell types are formed in response to DNA damage. The findings of this study demonstrate that the levels of RecA can influence formation and dispersal of biofilms. RecA loss results in surface attachment and prominent biofilms, while elevated RecA leads to diminished attachment and dispersal. These findings suggest that the challenge to treat A. baumannii infections may be explained by the induction of the DDR, common during infection, as well as the delicate balance between maintaining biofilms in low RecA cells and promoting mutagenesis and dispersal in high RecA cells. This study underscores the importance of understanding the fundamental biology of bacteria to develop more effective treatments for infections.
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Affiliation(s)
- Carly Ching
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Merlin Brychcy
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Brian Nguyen
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Paul Muller
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | | | - Margaret Downs
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Samuel Regan
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Breanna Isley
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - William Fowle
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Yunrong Chai
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Veronica G Godoy
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
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2
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Vuotto C, Donelli G, Buckley A, Chilton C. Clostridioides difficile Biofilm. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:249-272. [PMID: 38175479 DOI: 10.1007/978-3-031-42108-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clostridioides difficile infection (CDI), previously Clostridium difficile infection, is a symptomatic infection of the large intestine caused by the spore-forming anaerobic, gram-positive bacterium Clostridioides difficile. CDI is an important healthcare-associated disease worldwide, characterized by high levels of recurrence, morbidity, and mortality. CDI is observed at a higher rate in immunocompromised patients after antimicrobial therapy, with antibiotics disrupting the commensal microbiota and promoting C. difficile colonization of the gastrointestinal tract.A rise in clinical isolates resistant to multiple antibiotics and the reduced susceptibility to the most commonly used antibiotic molecules have made the treatment of CDI more complicated, allowing the persistence of C. difficile in the intestinal environment.Gut colonization and biofilm formation have been suggested to contribute to the pathogenesis and persistence of C. difficile. In fact, biofilm growth is considered as a serious threat because of the related antimicrobial tolerance that makes antibiotic therapy often ineffective. This is the reason why the involvement of C. difficile biofilm in the pathogenesis and recurrence of CDI is attracting more and more interest, and the mechanisms underlying biofilm formation of C. difficile as well as the role of biofilm in CDI are increasingly being studied by researchers in the field.Findings on C. difficile biofilm, possible implications in CDI pathogenesis and treatment, efficacy of currently available antibiotics in treating biofilm-forming C. difficile strains, and some antimicrobial alternatives under investigation will be discussed here.
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Affiliation(s)
- Claudia Vuotto
- Microbial Biofilm Laboratory, IRCCS Fondazione Santa Lucia, Rome, Italy.
| | | | - Anthony Buckley
- Microbiome and Nutritional Sciences Group, School of Food Science & Nutrition, University of Leeds, Leeds, UK
| | - Caroline Chilton
- Healthcare Associated Infection Research Group, Section of Molecular Gastroenterology, Leeds Institute for Medical Research at St James, University of Leeds, Leeds, UK
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3
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Azrad M, Abu-Rahmoun L, Hamo Z, Peretz A. Associations of motility and auto-aggregation with biofilm-formation capacity levels in Clostridioidesdifficile. Microb Pathog 2024; 186:106490. [PMID: 38061667 DOI: 10.1016/j.micpath.2023.106490] [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: 09/10/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 01/02/2024]
Abstract
Clostridioides difficile (C. difficile) is responsible for one of the most common nosocomial infections worldwide. This work assessed associations between biofilm-formation capacity levels of C. difficile and cell viability, motility, flagella, motility and auto-aggregation in 118 clinical isolates. Biofilm production was assessed by the crystal violet method. Cell viability was determined by BacTiter-Glo™ Microbial Cell Viability Assay and live-imaging microscopy. Expression levels of LuxS, Cwp84, Spo0A, PilA, and FliC were measured by real-time PCR. Motility was visually assessed in agar tubes. Auto-aggregation levels were determined by OD600 measurements. Out of 118 isolates, 66 (56 %) were biofilm producers, with most being strong or moderate producers. Cell viability, motility and auto-aggregation positively correlated with biofilm-production capacity (p = 0.0001, p = 0.036 and p < 0.0001, respectively). Positive associations were found between pilA, fliC and luxS expression levels and biofilm-production capacity (p = 0.04, p = 0.01, p = 0.036, respectively). This is the first report of associations between biofilm-formation capacity and cell viability, pilA, fliC, and luxS gene expression, auto-aggregation and motility. These correlations should be further explored to expand knowledge on the regulation of C. difficile biofilm formation, and pathogenesis, which will have notable implications on treatment options.
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Affiliation(s)
- Maya Azrad
- Clinical Microbiology Laboratory, Tzafon Medical Center, Poriya, Israel
| | | | - Zohar Hamo
- Clinical Microbiology Laboratory, Tzafon Medical Center, Poriya, Israel
| | - Avi Peretz
- Clinical Microbiology Laboratory, Tzafon Medical Center, Poriya, Israel; Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel.
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4
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Muzyukina P, Shkaruta A, Guzman NM, Andreani J, Borges AL, Bondy-Denomy J, Maikova A, Semenova E, Severinov K, Soutourina O. Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile. mSphere 2023; 8:e0040123. [PMID: 38009936 PMCID: PMC10732046 DOI: 10.1128/msphere.00401-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/10/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Clostridioides difficile is the widespread anaerobic spore-forming bacterium that is a major cause of potentially lethal nosocomial infections associated with antibiotic therapy worldwide. Due to the increase in severe forms associated with a strong inflammatory response and higher recurrence rates, a current imperative is to develop synergistic and alternative treatments for C. difficile infections. In particular, phage therapy is regarded as a potential substitute for existing antimicrobial treatments. However, it faces challenges because C. difficile has highly active CRISPR-Cas immunity, which may be a specific adaptation to phage-rich and highly crowded gut environment. To overcome this defense, C. difficile phages must employ anti-CRISPR mechanisms. Here, we present the first anti-CRISPR protein that inhibits the CRISPR-Cas defense system in this pathogen. Our work offers insights into the interactions between C. difficile and its phages, paving the way for future CRISPR-based applications and development of effective phage therapy strategies combined with the engineering of virulent C. difficile infecting phages.
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Affiliation(s)
- Polina Muzyukina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Anton Shkaruta
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Noemi M. Guzman
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Jessica Andreani
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Adair L. Borges
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Anna Maikova
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Ekaterina Semenova
- Waksman Institute, Rutgers, State University of New Jersey, Piscataway, New Jersey, USA
| | - Konstantin Severinov
- Waksman Institute, Rutgers, State University of New Jersey, Piscataway, New Jersey, USA
- Institute of Molecular Genetics, Kurchatov National Research Center, Moscow, Russia
| | - Olga Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Institut Universitaire de France (IUF), Paris, France
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Buddle JE, Fagan RP. Pathogenicity and virulence of Clostridioides difficile. Virulence 2023; 14:2150452. [PMID: 36419222 DOI: 10.1080/21505594.2022.2150452] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/02/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022] Open
Abstract
Clostridioides difficile is the most common cause of nosocomial antibiotic-associated diarrhea, and is responsible for a spectrum of diseases characterized by high levels of recurrence, morbidity, and mortality. Treatment is complex, since antibiotics constitute both the main treatment and the major risk factor for infection. Worryingly, resistance to multiple antibiotics is becoming increasingly widespread, leading to the classification of this pathogen as an urgent threat to global health. As a consummate opportunist, C. difficile is well equipped for promoting disease, owing to its arsenal of virulence factors: transmission of this anaerobe is highly efficient due to the formation of robust endospores, and an array of adhesins promote gut colonization. C. difficile produces multiple toxins acting upon gut epithelia, resulting in manifestations typical of diarrheal disease, and severe inflammation in a subset of patients. This review focuses on such virulence factors, as well as the importance of antimicrobial resistance and genome plasticity in enabling pathogenesis and persistence of this important pathogen.
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Affiliation(s)
- Jessica E Buddle
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Robert P Fagan
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, UK
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Rubio-Mendoza D, Martínez-Meléndez A, Maldonado-Garza HJ, Córdova-Fletes C, Garza-González E. Review of the Impact of Biofilm Formation on Recurrent Clostridioides difficile Infection. Microorganisms 2023; 11:2525. [PMID: 37894183 PMCID: PMC10609348 DOI: 10.3390/microorganisms11102525] [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: 09/05/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Clostridioides difficile infection (CDI) may recur in approximately 10-30% of patients, and the risk of recurrence increases with each successive recurrence, reaching up to 65%. C. difficile can form biofilm with approximately 20% of the bacterial genome expressed differently between biofilm and planktonic cells. Biofilm plays several roles that may favor recurrence; for example, it may act as a reservoir of spores, protect the vegetative cells from the activity of antibiotics, and favor the formation of persistent cells. Moreover, the expression of several virulence genes, including TcdA and TcdB toxins, has been associated with recurrence. Several systems and structures associated with adhesion and biofilm formation have been studied in C. difficile, including cell-wall proteins, quorum sensing (including LuxS and Agr), Cyclic di-GMP, type IV pili, and flagella. Most antibiotics recommended for the treatment of CDI do not have activity on spores and do not eliminate biofilm. Therapeutic failure in R-CDI has been associated with the inadequate concentration of drugs in the intestinal tract and the antibiotic resistance of a biofilm. This makes it challenging to eradicate C. difficile in the intestine, complicating antibacterial therapies and allowing non-eliminated spores to remain in the biofilm, increasing the risk of recurrence. In this review, we examine the role of biofilm on recurrence and the challenges of treating CDI when the bacteria form a biofilm.
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Affiliation(s)
- Daira Rubio-Mendoza
- Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico; (D.R.-M.); (H.J.M.-G.); (C.C.-F.)
| | - Adrián Martínez-Meléndez
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico;
| | - Héctor Jesús Maldonado-Garza
- Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico; (D.R.-M.); (H.J.M.-G.); (C.C.-F.)
| | - Carlos Córdova-Fletes
- Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico; (D.R.-M.); (H.J.M.-G.); (C.C.-F.)
| | - Elvira Garza-González
- Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico; (D.R.-M.); (H.J.M.-G.); (C.C.-F.)
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Dicks LMT. Biofilm Formation of Clostridioides difficile, Toxin Production and Alternatives to Conventional Antibiotics in the Treatment of CDI. Microorganisms 2023; 11:2161. [PMID: 37764005 PMCID: PMC10534356 DOI: 10.3390/microorganisms11092161] [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: 06/29/2023] [Revised: 08/16/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Clostridioides difficile is considered a nosocomial pathogen that flares up in patients exposed to antibiotic treatment. However, four out of ten patients diagnosed with C. difficile infection (CDI) acquired the infection from non-hospitalized individuals, many of whom have not been treated with antibiotics. Treatment of recurrent CDI (rCDI) with antibiotics, especially vancomycin (VAN) and metronidazole (MNZ), increases the risk of experiencing a relapse by as much as 70%. Fidaxomicin, on the other hand, proved more effective than VAN and MNZ by preventing the initial transcription of RNA toxin genes. Alternative forms of treatment include quorum quenching (QQ) that blocks toxin synthesis, binding of small anion molecules such as tolevamer to toxins, monoclonal antibodies, such as bezlotoxumab and actoxumab, bacteriophage therapy, probiotics, and fecal microbial transplants (FMTs). This review summarizes factors that affect the colonization of C. difficile and the pathogenicity of toxins TcdA and TcdB. The different approaches experimented with in the destruction of C. difficile and treatment of CDI are evaluated.
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Affiliation(s)
- Leon M T Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
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Dupuy B. Regulation of Clostridial Toxin Gene Expression: A Pasteurian Tradition. Toxins (Basel) 2023; 15:413. [PMID: 37505682 PMCID: PMC10467148 DOI: 10.3390/toxins15070413] [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: 05/09/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 07/29/2023] Open
Abstract
The alarming symptoms attributed to several potent clostridial toxins enabled the early identification of the causative agent of tetanus, botulism, and gas gangrene diseases, which belongs to the most famous species of pathogenic clostridia. Although Clostridioides difficile was identified early in the 20th century as producing important toxins, it was identified only 40 years later as the causative agent of important nosocomial diseases upon the advent of antibiotic therapies in hospital settings. Today, C. difficile is a leading public health issue, as it is the major cause of antibiotic-associated diarrhea in adults. In particular, severe symptoms within the spectrum of C. difficile infections are directly related to the levels of toxins produced in the host. This highlights the importance of understanding the regulation of toxin synthesis in the pathogenicity process of C. difficile, whose regulatory factors in response to the gut environment were first identified at the Institut Pasteur. Subsequently, the work of other groups in the field contributed to further deciphering the complex mechanisms controlling toxin production triggered by the intestinal dysbiosis states during infection. This review summarizes the Pasteurian contribution to clostridial toxin regulation studies.
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Affiliation(s)
- Bruno Dupuy
- Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
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Chandra H, Sorg JA, Hassett DJ, Sun X. Regulatory transcription factors of Clostridioides difficile pathogenesis with a focus on toxin regulation. Crit Rev Microbiol 2023; 49:334-349. [PMID: 35389761 PMCID: PMC11209739 DOI: 10.1080/1040841x.2022.2054307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 02/26/2022] [Accepted: 03/14/2022] [Indexed: 11/03/2022]
Abstract
Clostridioides difficile (CD), a nosocomial gut pathogen, produces two major exotoxins, TcdA and TcdB, which disrupt the gut epithelial barrier and induce inflammatory/immune responses, leading to symptoms ranging from mild diarrhoea to pseudomembranous colitis and potentially to death. The expression of toxins is regulated by various transcription factors (TFs) which are induced in response to CD physiological life stages, nutritional availability, and host environment. This review summarises our current understanding on the regulation of toxin expression by TFs that interconnect with pathways of flagellar synthesis, quorum sensing, motility, biofilm formation, sporulation, and phase variation. The pleiotropic roles of some key TFs suggest that toxin production is tightly linked to other cellular processes of the CD physiology.
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Affiliation(s)
- Harish Chandra
- Department of Environmental Microbiology, School of Environmental and Earth Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, India
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Joseph A. Sorg
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Daniel J Hassett
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
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Morais MLGDS, Santos MGC, Costa CL, Martins CS, Leitão RFDC, de Melo Pacífico D, Quesada-Gómez C, Castelo Branco D, Ferreira EDO, Brito GADC. Comparative biofilm-forming ability between Clostridioides difficile strains isolated in Latin America and the epidemic NAP1/027 strain. Front Cell Infect Microbiol 2022; 12:1033698. [PMID: 36619751 PMCID: PMC9815708 DOI: 10.3389/fcimb.2022.1033698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022] Open
Abstract
Introduction One of the challenges in treating Clostridioides difficile infection (CDI) is that the bacterium forms biofilms, a critical virulence mechanism known to promote antibiotic resistance and, as a result, consequently, a higher recurrence of the disease. The goal of this study was to compare the ability of three MLST Clade 2 strains to form a biofilm in vitro: ICC-45 (ribotype SLO231/UK[CE]821), a ST41 toxinotype IXb isolated in Brazil; and two epidemic NAP1/027/ST01 strains: NAP1/027/ST01 (LIBA5756), isolated during a 2010 outbreak in Costa Rica and the reference epidemic strain NAP1/027/ST01 (R20291); and ATCC700057, a non-toxigenic strain. Methods The ability of strains to form biofilm was evaluated using crystal violet staining. In addition, samples were stained with the Film Tracer biofilm matrix (Invitrogen®) and the biofilm matrix thickness was measured using confocal microscopy. The matrix architecture was determined using Scanning electron microscop. Confocal microscopy was used to detect the presence of toxin A (tcdA) using an anti-Clostridioides difficile TcdA antibody. The expression of virulence genes (tcdA, tcdB, tcdC, cdtB, spo0A, slpA, cwp66 and cwp84) was examined, as well as the effect of antibiotics metronidazole (MTZ) and vancomycin (VAN) on biofilm growth. Results All of the strains tested formed a moderate biofilm with 1.1 <DO570nm>3.5. After 72h, biofilm biomass of the NAP1/027/ST01 epidemic strains (LIBA5756 and R20291) was significantly higher than ICC-45 and ATCC 700057 biofilms, as confirmed by electron and confocal microscopy. At 120h, the LIBA5756 biofilm biomass decreased compared to other strains. The toxigenic strains R20291 or LIBA 5756 had higher expression of genes tcdA, tcdB, tcdC, cdtA, slpA and spo0A than ICC-45, but there were no significant differences in the expression levels of cdtB, cwp66 and cwp84. In epidemic strains, VAN and MTZ inhibited biofilm formation; however, in the ICC-45 strain, MIC concentrations of VAN and MIC and 4MIC of MTZ did not inhibit biofilm formation. Conclusion The three MLST Clade 2 isolated from different rybotipes, two of which were isolated from Latin America, are competent biofilm-forming bacteria, indicating their ability to induce C. difficile infection recurrence, making treatment difficult.
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Affiliation(s)
- Maria Luana Gaudencio dos Santos Morais
- Department of Morphology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil,Laboratory of Bacteriology, Department of Pathology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Mayara Gilde Castro Santos
- Laboratório de Biologia de Anaeróbios, Instituto de Microbiologia Paulo de Góes Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cecília Leite Costa
- Department of Morphology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil,Laboratory of Bacteriology, Department of Pathology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Conceição Silva Martins
- Department of Morphology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | | | - Dvison de Melo Pacífico
- Department of Morphology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Carlos Quesada-Gómez
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Débora Castelo Branco
- Laboratory of Bacteriology, Department of Pathology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Eliane de Oliveira Ferreira
- Laboratory of Bacteriology, Department of Pathology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Gerly Anne de Castro Brito
- Department of Morphology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil,*Correspondence: Gerly Anne de Castro Brito,
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Exploiting Biofilm Characteristics to Enhance Biological Nutrient Removal in Wastewater Treatment Plants. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12157561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Biological treatments are integral processes in wastewater treatment plants (WWTPs). They can be carried out using sludge or biofilm processes. Although the sludge process is effective for biological wastewater systems, it has some drawbacks that make it undesirable. Hence, biofilm processes have gained popularity, since they address the drawbacks of sludge treatments, such as the high rates of sludge production. Although biofilms have been reported to be essential for wastewater, few studies have reviewed the different ways in which the biofilm properties can be explored, especially for the benefit of wastewater treatment. Thus, this review explores the properties of biofilms that can be exploited to enhance biological wastewater systems. In this review, it is revealed that various biofilm properties, such as the extracellular polymeric substances (EPS), quorum sensing (Qs), and acylated homoserine lactones (AHLs), can be enhanced as a sustainable and cost-effective strategy to enhance the biofilm. Moreover, the exploitation of other biofilm properties such as the SOS, which is only reported in the medical field, with no literature reporting it in the context of wastewater treatment, is also recommended to improve the biofilm technology for wastewater treatment processes. Additionally, this review further elaborates on ways that these properties can be exploited to advance biofilm wastewater treatment systems. A special emphasis is placed on exploiting these properties in simultaneous nitrification and denitrification and biological phosphorus removal processes, which have been reported to be the most sensitive processes in biological wastewater treatment.
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Genome-Wide Identification of the LexA-Mediated DNA Damage Response in Streptomyces venezuelae. J Bacteriol 2022; 204:e0010822. [PMID: 35862789 PMCID: PMC9380542 DOI: 10.1128/jb.00108-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
DNA damage triggers a widely conserved stress response in bacteria called the SOS response, which involves two key regulators, the activator RecA and the transcriptional repressor LexA. Despite the wide conservation of the SOS response, the number of genes controlled by LexA varies considerably between different organisms. The filamentous soil-dwelling bacteria of the genus Streptomyces contain LexA and RecA homologs, but their roles in Streptomyces have not been systematically studied. Here, we demonstrate that RecA and LexA are required for the survival of Streptomyces venezuelae during DNA-damaging conditions and for normal development during unperturbed growth. Monitoring the activity of a fluorescent recA promoter fusion and LexA protein levels revealed that the activation of the SOS response is delayed in S. venezuelae. By combining global transcriptional profiling and chromatin immunoprecipitation sequencing (ChIP-seq) analysis, we determined the LexA regulon and defined the core set of DNA damage repair genes that are expressed in response to treatment with the DNA-alkylating agent mitomycin C. Our results show that DNA damage-induced degradation of LexA results in the differential regulation of LexA target genes. Using surface plasmon resonance, we further confirmed the LexA DNA binding motif (SOS box) and demonstrated that LexA displays tight but distinct binding affinities to its target promoters, indicating a graded response to DNA damage. IMPORTANCE The transcriptional regulator LexA functions as a repressor of the bacterial SOS response, which is induced under DNA-damaging conditions. This results in the expression of genes important for survival and adaptation. Here, we report the regulatory network controlled by LexA in the filamentous antibiotic-producing Streptomyces bacteria and establish the existence of the SOS response in Streptomyces. Collectively, our work reveals significant insights into the DNA damage response in Streptomyces that will promote further studies to understand how these important bacteria adapt to their environment.
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Jaramillo AVC, Cory MB, Li A, Kohli RM, Wuest WM. Exploration of inhibitors of the bacterial LexA repressor-protease. Bioorg Med Chem Lett 2022; 65:128702. [PMID: 35351585 DOI: 10.1016/j.bmcl.2022.128702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 11/25/2022]
Abstract
Resistant and tolerant bacterial infections lead to billions in healthcare costs and cause hundreds of thousands of deaths each year. The bulk of current antibiotic research efforts focus on molecules which, although novel, are not immune from acquired resistance and seldomly affect tolerant populations. The bacterial SOS response has been implicated in several resistance and tolerance mechanisms, making it an attractive antibiotic target. Using small molecule inhibitors targeting a key step in the deployment of the SOS response, our approach focused on preventing the deployment of mechanisms such as biofilm formation, horizontal gene transfer, and error-prone DNA repair. Herein we report the synthesis and testing of analogs of a triazole-containing tricyclic inhibitor of LexA proteolysis, the key event in the SOS response. Our results hint that our inhibitor's may function by adopting a β-hairpin conformation, reminiscent of the native cleavage loop of LexA.
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Affiliation(s)
| | - Michael B Cory
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Allen Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - William M Wuest
- Department of Chemistry, Emory University, Atlanta, GA, USA.
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Azithromycin can induce SOS response and horizontal gene transfer of SXT element in Vibrio cholerae. Mol Biol Rep 2022; 49:4737-4748. [DOI: 10.1007/s11033-022-07323-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
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15
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Regulation of Clostridioides difficile toxin production. Curr Opin Microbiol 2022; 65:95-100. [PMID: 34781095 PMCID: PMC8792210 DOI: 10.1016/j.mib.2021.10.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/19/2021] [Accepted: 10/25/2021] [Indexed: 02/03/2023]
Abstract
Clostridioides difficile produces toxins TcdA and TcdB during infection. Since the severity of the illness is directly correlated with the level of toxins produced, researchers have long been interested in the regulation mechanisms of toxin production. The advent of new genetics and mutagenesis technologies in C. difficile has allowed a slew of new investigations in the last decade, which considerably improved our understanding of this crucial regulatory network. The current body of work shows that the toxin regulatory network overlaps with the regulatory networks of sporulation, motility, and key metabolic pathways. This implies that toxin production is a complicated process initiated by bacteria in response to numerous host factors during infection. We summarize the existing knowledge about the toxin gene regulatory network here.
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Tremblay YD, Dupuy B. The blueprint for building a biofilm the Clostridioides difficile way. Curr Opin Microbiol 2021; 66:39-45. [PMID: 34933207 DOI: 10.1016/j.mib.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/25/2021] [Accepted: 12/06/2021] [Indexed: 11/27/2022]
Abstract
Clostridioides difficile is an opportunistic pathogen that causes by a high rate of recurrent infections. Persistence in the gastrointestinal tract is thought to be mediated by sporulation and/or biofilm formation. There is an increase interest in C. difficile biofilm formation and recent findings have provided a framework to model surface-attached biofilm formation. For in vitro biofilm formation, C. difficile must undergo a metabolic reprogramming as it enters stationary phase. This helps maintain long-term viability and increases responsiveness to signals leading to biofilm formation. Metabolic reprogramming and biofilm formation requires several regulatory factors and these overlap with the sporulation cascade. Despite recent advances, further research is needed to answer outstanding questions in the field.
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Affiliation(s)
- Yannick Dn Tremblay
- Institut Pasteur, Université de Paris, UMR-CNRS 2001, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France; Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada.
| | - Bruno Dupuy
- Institut Pasteur, Université de Paris, UMR-CNRS 2001, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France.
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Metabolic adaption to extracellular pyruvate triggers biofilm formation in Clostridioides difficile. THE ISME JOURNAL 2021; 15:3623-3635. [PMID: 34155333 PMCID: PMC8630010 DOI: 10.1038/s41396-021-01042-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
Clostridioides difficile infections are associated with gut microbiome dysbiosis and are the leading cause of hospital-acquired diarrhoea. The infectious process is strongly influenced by the microbiota and successful infection relies on the absence of specific microbiota-produced metabolites. Deoxycholate and short-chain fatty acids are microbiota-produced metabolites that limit the growth of C. difficile and protect the host against this infection. In a previous study, we showed that deoxycholate causes C. difficile to form strongly adherent biofilms after 48 h. Here, our objectives were to identify and characterize key molecules and events required for biofilm formation in the presence of deoxycholate. We applied time-course transcriptomics and genetics to identify sigma factors, metabolic processes and type IV pili that drive biofilm formation. These analyses revealed that extracellular pyruvate induces biofilm formation in the presence of deoxycholate. In the absence of deoxycholate, pyruvate supplementation was sufficient to induce biofilm formation in a process that was dependent on pyruvate uptake by the membrane protein CstA. In the context of the human gut, microbiota-generated pyruvate is a metabolite that limits pathogen colonization. Taken together our results suggest that pyruvate-induced biofilm formation might act as a key process driving C. difficile persistence in the gut.
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Meza-Torres J, Auria E, Dupuy B, Tremblay YDN. Wolf in Sheep's Clothing: Clostridioides difficile Biofilm as a Reservoir for Recurrent Infections. Microorganisms 2021; 9:1922. [PMID: 34576818 PMCID: PMC8470499 DOI: 10.3390/microorganisms9091922] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 12/21/2022] Open
Abstract
The microbiota inhabiting the intestinal tract provide several critical functions to its host. Microorganisms found at the mucosal layer form organized three-dimensional structures which are considered to be biofilms. Their development and functions are influenced by host factors, host-microbe interactions, and microbe-microbe interactions. These structures can dictate the health of their host by strengthening the natural defenses of the gut epithelium or cause disease by exacerbating underlying conditions. Biofilm communities can also block the establishment of pathogens and prevent infectious diseases. Although these biofilms are important for colonization resistance, new data provide evidence that gut biofilms can act as a reservoir for pathogens such as Clostridioides difficile. In this review, we will look at the biofilms of the intestinal tract, their contribution to health and disease, and the factors influencing their formation. We will then focus on the factors contributing to biofilm formation in C. difficile, how these biofilms are formed, and their properties. In the last section, we will look at how the gut microbiota and the gut biofilm influence C. difficile biofilm formation, persistence, and transmission.
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Affiliation(s)
- Jazmin Meza-Torres
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
| | - Emile Auria
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
| | - Yannick D. N. Tremblay
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
- Health Sciences Building, Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK S7N 5E5, Canada
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19
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Abstract
Clostridiodes difficile (C. difficile) was ranked an “urgent threat” by the Centers for Disease Control and Prevention (CDC) in 2019. C. difficile infection (CDI) is the most common healthcare-associated infection (HAI) in the United States of America as well as the leading cause of antibiotic-associated gastrointestinal disease. C. difficile is a gram-positive, rod-shaped, spore-forming, anaerobic bacterium that causes infection of the epithelial lining of the gut. CDI occurs most commonly after disruption of the human gut microflora following the prolonged use of broad-spectrum antibiotics. However, the recurrent nature of this disease has led to the hypothesis that biofilm formation may play a role in its pathogenesis. Biofilms are sessile communities of bacteria protected from extracellular stresses by a matrix of self-produced proteins, polysaccharides, and extracellular DNA. Biofilm regulation in C. difficile is still incompletely understood, and its role in disease recurrence has yet to be fully elucidated. However, many factors have been found to influence biofilm formation in C. difficile, including motility, adhesion, and hydrophobicity of the bacterial cells. Small changes in one of these systems can greatly influence biofilm formation. Therefore, the biofilm regulatory system would need to coordinate all these systems to create optimal biofilm-forming physiology under appropriate environmental conditions. The coordination of these systems is complex and multifactorial, and any analysis must take into consideration the influences of the stress response, quorum sensing (QS), and gene regulation by second messenger molecule cyclic diguanosine monophosphate (c-di-GMP). However, the differences in biofilm-forming ability between C. difficile strains such as 630 and the “hypervirulent” strain, R20291, make it difficult to assign a “one size fits all” mechanism to biofilm regulation in C. difficile. This review seeks to consolidate published data regarding the regulation of C. difficile biofilms in order to identify gaps in knowledge and propose directions for future study. Clostridioides difficile (C. difficile) is an opportunistic bacterial pathogen that causes infection of the human gut epithelium following disruption of the normal gut microflora, usually by broad-spectrum antibiotics. C. difficile infection (CDI) is recurrent in 20% to 30% of cases and can lead to significant health-related complications such as pseudomembranous colitis and, in severe cases, death. The impact and cost of this pathogen on healthcare systems are significant, and some aspects of the pathogen’s lifestyle in the host are, as yet, unknown. It is hypothesised that C. difficile exists in the gut as a biofilm due to the infection’s severity and recurrent nature. The biofilm mode of bacterial growth can protect the cells from external factors such as antibiotic treatment, physiological processes, and the immune system. However, biofilm regulation in C. difficile is not yet fully characterised, and in this review, we consolidate published primary research on C. difficile biofilm regulation to gain a comprehensive overview of the factors involved and how they may interact to enable biofilm development within a host.
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20
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Sheng DH, Wang Y, Wu SG, Duan RQ, Li YZ. The Regulation of LexA on UV-Induced SOS Response in Myxococcus xanthus Based on Transcriptome Analysis. J Microbiol Biotechnol 2021; 31:912-920. [PMID: 34024894 PMCID: PMC9705874 DOI: 10.4014/jmb.2103.03047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 12/15/2022]
Abstract
SOS response is a conserved response to DNA damage in prokaryotes and is negatively regulated by LexA protein, which recognizes specifically an "SOS-box" motif present in the promoter region of SOS genes. Myxococcus xanthus DK1622 possesses a lexA gene, and while the deletion of lexA had no significant effect on either bacterial morphology, UV-C resistance, or sporulation, it did delay growth. UV-C radiation resulted in 651 upregulated genes in M. xanthus, including the typical SOS genes lexA, recA, uvrA, recN and so on, mostly enriched in the pathways of DNA replication and repair, secondary metabolism, and signal transduction. The UV-irradiated lexA mutant also showed the induced expression of SOS genes and these SOS genes enriched into a similar pathway profile to that of wild-type strain. Without irradiation treatment, the absence of LexA enhanced the expression of 122 genes that were not enriched in any pathway. Further analysis of the promoter sequence revealed that in the 122 genes, only the promoters of recA2, lexA and an operon composed of three genes (pafB, pafC and cyaA) had SOS box sequence to which the LexA protein is bound directly. These results update our current understanding of SOS response in M. xanthus and show that UV induces more genes involved in secondary metabolism and signal transduction in addition to DNA replication and repair; and while the canonical LexA-dependent regulation on SOS response has shrunk, only 5 SOS genes are directly repressed by LexA.
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Affiliation(s)
- Duo-hong Sheng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China,
D-h. Sheng Phone: +86-532-58631538 E-mail:
| | - Ye Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China
| | - Shu-ge Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China
| | - Rui-qin Duan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China
| | - Yue-zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China,Corresponding authors Y.Z. Li Phone: +86-532-58631539 E-mail:
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21
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Brauer M, Lassek C, Hinze C, Hoyer J, Becher D, Jahn D, Sievers S, Riedel K. What's a Biofilm?-How the Choice of the Biofilm Model Impacts the Protein Inventory of Clostridioides difficile. Front Microbiol 2021; 12:682111. [PMID: 34177868 PMCID: PMC8225356 DOI: 10.3389/fmicb.2021.682111] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/12/2021] [Indexed: 12/18/2022] Open
Abstract
The anaerobic pathogen Clostridioides difficile is perfectly equipped to survive and persist inside the mammalian intestine. When facing unfavorable conditions C. difficile is able to form highly resistant endospores. Likewise, biofilms are currently discussed as form of persistence. Here a comprehensive proteomics approach was applied to investigate the molecular processes of C. difficile strain 630Δerm underlying biofilm formation. The comparison of the proteome from two different forms of biofilm-like growth, namely aggregate biofilms and colonies on agar plates, revealed major differences in the formation of cell surface proteins, as well as enzymes of its energy and stress metabolism. For instance, while the obtained data suggest that aggregate biofilm cells express both flagella, type IV pili and enzymes required for biosynthesis of cell-surface polysaccharides, the S-layer protein SlpA and most cell wall proteins (CWPs) encoded adjacent to SlpA were detected in significantly lower amounts in aggregate biofilm cells than in colony biofilms. Moreover, the obtained data suggested that aggregate biofilm cells are rather actively growing cells while colony biofilm cells most likely severely suffer from a lack of reductive equivalents what requires induction of the Wood-Ljungdahl pathway and C. difficile’s V-type ATPase to maintain cell homeostasis. In agreement with this, aggregate biofilm cells, in contrast to colony biofilm cells, neither induced toxin nor spore production. Finally, the data revealed that the sigma factor SigL/RpoN and its dependent regulators are noticeably induced in aggregate biofilms suggesting an important role of SigL/RpoN in aggregate biofilm formation.
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Affiliation(s)
- Madita Brauer
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christian Lassek
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christian Hinze
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Juliane Hoyer
- Department for Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Department for Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Susanne Sievers
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
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22
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Engevik MA, Engevik AC, Engevik KA, Auchtung JM, Chang-Graham AL, Ruan W, Luna RA, Hyser JM, Spinler JK, Versalovic J. Mucin-Degrading Microbes Release Monosaccharides That Chemoattract Clostridioides difficile and Facilitate Colonization of the Human Intestinal Mucus Layer. ACS Infect Dis 2021; 7:1126-1142. [PMID: 33176423 DOI: 10.1021/acsinfecdis.0c00634] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
It is widely accepted that the pathogen Clostridioides difficile exploits an intestinal environment with an altered microbiota, but the details of these microbe-microbe interactions are unclear. Adherence and colonization of mucus has been demonstrated for several enteric pathogens and it is possible that mucin-associated microbes may be working in concert with C. difficile. We showed that C. difficile ribotype-027 adheres to MUC2 glycans and using fecal bioreactors, we identified that C. difficile associates with several mucin-degrading microbes. C. difficile was found to chemotax toward intestinal mucus and its glycan components, demonstrating that C. difficile senses the mucus layer. Although C. difficile lacks the glycosyl hydrolases required to degrade mucin glycans, coculturing C. difficile with the mucin-degrading Akkermansia muciniphila, Bacteroides thetaiotaomicron, and Ruminococcus torques allowed C. difficile to grow in media that lacked glucose but contained purified MUC2. Collectively, these studies expand our knowledge on how intestinal microbes support C. difficile.
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Affiliation(s)
- Melinda A. Engevik
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - Amy C. Engevik
- Department of Surgery, Vanderbilt University School of Medicine, Nashville Tennessee 37232, United States
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville Tennessee 37232, United States
| | - Kristen A. Engevik
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
| | - Jennifer M. Auchtung
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Food Science and Technology, University of Nebraska—Lincoln, Lincoln Nebraska 68588, United States
| | - Alexandra L. Chang-Graham
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
| | - Wenly Ruan
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - Ruth Ann Luna
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - Joseph M. Hyser
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
| | - Jennifer K. Spinler
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - James Versalovic
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
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Hu WS, Woo DU, Kang YJ, Koo OK. Biofilm and Spore Formation of Clostridium perfringens and Its Resistance to Disinfectant and Oxidative Stress. Antibiotics (Basel) 2021; 10:antibiotics10040396. [PMID: 33917564 PMCID: PMC8067515 DOI: 10.3390/antibiotics10040396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/05/2021] [Accepted: 04/01/2021] [Indexed: 11/24/2022] Open
Abstract
Clostridium perfringens is a major human pathogen that causes gastroenteritis via enterotoxin production and has the ability to form spores and biofilms for environmental persistence and disease transmission. This study aimed to compare the disinfectant and environmental resistance properties of C. perfringens vegetative cells and spores in planktonic and sessile conditions, and to examine the nucleotide polymorphisms and transcription under sessile conditions in C. perfringens strains isolated from meat. The sporulation rate of sessile C. perfringens TYJAM-D-66 (cpe+) was approximately 19% at day 5, while those of CMM-C-80 (cpe−) and SDE-B-202 (cpe+) were only 0.26% and 0.67%, respectively, at day 7. When exposed to aerobic conditions for 36 h, TYJAM-D-66, CMM-C-80, and SDE-B-202 vegetative cells showed 1.70 log, 5.36 log, and 5.67 log reductions, respectively. After treatment with sodium hypochlorite, the survival rates of TYJAM-D-66 vegetative cells (53.6%) and spores (82.3%) in biofilms were higher than those of planktonic cells (9.23%). Biofilm- and spore-related genes showed different expression within TYJAM-D-66 (–4.66~113.5), CMM-C-80 (–3.02~2.49), and SDE-B-202 (–5.07~2.73). Our results indicate the resistance of sessile cells and spores of C. perfringens upon exposure to stress conditions after biofilm formation.
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Affiliation(s)
- Wen Si Hu
- Department of Food Science and Engineering, Liaocheng University, Liaocheng 252059, China;
| | - Dong U Woo
- Division of Life Science Department, Gyeongsang National University, Jinju 52828, Korea; (D.U.W.); (Y.J.K.)
- Division of Bio & Medical Big Data Department (BK4 Program), Gyeongsang National University, Jinju 52828, Korea
| | - Yang Jae Kang
- Division of Life Science Department, Gyeongsang National University, Jinju 52828, Korea; (D.U.W.); (Y.J.K.)
- Division of Bio & Medical Big Data Department (BK4 Program), Gyeongsang National University, Jinju 52828, Korea
| | - Ok Kyung Koo
- Department of Food and Nutrition, Gyeongsang National University, Jinju 52828, Korea
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea
- Correspondence: ; Tel.: +82-55-772-1441
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24
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Frost LR, Cheng JKJ, Unnikrishnan M. Clostridioides difficile biofilms: A mechanism of persistence in the gut? PLoS Pathog 2021; 17:e1009348. [PMID: 33705497 PMCID: PMC7951904 DOI: 10.1371/journal.ppat.1009348] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Lucy R. Frost
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Jeffrey K. J. Cheng
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Meera Unnikrishnan
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
- * E-mail:
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25
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Dawson LF, Peltier J, Hall CL, Harrison MA, Derakhshan M, Shaw HA, Fairweather NF, Wren BW. Extracellular DNA, cell surface proteins and c-di-GMP promote biofilm formation in Clostridioides difficile. Sci Rep 2021; 11:3244. [PMID: 33547340 PMCID: PMC7865049 DOI: 10.1038/s41598-020-78437-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
Clostridioides difficile is the leading cause of nosocomial antibiotic-associated diarrhoea worldwide, yet there is little insight into intestinal tract colonisation and relapse. In many bacterial species, the secondary messenger cyclic-di-GMP mediates switching between planktonic phase, sessile growth and biofilm formation. We demonstrate that c-di-GMP promotes early biofilm formation in C. difficile and that four cell surface proteins contribute to biofilm formation, including two c-di-GMP regulated; CD2831 and CD3246, and two c-di-GMP-independent; CD3392 and CD0183. We demonstrate that C. difficile biofilms are composed of extracellular DNA (eDNA), cell surface and intracellular proteins, which form a protective matrix around C. difficile vegetative cells and spores, as shown by a protective effect against the antibiotic vancomycin. We demonstrate a positive correlation between biofilm biomass, sporulation frequency and eDNA abundance in all five C. difficile lineages. Strains 630 (RT012), CD305 (RT023) and M120 (RT078) contain significantly more eDNA in their biofilm matrix than strains R20291 (RT027) and M68 (RT017). DNase has a profound effect on biofilm integrity, resulting in complete disassembly of the biofilm matrix, inhibition of biofilm formation and reduced spore germination. The addition of exogenous DNase could be exploited in treatment of C. difficile infection and relapse, to improve antibiotic efficacy.
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Affiliation(s)
- Lisa F Dawson
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK.
| | - Johann Peltier
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Catherine L Hall
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Mark A Harrison
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Maria Derakhshan
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Helen A Shaw
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
- National Institute for Biological Standards and Control, Potters Bar, UK
| | - Neil F Fairweather
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Brendan W Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
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Yekani M, Baghi HB, Vahed SZ, Ghanbari H, Hosseinpur R, Azargun R, Azimi S, Memar MY. Tightly controlled response to oxidative stress; an important factor in the tolerance of Bacteroides fragilis. Res Microbiol 2021; 172:103798. [PMID: 33485914 DOI: 10.1016/j.resmic.2021.103798] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/01/2022]
Abstract
The exposure of Bacteroides fragilis to highly oxygenated tissues induces an oxidative stress due to a shift from the reduced condition of the gastrointestinal tract to an aerobic environment of host tissues. The potent and effective responses to reactive oxygen species (ROS) make the B. fragilis tolerant to atmospheric oxygen for several days. The response to oxidative stress in B. fragilis is a complicated event that is induced and regulated by different agents. In this review, we will focus on the B. fragilis response to oxidative stress and present an overview of the regulators of responses to oxidative stress in this bacterium.
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Affiliation(s)
- Mina Yekani
- Department of Microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Hadi Ghanbari
- Department of Pharmacognosy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Rasul Hosseinpur
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Robab Azargun
- Department of Microbiology, Faculty of Medicine, Maragheh University of Medical Sciences, Maragheh, Iran
| | - Somayeh Azimi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Microbiology Department, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Memar MY, Yekani M, Celenza G, Poortahmasebi V, Naghili B, Bellio P, Baghi HB. The central role of the SOS DNA repair system in antibiotics resistance: A new target for a new infectious treatment strategy. Life Sci 2020; 262:118562. [PMID: 33038378 DOI: 10.1016/j.lfs.2020.118562] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/15/2020] [Accepted: 10/01/2020] [Indexed: 01/19/2023]
Abstract
Bacteria have a considerable ability and potential to acquire resistance against antimicrobial agents by acting diverse mechanisms such as target modification or overexpression, multidrug transporter systems, and acquisition of drug hydrolyzing enzymes. Studying the mechanisms of bacterial cell physiology is mandatory for the development of novel strategies to control the antimicrobial resistance phenomenon, as well as for the control of infections in clinics. The SOS response is a cellular DNA repair mechanism that has an essential role in the bacterial biologic process involved in resistance to antibiotics. The activation of the SOS network increases the resistance and tolerance of bacteria to stress and, as a consequence, to antimicrobial agents. Therefore, SOS can be an applicable target for the discovery of new antimicrobial drugs. In the present review, we focus on the central role of SOS response in bacterial resistance mechanisms and its potential as a new target for control of resistant pathogens.
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Affiliation(s)
- Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Students' Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mina Yekani
- Department of Microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy.
| | - Vahdat Poortahmasebi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrooz Naghili
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Podlesek Z, Žgur Bertok D. The DNA Damage Inducible SOS Response Is a Key Player in the Generation of Bacterial Persister Cells and Population Wide Tolerance. Front Microbiol 2020; 11:1785. [PMID: 32849403 PMCID: PMC7417476 DOI: 10.3389/fmicb.2020.01785] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/08/2020] [Indexed: 12/28/2022] Open
Abstract
Population-wide tolerance and persisters enable susceptible bacterial cells to endure hostile environments, including antimicrobial exposure. The SOS response can play a significant role in the generation of persister cells, population-wide tolerance, and shielding. The SOS pathway is an inducible DNA damage repair system that is also pivotal for bacterial adaptation, pathogenesis, and diversification. In addition to the two key SOS regulators, LexA and RecA, some other stressors and stress responses can control SOS factors. Bacteria are exposed to DNA-damaging agents and other environmental and intracellular factors, including cigarette smoke, that trigger the SOS response at a number of sites within the host. The Escherichia coli TisB/IstR module is as yet the only known SOS-regulated toxin–antitoxin module involved in persister formation. Nevertheless, the SOS response plays a key role in the formation of biofilms that are highly recalcitrant to antimicrobials and can be abundant in persisters. Furthermore, the dynamic biofilm environment generates DNA-damaging factors that trigger the SOS response within the biofilm, fueling bacterial adaptation and diversification. This review highlights the SOS response in relation to antimicrobial recalcitrance to antimicrobials in four clinically significant species, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Mycobacterium tuberculosis.
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Affiliation(s)
- Zdravko Podlesek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Darja Žgur Bertok
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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29
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Llama‐Palacios A, Potupa O, Sánchez MC, Figuero E, Herrera D, Sanz M. Proteomic analysis ofFusobacterium nucleatumgrowth in biofilm versus planktonic state. Mol Oral Microbiol 2020; 35:168-180. [DOI: 10.1111/omi.12303] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/01/2020] [Accepted: 06/11/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Arancha Llama‐Palacios
- Oral Microbiology Laboratory at the Faculty of Odontology University Complutense Madrid Spain
- ETEP (Etiology and Therapy of Periodontal Diseases) Research Group University Complutense Madrid Spain
| | - Oksana Potupa
- Oral Microbiology Laboratory at the Faculty of Odontology University Complutense Madrid Spain
| | - María C. Sánchez
- Oral Microbiology Laboratory at the Faculty of Odontology University Complutense Madrid Spain
- ETEP (Etiology and Therapy of Periodontal Diseases) Research Group University Complutense Madrid Spain
| | - Elena Figuero
- ETEP (Etiology and Therapy of Periodontal Diseases) Research Group University Complutense Madrid Spain
| | - David Herrera
- ETEP (Etiology and Therapy of Periodontal Diseases) Research Group University Complutense Madrid Spain
| | - Mariano Sanz
- ETEP (Etiology and Therapy of Periodontal Diseases) Research Group University Complutense Madrid Spain
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Marx P, Sang Y, Qin H, Wang Q, Guo R, Pfeifer C, Kreth J, Merritt J. Environmental stress perception activates structural remodeling of extant Streptococcus mutans biofilms. NPJ Biofilms Microbiomes 2020; 6:17. [PMID: 32221309 PMCID: PMC7101444 DOI: 10.1038/s41522-020-0128-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/12/2020] [Indexed: 01/28/2023] Open
Abstract
Transcription regulators from the LexA-like Protein Superfamily control a highly diverse assortment of genetic pathways in response to environmental stress. All characterized members of this family modulate their functionality and stability via a strict coordination with the coprotease function of RecA. Using the LexA-like protein IrvR from Streptococcus mutans, we demonstrate an exception to the RecA paradigm and illustrate how this evolutionary innovation has been coopted to diversify the stress responsiveness of S. mutans biofilms. Using a combination of genetics and biophysical measurements, we demonstrate how non-SOS stresses and SOS stresses each trigger separate regulatory mechanisms that stimulate production of a surface lectin responsible for remodeling the viscoelastic properties of extant biofilms during episodes of environmental stress. These studies demonstrate how changes in the external environment or even anti-biofilm therapeutic agents can activate biofilm-specific adaptive mechanisms responsible for bolstering the integrity of established biofilm communities. Such changes in biofilm community structure are likely to play central roles in the notorious recalcitrance of biofilm infections.
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Affiliation(s)
- Patrick Marx
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Yu Sang
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Hua Qin
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Qingjing Wang
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Rongkai Guo
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Carmem Pfeifer
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Jens Kreth
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Justin Merritt
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239 USA
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Dubois T, Tremblay YDN, Hamiot A, Martin-Verstraete I, Deschamps J, Monot M, Briandet R, Dupuy B. A microbiota-generated bile salt induces biofilm formation in Clostridium difficile. NPJ Biofilms Microbiomes 2019; 5:14. [PMID: 31098293 PMCID: PMC6509328 DOI: 10.1038/s41522-019-0087-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 04/18/2019] [Indexed: 12/11/2022] Open
Abstract
Clostridium difficile is a major cause of nosocomial infections. Bacterial persistence in the gut is responsible for infection relapse; sporulation and other unidentified mechanisms contribute to this process. Intestinal bile salts cholate and deoxycholate stimulate spore germination, while deoxycholate kills vegetative cells. Here, we report that sub-lethal concentrations of deoxycholate stimulate biofilm formation, which protects C. difficile from antimicrobial compounds. The biofilm matrix is composed of extracellular DNA and proteinaceous factors that promote biofilm stability. Transcriptomic analysis indicates that deoxycholate induces metabolic pathways and cell envelope reorganization, and represses toxin and spore production. In support of the transcriptomic analysis, we show that global metabolic regulators and an uncharacterized lipoprotein contribute to deoxycholate-induced biofilm formation. Finally, Clostridium scindens enhances biofilm formation of C. difficile by converting cholate into deoxycholate. Together, our results suggest that deoxycholate is an intestinal signal that induces C. difficile persistence and may increase the risk of relapse.
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Affiliation(s)
- Thomas Dubois
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Present Address: INRA, UMR UMET, Villeneuve d’Ascq, France
| | - Yannick D. N. Tremblay
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Audrey Hamiot
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Present Address: INRA, UMR UMET, Villeneuve d’Ascq, France
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Julien Deschamps
- Institut Micalis, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Marc Monot
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Romain Briandet
- Institut Micalis, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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Mrázek J, Karls AC. In silico simulations of occurrence of transcription factor binding sites in bacterial genomes. BMC Evol Biol 2019; 19:67. [PMID: 30823869 PMCID: PMC6397444 DOI: 10.1186/s12862-019-1381-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 02/01/2019] [Indexed: 11/16/2022] Open
Abstract
Background Interactions between transcription factors and their specific binding sites are a key component of regulation of gene expression. Until recently, it was generally assumed that most bacterial transcription factor binding sites are located at or near promoters. However, several recent works utilizing high-throughput technology to detect transcription factor binding sites in bacterial genomes found a large number of binding sites in unexpected locations, particularly inside genes, as opposed to known or expected promoter regions. While some of these intragenic binding sites likely have regulatory functions, an alternative scenario is that many of these binding sites arise by chance in the absence of selective constraints. The latter possibility was supported by in silico simulations for σ54 binding sites in Salmonella. Results In this work, we extend these simulations to more than forty transcription factors from E. coli and other bacteria. The results suggest that binding sites for all analyzed transcription factors are likely to arise throughout the genome by random genetic drift and many transcription factor binding sites found in genomes may not have specific regulatory functions. In addition, when comparing observed and expected patterns of occurrence of binding sites in genomes, we observed distinct differences among different transcription factors. Conclusions We speculate that transcription factor binding sites randomly occurring throughout the genome could be beneficial in promoting emergence of new regulatory interactions and thus facilitating evolution of gene regulatory networks. Electronic supplementary material The online version of this article (10.1186/s12862-019-1381-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jan Mrázek
- Department of Microbiology, University of Georgia, Athens, GA, USA. .,Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
| | - Anna C Karls
- Department of Microbiology, University of Georgia, Athens, GA, USA
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Generation of Markerless Deletions in the Nosocomial Pathogen Clostridium difficile by Induction of DNA Double-Strand Breaks. Appl Environ Microbiol 2019; 85:AEM.02055-18. [PMID: 30478235 PMCID: PMC6344619 DOI: 10.1128/aem.02055-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/17/2018] [Indexed: 02/08/2023] Open
Abstract
Most sequenced bacterial genomes contain genes encoding proteins of unknown or hypothetical function. To identify a phenotype for mutations in such genes, deletion is the preferred method for mutagenesis because it reduces the likelihood of polar effects, although it does not eliminate the possibility. Allelic exchange to produce deletions is dependent on the length of homologous regions used to generate merodiploids. Shorter regions of homology resolve at lower frequencies. The work presented here demonstrates the utility of inducing DNA double-strand breaks to increase the frequency of merodiploid resolution in Clostridium difficile. Using this approach, we reveal the roles of two genes, encoding homologues of AddAB, in survival following DNA damage. The method is readily applicable to the production of deletions in C. difficile and expands the toolbox available for genetic analysis of this important anaerobic pathogen. Clostridium difficile is an important nosocomial pathogen associated with potentially fatal disease induced by the use of antibiotics. Genetic characterization of such clinically important bacteria is often hampered by lack of availability of suitable tools. Here, we describe the use of I-SceI to induce DNA double-strand breaks, which increase the frequency of allelic exchange and enable the generation of markerless deletions in C. difficile. The usefulness of the system is illustrated by the deletion of genes encoding putative AddAB homologues. The ΔaddAB mutants are sensitive to ultraviolet light and the antibiotic metronidazole, indicating a role in homologous recombination and the repair of DNA breaks. Despite the impairment in recombination, the mutants are still proficient for induction of the SOS response. In addition, deletion of the fliC gene, and subsequent complementation, reveals the importance of potential regulatory elements required for expression of a downstream gene encoding the flagellin glycosyltransferase. IMPORTANCE Most sequenced bacterial genomes contain genes encoding proteins of unknown or hypothetical function. To identify a phenotype for mutations in such genes, deletion is the preferred method for mutagenesis because it reduces the likelihood of polar effects, although it does not eliminate the possibility. Allelic exchange to produce deletions is dependent on the length of homologous regions used to generate merodiploids. Shorter regions of homology resolve at lower frequencies. The work presented here demonstrates the utility of inducing DNA double-strand breaks to increase the frequency of merodiploid resolution in Clostridium difficile. Using this approach, we reveal the roles of two genes, encoding homologues of AddAB, in survival following DNA damage. The method is readily applicable to the production of deletions in C. difficile and expands the toolbox available for genetic analysis of this important anaerobic pathogen.
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Cyclic Diguanylate Regulates Virulence Factor Genes via Multiple Riboswitches in Clostridium difficile. mSphere 2018; 3:3/5/e00423-18. [PMID: 30355665 PMCID: PMC6200980 DOI: 10.1128/msphere.00423-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In Clostridium difficile, the signaling molecule c-di-GMP regulates multiple processes affecting its ability to cause disease, including swimming and surface motility, biofilm formation, toxin production, and intestinal colonization. In this study, we used RNA-seq to define the transcriptional regulon of c-di-GMP in C. difficile. Many new targets of c-di-GMP regulation were identified, including multiple putative colonization factors. Transcriptional analyses revealed a prominent role for riboswitches in c-di-GMP signaling. Only a subset of the 16 previously predicted c-di-GMP riboswitches were functional in vivo and displayed potential variability in their response kinetics to c-di-GMP. This work underscores the importance of studying c-di-GMP riboswitches in a relevant biological context and highlights the role of the riboswitches in controlling gene expression in C. difficile. The intracellular signaling molecule cyclic diguanylate (c-di-GMP) regulates many processes in bacteria, with a central role in controlling the switch between motile and nonmotile lifestyles. Recent work has shown that in Clostridium difficile (also called Clostridioides difficile), c-di-GMP regulates swimming and surface motility, biofilm formation, toxin production, and intestinal colonization. In this study, we determined the transcriptional regulon of c-di-GMP in C. difficile, employing overexpression of a diguanylate cyclase gene to artificially manipulate intracellular c-di-GMP. Consistent with prior work, c-di-GMP regulated the expression of genes involved in swimming and surface motility. c-di-GMP also affected the expression of multiple genes encoding cell envelope proteins, several of which affected biofilm formation in vitro. A substantial proportion of the c-di-GMP regulon appears to be controlled either directly or indirectly via riboswitches. We confirmed the functionality of 11 c-di-GMP riboswitches, demonstrating their effects on downstream gene expression independent of the upstream promoters. The class I riboswitches uniformly functioned as “off” switches in response to c-di-GMP, while class II riboswitches acted as “on” switches. Transcriptional analyses of genes 3′ of c-di-GMP riboswitches over a broad range of c-di-GMP levels showed that relatively modest changes in c-di-GMP levels are capable of altering gene transcription, with concomitant effects on microbial behavior. This work expands the known c-di-GMP signaling network in C. difficile and emphasizes the role of the riboswitches in controlling known and putative virulence factors in C. difficile. IMPORTANCE In Clostridium difficile, the signaling molecule c-di-GMP regulates multiple processes affecting its ability to cause disease, including swimming and surface motility, biofilm formation, toxin production, and intestinal colonization. In this study, we used RNA-seq to define the transcriptional regulon of c-di-GMP in C. difficile. Many new targets of c-di-GMP regulation were identified, including multiple putative colonization factors. Transcriptional analyses revealed a prominent role for riboswitches in c-di-GMP signaling. Only a subset of the 16 previously predicted c-di-GMP riboswitches were functional in vivo and displayed potential variability in their response kinetics to c-di-GMP. This work underscores the importance of studying c-di-GMP riboswitches in a relevant biological context and highlights the role of the riboswitches in controlling gene expression in C. difficile.
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Mechanisms of Bacterial Tolerance and Persistence in the Gastrointestinal and Respiratory Environments. Clin Microbiol Rev 2018; 31:31/4/e00023-18. [PMID: 30068737 DOI: 10.1128/cmr.00023-18] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Pathogens that infect the gastrointestinal and respiratory tracts are subjected to intense pressure due to the environmental conditions of the surroundings. This pressure has led to the development of mechanisms of bacterial tolerance or persistence which enable microorganisms to survive in these locations. In this review, we analyze the general stress response (RpoS mediated), reactive oxygen species (ROS) tolerance, energy metabolism, drug efflux pumps, SOS response, quorum sensing (QS) bacterial communication, (p)ppGpp signaling, and toxin-antitoxin (TA) systems of pathogens, such as Escherichia coli, Salmonella spp., Vibrio spp., Helicobacter spp., Campylobacter jejuni, Enterococcus spp., Shigella spp., Yersinia spp., and Clostridium difficile, all of which inhabit the gastrointestinal tract. The following respiratory tract pathogens are also considered: Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, Burkholderia cenocepacia, and Mycobacterium tuberculosis Knowledge of the molecular mechanisms regulating the bacterial tolerance and persistence phenotypes is essential in the fight against multiresistant pathogens, as it will enable the identification of new targets for developing innovative anti-infective treatments.
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Kumar A, Kirti A, Rajaram H. Regulation of multiple abiotic stress tolerance by LexA in the cyanobacterium Anabaena sp. strain PCC7120. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:S1874-9399(18)30185-8. [PMID: 30055321 DOI: 10.1016/j.bbagrm.2018.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/15/2018] [Accepted: 07/19/2018] [Indexed: 11/28/2022]
Abstract
The paradigm of involvement of LexA in regulation of only SOS-response in bacteria through the down-regulation of DNA repair genes was challenged in the unicellular cyanobacterium, Synechocystis PCC6803, wherein it was originally shown not to be associated with DNA repair and later also involved in management of carbon-starvation through up-regulation of C-metabolism genes. In the filamentous cyanobacterium, Anabaena sp. strain PCC7120, global stress management role for LexA and a consensus LexA-binding box (AnLexA-box) has been established using a LexA-overexpressing recombinant strain, AnlexA+. High levels of LexA rendered Anabaena cells sensitive to different DNA damage and oxidative stress-inducing agents, through the transcriptional down-regulation of the genes involved in DNA repair and alleviation of oxidative stress. LexA overexpression enhanced the ability of Anabaena to tolerate C-depletion, induced by inhibiting photosynthesis, by up-regulating genes involved in C-fixation and down-regulating those involved in C-breakdown, while maintaining the overall photosynthetic efficiency. A consensus LexA-binding box, AnLexA-box [AGT-N4-11-ACT] was identified upstream of both up- and down-regulated genes using a subset of Anabaena genes identified on the basis of proteomic analysis of AnlexA+ strain along with a few DNA repair genes. A short genome search revealed the presence of AnLexA box in at least 40 more genes, with functional roles in fatty acid biosynthesis, toxin-antitoxin systems in addition to DNA repair, oxidative stress, metal tolerance and C-metabolism. Thus, Anabaena LexA modulates the tolerance to multitude of stresses through transcriptional up/down-regulation of their functional genes directly by binding to the AnLexA Box present in their promoter region.
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Affiliation(s)
- Arvind Kumar
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Trombay, Mumbai 400094, India
| | - Anurag Kirti
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Hema Rajaram
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Trombay, Mumbai 400094, India.
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Pantaléon V, Monot M, Eckert C, Hoys S, Collignon A, Janoir C, Candela T. Clostridium difficile forms variable biofilms on abiotic surface. Anaerobe 2018; 53:34-37. [PMID: 29859742 DOI: 10.1016/j.anaerobe.2018.05.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 05/14/2018] [Accepted: 05/18/2018] [Indexed: 01/06/2023]
Abstract
Clostridium difficile can form biofilms. Thirty-seven strains were characterized for their ability to form a biofilm, adhesion on an inert surface and hydrophobicity. No correlation between the ability to form a biofilm and the strain virulence was highlighted. However, non-motile strains were not able to form a high biofilm.
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Affiliation(s)
- V Pantaléon
- EA4043 Unité Bactéries Pathogènes et Santé (UBaPS), Université Paris-Sud, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - M Monot
- Département de Microbiologie, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, Paris, France; Département de Microbiologie et d'infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada; Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - C Eckert
- National Reference Laboratory for C. difficile, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine, Paris, France; Sorbonne Université, Centre d'immunologie et des Maladies Infectieuses-Paris, Cimi-Paris, Département de Bactériologie, AP-HP, Hôpitaux Universitaires de l'Est Parisien, F-75012 Paris, France
| | - S Hoys
- EA4043 Unité Bactéries Pathogènes et Santé (UBaPS), Université Paris-Sud, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - A Collignon
- EA4043 Unité Bactéries Pathogènes et Santé (UBaPS), Université Paris-Sud, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - C Janoir
- EA4043 Unité Bactéries Pathogènes et Santé (UBaPS), Université Paris-Sud, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - T Candela
- EA4043 Unité Bactéries Pathogènes et Santé (UBaPS), Université Paris-Sud, Université Paris-Saclay, 92290 Châtenay-Malabry, France.
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Abstract
Bacteria switch between free-living and a multicellular state, known as biofilms, in response to cellular and environmental cues. It is important to understand how these cues influence biofilm development as biofilms are not only ubiquitous in nature but are also causative agents of infectious diseases. It is often believed that any stress triggers biofilm formation as a means of bacterial protection. In this study, we propose a new mechanism for how cellular and environmental DNA damage may influence biofilm formation. We demonstrate that Bacillus subtilis prevents biofilm formation and cell differentiation when stressed by oxidative DNA damage. We show that during B. subtilis biofilm development, a subpopulation of cells accumulates reactive oxygen species, which triggers the DNA damage response. Surprisingly, DNA damage response induction shuts off matrix genes whose products permit individual cells to stick together within a biofilm. We further revealed that DDRON cells and matrix producers are mutually exclusive and spatially separated within the biofilm, and that a developmental checkpoint protein, Sda, mediates the exclusiveness. We believe this represents an alternative survival strategy, ultimately allowing cells to escape the multicellular community when in danger. Exposure to chemicals that damage DNA makes Bacillus subtilis bacteria turn off genes that maintain the biofilm state, releasing some bacteria. This mechanism to free cells from a biofilm is surprising, as biofilms holding bacteria together are generally considered to form as a protective mechanism for the bacteria. Yunrong Chai and colleagues at Northeastern University in Boston, USA, detected the surprising behavior in biofilms exposed to superoxide—a chemical species that damages DNA. They suggest that when the potential for damage to bacterial DNA reaches a threshold it signals that the environment is not suitable for cells to remain in the entrapped biofilm form, triggering disruption of the biofilm as a survival strategy. This response to DNA damage may be relevant to clinical conditions as biofilms are involved in many infectious diseases.
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Biofilm Formation by Clostridium ljungdahlii Is Induced by Sodium Chloride Stress: Experimental Evaluation and Transcriptome Analysis. PLoS One 2017; 12:e0170406. [PMID: 28118386 PMCID: PMC5261816 DOI: 10.1371/journal.pone.0170406] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/04/2017] [Indexed: 01/08/2023] Open
Abstract
The acetogen Clostridium ljungdahlii is capable of syngas fermentation and microbial electrosynthesis. Biofilm formation could benefit both these applications, but was not yet reported for C. ljungdahlii. Biofilm formation does not occur under standard growth conditions, but attachment or aggregation could be induced by different stresses. The strongest biofilm formation was observed with the addition of sodium chloride. After 3 days of incubation, the biomass volume attached to a plastic surface was 20 times higher with than without the addition of 200 mM NaCl to the medium. The addition of NaCl also resulted in biofilm formation on glass, graphite and glassy carbon, the latter two being often used electrode materials for microbial electrosynthesis. Biofilms were composed of extracellular proteins, polysaccharides, as well as DNA, while pilus-like appendages were observed with, but not without, the addition of NaCl. A transcriptome analysis comparing planktonic (no NaCl) and biofilm (NaCl addition) cells showed that C. ljungdahlii coped with the salt stress by the upregulation of the general stress response, Na+ export and osmoprotectant accumulation. A potential role for poly-N-acetylglucosamines and D-alanine in biofilm formation was found. Flagellar motility was downregulated, while putative type IV pili biosynthesis genes were not expressed. Moreover, the gene expression analysis suggested the involvement of the transcriptional regulators LexA, Spo0A and CcpA in stress response and biofilm formation. This study showed that NaCl addition might be a valuable strategy to induce biofilm formation by C. ljungdahlii, which can improve the efficacy of syngas fermentation and microbial electrosynthesis applications.
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Systematically Altering Bacterial SOS Activity under Stress Reveals Therapeutic Strategies for Potentiating Antibiotics. mSphere 2016; 1:mSphere00163-16. [PMID: 27536734 PMCID: PMC4980697 DOI: 10.1128/msphere.00163-16] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 07/19/2016] [Indexed: 11/20/2022] Open
Abstract
Our antibiotic arsenal is becoming depleted, in part, because bacteria have the ability to rapidly adapt and acquire resistance to our best agents. The SOS pathway, a widely conserved DNA damage stress response in bacteria, is activated by many antibiotics and has been shown to play central role in promoting survival and the evolution of resistance under antibiotic stress. As a result, targeting the SOS response has been proposed as an adjuvant strategy to revitalize our current antibiotic arsenal. However, the optimal molecular targets and partner antibiotics for such an approach remain unclear. In this study, focusing on the two key regulators of the SOS response, LexA and RecA, we provide the first comprehensive assessment of how to target the SOS response in order to increase bacterial susceptibility and reduce mutagenesis under antibiotic treatment. The bacterial SOS response is a DNA damage repair network that is strongly implicated in both survival and acquired drug resistance under antimicrobial stress. The two SOS regulators, LexA and RecA, have therefore emerged as potential targets for adjuvant therapies aimed at combating resistance, although many open questions remain. For example, it is not well understood whether SOS hyperactivation is a viable therapeutic approach or whether LexA or RecA is a better target. Furthermore, it is important to determine which antimicrobials could serve as the best treatment partners with SOS-targeting adjuvants. Here we derived Escherichia coli strains that have mutations in either lexA or recA genes in order to cover the full spectrum of possible SOS activity levels. We then systematically analyzed a wide range of antimicrobials by comparing the mean inhibitory concentrations (MICs) and induced mutation rates for each drug-strain combination. We first show that significant changes in MICs are largely confined to DNA-damaging antibiotics, with strains containing a constitutively repressed SOS response impacted to a greater extent than hyperactivated strains. Second, antibiotic-induced mutation rates were suppressed when SOS activity was reduced, and this trend was observed across a wider spectrum of antibiotics. Finally, perturbing either LexA or RecA proved to be equally viable strategies for targeting the SOS response. Our work provides support for multiple adjuvant strategies, while also suggesting that the combination of an SOS inhibitor with a DNA-damaging antibiotic could offer the best potential for lowering MICs and decreasing acquired drug resistance. IMPORTANCE Our antibiotic arsenal is becoming depleted, in part, because bacteria have the ability to rapidly adapt and acquire resistance to our best agents. The SOS pathway, a widely conserved DNA damage stress response in bacteria, is activated by many antibiotics and has been shown to play central role in promoting survival and the evolution of resistance under antibiotic stress. As a result, targeting the SOS response has been proposed as an adjuvant strategy to revitalize our current antibiotic arsenal. However, the optimal molecular targets and partner antibiotics for such an approach remain unclear. In this study, focusing on the two key regulators of the SOS response, LexA and RecA, we provide the first comprehensive assessment of how to target the SOS response in order to increase bacterial susceptibility and reduce mutagenesis under antibiotic treatment.
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Martin-Verstraete I, Peltier J, Dupuy B. The Regulatory Networks That Control Clostridium difficile Toxin Synthesis. Toxins (Basel) 2016; 8:E153. [PMID: 27187475 PMCID: PMC4885068 DOI: 10.3390/toxins8050153] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 05/03/2016] [Accepted: 05/05/2016] [Indexed: 12/19/2022] Open
Abstract
The pathogenic clostridia cause many human and animal diseases, which typically arise as a consequence of the production of potent exotoxins. Among the enterotoxic clostridia, Clostridium difficile is the main causative agent of nosocomial intestinal infections in adults with a compromised gut microbiota caused by antibiotic treatment. The symptoms of C. difficile infection are essentially caused by the production of two exotoxins: TcdA and TcdB. Moreover, for severe forms of disease, the spectrum of diseases caused by C. difficile has also been correlated to the levels of toxins that are produced during host infection. This observation strengthened the idea that the regulation of toxin synthesis is an important part of C. difficile pathogenesis. This review summarizes our current knowledge about the regulators and sigma factors that have been reported to control toxin gene expression in response to several environmental signals and stresses, including the availability of certain carbon sources and amino acids, or to signaling molecules, such as the autoinducing peptides of quorum sensing systems. The overlapping regulation of key metabolic pathways and toxin synthesis strongly suggests that toxin production is a complex response that is triggered by bacteria in response to particular states of nutrient availability during infection.
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Affiliation(s)
- Isabelle Martin-Verstraete
- Laboratoire Pathogenèse des Bactéries Anaérobes, Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux Paris, Paris 75015, France.
- UFR Sciences du vivant, University Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris 75015, France.
| | - Johann Peltier
- Laboratoire Pathogenèse des Bactéries Anaérobes, Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux Paris, Paris 75015, France.
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobes, Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux Paris, Paris 75015, France.
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Kizawa A, Kawahara A, Takimura Y, Nishiyama Y, Hihara Y. RNA-seq Profiling Reveals Novel Target Genes of LexA in the Cyanobacterium Synechocystis sp. PCC 6803. Front Microbiol 2016; 7:193. [PMID: 26925056 PMCID: PMC4759255 DOI: 10.3389/fmicb.2016.00193] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/04/2016] [Indexed: 11/13/2022] Open
Abstract
LexA is a well-established transcriptional repressor of SOS genes induced by DNA damage in Escherichia coli and other bacterial species. However, LexA in the cyanobacterium Synechocystis sp. PCC 6803 has been suggested not to be involved in SOS response. In this study, we performed RNA-seq analysis of the wild-type strain and the lexA-disrupted mutant to obtain the comprehensive view of LexA-regulated genes in Synechocystis. Disruption of lexA positively or negatively affected expression of genes related to various cellular functions such as phototactic motility, accumulation of the major compatible solute glucosylglycerol and subunits of bidirectional hydrogenase, photosystem I, and phycobilisome complexes. We also observed increase in the expression level of genes related to iron and manganese uptake in the mutant at the later stage of cultivation. However, none of the genes related to DNA metabolism were affected by disruption of lexA. DNA gel mobility shift assay using the recombinant LexA protein suggested that LexA binds to the upstream region of pilA7, pilA9, ggpS, and slr1670 to directly regulate their expression, but changes in the expression level of photosystem I genes by disruption of lexA is likely a secondary effect.
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Affiliation(s)
- Ayumi Kizawa
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University Saitama, Japan
| | - Akihito Kawahara
- Biological Science Laboratories, KAO Corporation Wakayama, Japan
| | - Yasushi Takimura
- Biological Science Laboratories, KAO Corporation Wakayama, Japan
| | - Yoshitaka Nishiyama
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University Saitama, Japan
| | - Yukako Hihara
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama UniversitySaitama, Japan; Core Research of Evolutional Science and Technology, Japan Science and Technology AgencySaitama, Japan
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