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Sánchez-Jiménez A, Llamas MA, Marcos-Torres FJ. Transcriptional Regulators Controlling Virulence in Pseudomonas aeruginosa. Int J Mol Sci 2023; 24:11895. [PMID: 37569271 PMCID: PMC10418997 DOI: 10.3390/ijms241511895] [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: 07/04/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 08/13/2023] Open
Abstract
Pseudomonas aeruginosa is a pathogen capable of colonizing virtually every human tissue. The host colonization competence and versatility of this pathogen are powered by a wide array of virulence factors necessary in different steps of the infection process. This includes factors involved in bacterial motility and attachment, biofilm formation, the production and secretion of extracellular invasive enzymes and exotoxins, the production of toxic secondary metabolites, and the acquisition of iron. Expression of these virulence factors during infection is tightly regulated, which allows their production only when they are needed. This process optimizes host colonization and virulence. In this work, we review the intricate network of transcriptional regulators that control the expression of virulence factors in P. aeruginosa, including one- and two-component systems and σ factors. Because inhibition of virulence holds promise as a target for new antimicrobials, blocking the regulators that trigger the production of virulence determinants in P. aeruginosa is a promising strategy to fight this clinically relevant pathogen.
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Affiliation(s)
| | - María A. Llamas
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain;
| | - Francisco Javier Marcos-Torres
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain;
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2
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Otero-Asman JR, Sánchez-Jiménez A, Bastiaansen KC, Wettstadt S, Civantos C, García-Puente A, Bitter W, Llamas MA. The Prc and CtpA proteases modulate cell-surface signaling activity and virulence in Pseudomonas aeruginosa. iScience 2023; 26:107216. [PMID: 37534181 PMCID: PMC10392083 DOI: 10.1016/j.isci.2023.107216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/17/2023] [Accepted: 06/22/2023] [Indexed: 08/04/2023] Open
Abstract
Cell-surface signaling (CSS) is a signal transfer system of Gram-negative bacteria that produces the activation of an extracytoplasmic function σ factor (σECF) in the cytosol in response to an extracellular signal. Activation requires the regulated and sequential proteolysis of the σECF-associated anti-σ factor, and the function of the Prc and RseP proteases. In this work, we have identified another protease that modulates CSS activity, namely the periplasmic carboxyl-terminal processing protease CtpA. CtpA functions upstream of Prc in the proteolytic cascade and seems to prevent the Prc-mediated proteolysis of the CSS anti-σ factor. Importantly, using zebrafish embryos and the A549 lung epithelial cell line as hosts, we show that mutants in the rseP and ctpA proteases of the human pathogen Pseudomonas aeruginosa are considerably attenuated in virulence while the prc mutation increases virulence likely by enhancing the production of membrane vesicles.
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Affiliation(s)
- Joaquín R. Otero-Asman
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Ana Sánchez-Jiménez
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Karlijn C. Bastiaansen
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
- Department of Medical Microbiology and Infection Control, Amsterdam University medical centres, location VU University, 1081 HV Amsterdam, The Netherlands
| | - Sarah Wettstadt
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Cristina Civantos
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Alicia García-Puente
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, Amsterdam University medical centres, location VU University, 1081 HV Amsterdam, The Netherlands
| | - María A. Llamas
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
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3
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Salvà-Serra F, Jaén-Luchoro D, Marathe NP, Adlerberth I, Moore ERB, Karlsson R. Responses of carbapenemase-producing and non-producing carbapenem-resistant Pseudomonas aeruginosa strains to meropenem revealed by quantitative tandem mass spectrometry proteomics. Front Microbiol 2023; 13:1089140. [PMID: 36845973 PMCID: PMC9948630 DOI: 10.3389/fmicb.2022.1089140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/08/2022] [Indexed: 02/11/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen with increasing incidence of multidrug-resistant strains, including resistance to last-resort antibiotics, such as carbapenems. Resistances are often due to complex interplays of natural and acquired resistance mechanisms that are enhanced by its large regulatory network. This study describes the proteomic responses of two carbapenem-resistant P. aeruginosa strains of high-risk clones ST235 and ST395 to subminimal inhibitory concentrations (sub-MICs) of meropenem by identifying differentially regulated proteins and pathways. Strain CCUG 51971 carries a VIM-4 metallo-β-lactamase or 'classical' carbapenemase; strain CCUG 70744 carries no known acquired carbapenem-resistance genes and exhibits 'non-classical' carbapenem-resistance. Strains were cultivated with different sub-MICs of meropenem and analyzed, using quantitative shotgun proteomics based on tandem mass tag (TMT) isobaric labeling, nano-liquid chromatography tandem-mass spectrometry and complete genome sequences. Exposure of strains to sub-MICs of meropenem resulted in hundreds of differentially regulated proteins, including β-lactamases, proteins associated with transport, peptidoglycan metabolism, cell wall organization, and regulatory proteins. Strain CCUG 51971 showed upregulation of intrinsic β-lactamases and VIM-4 carbapenemase, while CCUG 70744 exhibited a combination of upregulated intrinsic β-lactamases, efflux pumps, penicillin-binding proteins and downregulation of porins. All components of the H1 type VI secretion system were upregulated in strain CCUG 51971. Multiple metabolic pathways were affected in both strains. Sub-MICs of meropenem cause marked changes in the proteomes of carbapenem-resistant strains of P. aeruginosa exhibiting different resistance mechanisms, involving a wide range of proteins, many uncharacterized, which might play a role in the susceptibility of P. aeruginosa to meropenem.
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Affiliation(s)
- Francisco Salvà-Serra
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden,Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden,Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain,*Correspondence: Francisco Salvà-Serra, ✉
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | | | - Ingegerd Adlerberth
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Edward R. B. Moore
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden,Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Roger Karlsson
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden,Nanoxis Consulting AB, Gothenburg, Sweden,Roger Karlsson, ✉
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Pokharel K, Dawadi BR, Shrestha LB. Role of Biofilm in Bacterial Infection and Antimicrobial Resistance. JNMA J Nepal Med Assoc 2022; 60:836-840. [PMID: 36705135 PMCID: PMC9794942 DOI: 10.31729/jnma.7580] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 08/25/2022] [Indexed: 01/31/2023] Open
Abstract
Biofilm refers to the complex, sessile communities of microbes found either attached to a surface or buried firmly in an extracellular matrix as aggregates. Microbial flora which produces biofilm manifests an altered growth rate and transcribes genes that provide them resistance to antimicrobial and host immune systems. Biofilms protect the invading bacteria against the immune system of the host via impaired activation of phagocytes and the complement system. Biofilm-producing isolates showed greater multidrug resistance than non-biofilm producers. Biofilm causes antibiotic resistance through processes like chromosomally encoded resistant genes, restriction of antibiotics, reduction of growth rate, and host immunity. Biofilm formation is responsible for the development of superbugs like methicillin-resistant Staphylococcus aureus, vancomycin-resistant Staphylococcus aureus, and metallo-beta-lactamase producing Pseudomonas aeruginosa. Regular monitoring of antimicrobial resistance and maintaining hygiene, especially in hospitalized patients are required to control biofilm-related infections in order to prevent antimicrobial resistance.
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Affiliation(s)
- Khilasa Pokharel
- Department of Microbiology, Kathmandu Medical College and Teaching Hospital, Sinamangal, Kathmandu, Nepal,Correspondence: Dr Khilasa Pokharel, Department of Microbiology, Kathmandu Medical College and Teaching Hospital, Kathmandu, Nepal. , Phone: +977-9841437466
| | - Bishwa Raj Dawadi
- Department of Emergency Medicine, Grande International Hospital, Dhapasi, Kathmandu, Nepal
| | - Lok Bahadur Shrestha
- School of Medical Sciences and The Kirby Institute, University of New South Wales, Sydney, Australia
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5
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Xin G, Zhao L, Zhuang Z, Wang X, Fu Q, Huang H, Huang L, Qin Y, Zhang J, Zhang J, Yan Q. Function of the rpoD gene in Pseudomonas plecoglossicida pathogenicity and Epinephelus coioides immune response. FISH & SHELLFISH IMMUNOLOGY 2022; 127:427-436. [PMID: 35779810 DOI: 10.1016/j.fsi.2022.06.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Pseudomonas plecoglossicida is a Gram-negative pathogenic bacterium that causes visceral white spot disease in several marine fish species, resulting in high mortality and financial loss. Based on previous RNA sequencing (RNA-seq) results, rpoD gene expression is significantly up-regulated in P. plecoglossicida during infection, indicating that rpoD may contribute to bacterial pathogenicity. To investigate the role of this gene, five specific short hairpin RNAs (shRNAs) were designed and synthesized based on the rpoD gene sequence, with all five mutants exhibiting a significant decrease in rpoD gene expression in P. plecoglossicida. The mutant with the highest silencing efficiency (89.2%) was chosen for further study. Compared with the wild-type (WT) P. plecoglossicida strain NZBD9, silencing rpoD in the rpoD-RNA interference (RNAi) strain resulted in a significant decrease in growth, motility, chemotaxis, adhesion, and biofilm formation in P. plecoglossicida. Silencing of rpoD also resulted in a 25% increase in the survival rate, a one-day delay in the onset of death, and a significant decrease in the number of white spots on the spleen surface of infected orange-spotted groupers (Epinephelus coioides). In addition, rpoD expression and pathogen load were significantly lower in the spleens of E. coioides infected with the rpoD-RNAi strain than with the WT strain of P. plecoglossicida. We performed RNA-seq of E. coioides spleens infected with different P. plecoglossicida strains. Results showed that rpoD silencing in P. plecoglossicida led to a significant change in the infected spleen transcriptomes. In addition, comparative transcriptome analysis showed that silencing rpoD caused significant changes in complement and coagulation cascades and the IL-17 signaling pathway. Thus, this study revealed the effects of the rpoD gene on P. plecoglossicida pathogenicity and identified the main pathway involved in the immune response of E. coioides.
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Affiliation(s)
- Ge Xin
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
| | - Lingmin Zhao
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
| | - Zhixia Zhuang
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen, Fujian, 361024, China
| | - Xiaoru Wang
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen, Fujian, 361024, China
| | - Qi Fu
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen, Fujian, 361024, China
| | - Huabin Huang
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen, Fujian, 361024, China
| | - Lixing Huang
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
| | - Yingxue Qin
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
| | - Jiaonan Zhang
- Key Laboratory of Special Aquatic Feed for Fujian, Fujian Tianma Technology Company Limited, Fuzhou, Fujian, 350308, China
| | - Jiaolin Zhang
- Key Laboratory of Special Aquatic Feed for Fujian, Fujian Tianma Technology Company Limited, Fuzhou, Fujian, 350308, China
| | - Qingpi Yan
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China.
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6
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Cell Envelope Stress Response in Pseudomonas aeruginosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:147-184. [DOI: 10.1007/978-3-031-08491-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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Dou Y, Rutanhira H, Schormann N, Deivanayagam C, Fletcher HM. PG1659 functions as anti-sigma factor to extracytoplasmic function sigma factor RpoE in Porphyromonas gingivalis W83. Mol Oral Microbiol 2021; 36:80-91. [PMID: 33377315 DOI: 10.1111/omi.12329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022]
Abstract
Anti-sigma factors play a critical role in regulating the expression of sigma factors in response to environmental stress signals. PG1659 is cotranscribed with an upstream gene PG1660 (rpoE), which encodes for a sigma factor that plays an important role in oxidative stress resistance and the virulence regulatory network of P. gingivalis. PG1659, which is annotated as a hypothetical gene, is evaluated in this study. PG1659, composed of 130 amino acids, is predicted to be transmembrane protein with a single calcium (Ca2+ ) binding site. In P. gingivalis FLL358 (ΔPG1659::ermF), the rpoE gene was highly upregulated compared to the wild-type W83 strain. RpoE-induced genes were also upregulated in the PG1659-defective isogenic mutant. Both protein-protein pull-down and bacterial two-hybrid assays revealed that the PG1659 protein could interact with/bind RpoE. The N-terminal domain of PG1659, representing the cytoplasmic fragment of the protein, is critical for interaction with RpoE. In the presence of PG1659, the initiation of transcription by the RpoE sigma factor was inhibited. Taken together, our data suggest that PG1659 is an anti-sigma factor which plays an important regulatory role in the modulation of the sigma factor RpoE in P. gingivalis.
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Affiliation(s)
- Yuetan Dou
- Department of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Hiel Rutanhira
- Department of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Norbert Schormann
- Department of Biochemistry and Molecular Genetics, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Champion Deivanayagam
- Department of Biochemistry and Molecular Genetics, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hansel M Fletcher
- Department of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, CA, USA
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8
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Travis BA, Ramsey KM, Prezioso SM, Tallo T, Wandzilak JM, Hsu A, Borgnia M, Bartesaghi A, Dove SL, Brennan RG, Schumacher MA. Structural Basis for Virulence Activation of Francisella tularensis. Mol Cell 2021; 81:139-152.e10. [PMID: 33217319 PMCID: PMC7959165 DOI: 10.1016/j.molcel.2020.10.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/25/2020] [Accepted: 10/22/2020] [Indexed: 01/25/2023]
Abstract
The bacterium Francisella tularensis (Ft) is one of the most infectious agents known. Ft virulence is controlled by a unique combination of transcription regulators: the MglA-SspA heterodimer, PigR, and the stress signal, ppGpp. MglA-SspA assembles with the σ70-associated RNAP holoenzyme (RNAPσ70), forming a virulence-specialized polymerase. These factors activate Francisella pathogenicity island (FPI) gene expression, which is required for virulence, but the mechanism is unknown. Here we report FtRNAPσ70-promoter-DNA, FtRNAPσ70-(MglA-SspA)-promoter DNA, and FtRNAPσ70-(MglA-SspA)-ppGpp-PigR-promoter DNA cryo-EM structures. Structural and genetic analyses show MglA-SspA facilitates σ70 binding to DNA to regulate virulence and virulence-enhancing genes. Our Escherichia coli RNAPσ70-homodimeric EcSspA structure suggests this is a general SspA-transcription regulation mechanism. Strikingly, our FtRNAPσ70-(MglA-SspA)-ppGpp-PigR-DNA structure reveals ppGpp binding to MglA-SspA tethers PigR to promoters. PigR in turn recruits FtRNAP αCTDs to DNA UP elements. Thus, these studies unveil a unique mechanism for Ft pathogenesis involving a virulence-specialized RNAP that employs two (MglA-SspA)-based strategies to activate virulence genes.
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Affiliation(s)
- Brady A Travis
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kathryn M Ramsey
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Cell and Molecular Biology and Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Samantha M Prezioso
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Tallo
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jamie M Wandzilak
- Department of Cell and Molecular Biology and Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Allen Hsu
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Mario Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Alberto Bartesaghi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Simon L Dove
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Richard G Brennan
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.
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Varadarajan AR, Allan RN, Valentin JDP, Castañeda Ocampo OE, Somerville V, Pietsch F, Buhmann MT, West J, Skipp PJ, van der Mei HC, Ren Q, Schreiber F, Webb JS, Ahrens CH. An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1. NPJ Biofilms Microbiomes 2020; 6:46. [PMID: 33127897 PMCID: PMC7603352 DOI: 10.1038/s41522-020-00154-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 10/07/2020] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas aeruginosa MPAO1 is the parental strain of the widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and biofilm-associated antibiotic resistance. Our model employs a genomics-driven workflow to assemble the complete MPAO1 genome, identify unique and conserved genes by comparative genomics with the PAO1 reference strain and genes missed within existing assemblies by proteogenomics. Among over 200 unique MPAO1 genes, we identified six general essential genes that were overlooked when mapping public Tn-seq data sets against PAO1, including an antitoxin. Genomic data were integrated with phenotypic data from an experimental workflow using a user-friendly, soft lithography-based microfluidic flow chamber for biofilm growth and a screen with the Tn-mutant library in microtiter plates. The screen identified hitherto unknown genes involved in biofilm growth and antibiotic resistance. Experiments conducted with the flow chamber across three laboratories delivered reproducible data on P. aeruginosa biofilms and validated the function of both known genes and genes identified in the Tn-mutant screens. Differential protein abundance data from planktonic cells versus biofilm confirmed the upregulation of candidates known to affect biofilm formation, of structural and secreted proteins of type VI secretion systems, and provided proteogenomic evidence for some missed MPAO1 genes. This integrated, broadly applicable model promises to improve the mechanistic understanding of biofilm formation, antimicrobial tolerance, and resistance evolution in biofilms.
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Affiliation(s)
- Adithi R Varadarajan
- Research Group Molecular Diagnostics Genomics & Bioinformatics, Agroscope and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland.
| | - Raymond N Allan
- School of Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- National Biofilms Innovation Centre, University of Southampton, Southampton, SO17 1BJ, UK
- School of Pharmacy, Faculty of Health and Life Sciences, De Montfort University, Leicester, LE1 9BH, UK
| | - Jules D P Valentin
- Laboratory for Biointerfaces, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland
- Department of BioMedical Engineering, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Olga E Castañeda Ocampo
- Department of BioMedical Engineering, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Vincent Somerville
- Research Group Molecular Diagnostics Genomics & Bioinformatics, Agroscope and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Franziska Pietsch
- Division of Biodeterioration and Reference Organisms, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | - Matthias T Buhmann
- Laboratory for Biointerfaces, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland
| | - Jonathan West
- Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK
- Centre for Hybrid Biodevices, University of Southampton, Southampton, SO17 1BJ, UK
| | - Paul J Skipp
- Centre for Proteomics Research, University of Southampton, Southampton, SO17 1BJ, UK
| | - Henny C van der Mei
- Department of BioMedical Engineering, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Qun Ren
- Laboratory for Biointerfaces, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland
| | - Frank Schreiber
- Division of Biodeterioration and Reference Organisms, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | - Jeremy S Webb
- School of Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- National Biofilms Innovation Centre, University of Southampton, Southampton, SO17 1BJ, UK
| | - Christian H Ahrens
- Research Group Molecular Diagnostics Genomics & Bioinformatics, Agroscope and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland.
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10
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Pieroni M. Nitric oxide-releasing cyclodextrins as biodegradable antibacterial scaffolds: a patent evaluation of US2019343869(A1). Expert Opin Ther Pat 2020; 30:901-905. [PMID: 32901572 DOI: 10.1080/13543776.2020.1822328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Antimicrobial resistance is one of the major scourges for health care worldwide; therefore, novel investigational approaches are needed to potentiate and preserve the current antibacterial arsenal. Cyclodextrins are known to improve the formulability of several different therapeutic agents. When functionalized with nitric oxide (NO) releasing groups, and suitably loaded with an antibacterial or antitumoral agents, they can exert additive activity, especially toward certain bacterial strains and cell cancer lines. AREAS COVERED US2019343869 describes NO-releasing cyclodextrins, a method for their synthesis, a composition that is based on them, and their application as anticancer or antibacterial agents, especially toward planktonic P. aeruginosa and the biofilm resulting from infection. Anticancer activity is measured against A549 cells. The amount of NO released is in the range of 0.5 μmol to 2.5 μmol per milligram of functionalized cyclodextrin with a half-life for NO release in a range of between about 0.7-4.2 hours. EXPERT OPINION The results support the use of NO-releasing cyclodextrins as a matrix for the delivery of antibacterial and anticancer drugs in a suitable formulation. However, antibacterial activity seems to be weak, and more focused studies are needed.
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Affiliation(s)
- Marco Pieroni
- P4T Group, University of Parma , Parma, Italy.,Department of Food and Drug, University of Parma , Parma, Italy
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11
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Otero-Asman JR, Wettstadt S, Bernal P, Llamas MA. Diversity of extracytoplasmic function sigma (σ ECF ) factor-dependent signaling in Pseudomonas. Mol Microbiol 2019; 112:356-373. [PMID: 31206859 DOI: 10.1111/mmi.14331] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2019] [Indexed: 12/23/2022]
Abstract
Pseudomonas bacteria are widespread and are found in soil and water, as well as pathogens of both plants and animals. The ability of Pseudomonas to colonize many different environments is facilitated by the multiple signaling systems these bacteria contain that allow Pseudomonas to adapt to changing circumstances by generating specific responses. Among others, signaling through extracytoplasmic function σ (σECF ) factors is extensively present in Pseudomonas. σECF factors trigger expression of functions required under particular conditions in response to specific signals. This manuscript reviews the phylogeny and biological roles of σECF factors in Pseudomonas, and highlights the diversity of σECF -signaling pathways of this genus in terms of function and activation. We show that Pseudomonas σECF factors belong to 16 different phylogenetic groups. Most of them are included within the iron starvation group and are mainly involved in iron acquisition. The second most abundant group is formed by RpoE-like σECF factors, which regulate the responses to cell envelope stress. Other groups controlling solvent tolerance, biofilm formation and the response to oxidative stress, among other functions, are present in lower frequency. The role of σECF factors in the virulence of Pseudomonas pathogenic species is described.
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Affiliation(s)
- Joaquín R Otero-Asman
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Sarah Wettstadt
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Patricia Bernal
- Department of Biology, Faculty of Sciences, Universidad Autónoma de Madrid, Madrid, Spain
| | - María A Llamas
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
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12
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Long GS, Hussen M, Dench J, Aris-Brosou S. Identifying genetic determinants of complex phenotypes from whole genome sequence data. BMC Genomics 2019; 20:470. [PMID: 31182025 PMCID: PMC6558885 DOI: 10.1186/s12864-019-5820-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/21/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND A critical goal in biology is to relate the phenotype to the genotype, that is, to find the genetic determinants of various traits. However, while simple monofactorial determinants are relatively easy to identify, the underpinnings of complex phenotypes are harder to predict. While traditional approaches rely on genome-wide association studies based on Single Nucleotide Polymorphism data, the ability of machine learning algorithms to find these determinants in whole proteome data is still not well known. RESULTS To better understand the applicability of machine learning in this case, we implemented two such algorithms, adaptive boosting (AB) and repeated random forest (RRF), and developed a chunking layer that facilitates the analysis of whole proteome data. We first assessed the performance of these algorithms and tuned them on an influenza data set, for which the determinants of three complex phenotypes (infectivity, transmissibility, and pathogenicity) are known based on experimental evidence. This allowed us to show that chunking improves runtimes by an order of magnitude. Based on simulations, we showed that chunking also increases sensitivity of the predictions, reaching 100% with as few as 20 sequences in a small proteome as in the influenza case (5k sites), but may require at least 30 sequences to reach 90% on larger alignments (500k sites). While RRF has less specificity than random forest, it was never <50%, and RRF sensitivity was significantly higher at smaller chunk sizes. We then used these algorithms to predict the determinants of three types of drug resistance (to Ciprofloxacin, Ceftazidime, and Gentamicin) in a bacterium, Pseudomonas aeruginosa. While both algorithms performed well in the case of the influenza data, results were more nuanced in the bacterial case, with RRF making more sensible predictions, with smaller errors rates, than AB. CONCLUSIONS Altogether, we demonstrated that ML algorithms can be used to identify genetic determinants in small proteomes (viruses), even when trained on small numbers of individuals. We further showed that our RRF algorithm may deserve more scrutiny, which should be facilitated by the decreasing costs of both sequencing and phenotyping of large cohorts of individuals.
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Affiliation(s)
- George S Long
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Mohammed Hussen
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Jonathan Dench
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Stéphane Aris-Brosou
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada. .,Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.
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Kamaruzzaman NF, Tan LP, Hamdan RH, Choong SS, Wong WK, Gibson AJ, Chivu A, Pina MDF. Antimicrobial Polymers: The Potential Replacement of Existing Antibiotics? Int J Mol Sci 2019; 20:E2747. [PMID: 31167476 PMCID: PMC6600223 DOI: 10.3390/ijms20112747] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/08/2019] [Accepted: 04/11/2019] [Indexed: 12/22/2022] Open
Abstract
Antimicrobial resistance is now considered a major global challenge; compromising medical advancements and our ability to treat infectious disease. Increased antimicrobial resistance has resulted in increased morbidity and mortality due to infectious diseases worldwide. The lack of discovery of novel compounds from natural products or new classes of antimicrobials, encouraged us to recycle discontinued antimicrobials that were previously removed from routine use due to their toxicity, e.g., colistin. Since the discovery of new classes of compounds is extremely expensive and has very little success, one strategy to overcome this issue could be the application of synthetic compounds that possess antimicrobial activities. Polymers with innate antimicrobial properties or that have the ability to be conjugated with other antimicrobial compounds create the possibility for replacement of antimicrobials either for the direct application as medicine or implanted on medical devices to control infection. Here, we provide the latest update on research related to antimicrobial polymers in the context of ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) pathogens. We summarise polymer subgroups: compounds containing natural peptides, halogens, phosphor and sulfo derivatives and phenol and benzoic derivatives, organometalic polymers, metal nanoparticles incorporated into polymeric carriers, dendrimers and polymer-based guanidine. We intend to enhance understanding in the field and promote further work on the development of polymer based antimicrobial compounds.
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Affiliation(s)
- Nor Fadhilah Kamaruzzaman
- Faculty of Veterinary Medicine, Locked bag 36, Universiti Malaysia Kelantan, Pengkalan Chepa 16100, Kelantan, Malaysia.
| | - Li Peng Tan
- Faculty of Veterinary Medicine, Locked bag 36, Universiti Malaysia Kelantan, Pengkalan Chepa 16100, Kelantan, Malaysia.
| | - Ruhil Hayati Hamdan
- Faculty of Veterinary Medicine, Locked bag 36, Universiti Malaysia Kelantan, Pengkalan Chepa 16100, Kelantan, Malaysia.
| | - Siew Shean Choong
- Faculty of Veterinary Medicine, Locked bag 36, Universiti Malaysia Kelantan, Pengkalan Chepa 16100, Kelantan, Malaysia.
| | - Weng Kin Wong
- School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia.
| | - Amanda Jane Gibson
- Royal Veterinary College, Pathobiology and Population Sciences, Hawkshead Lane, North Mymms, Hatfield AL9 7TA, UK.
| | - Alexandru Chivu
- UCL Centre for Nanotechnology and Regenerative Medicine, Division of Surgery & Interventional Science, University College London, London NW3 2PF, UK.
| | - Maria de Fatima Pina
- Medicines and Healthcare Regulatory Products Agency, 10 South Colonnade, Canary Wharf, London E14 4PU, UK.
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14
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Bouillet S, Ba M, Houot L, Iobbi-Nivol C, Bordi C. Connected partner-switches control the life style of Pseudomonas aeruginosa through RpoS regulation. Sci Rep 2019; 9:6496. [PMID: 31019225 PMCID: PMC6482189 DOI: 10.1038/s41598-019-42653-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/29/2019] [Indexed: 12/27/2022] Open
Abstract
Biofilm formation is a complex process resulting from the action of imbricated pathways in response to environmental cues. In this study, we showed that biofilm biogenesis in the opportunistic pathogen Pseudomonas aeruginosa depends on the availability of RpoS, the sigma factor regulating the general stress response in bacteria. Moreover, it was demonstrated that RpoS is post-translationally regulated by the HsbR-HsbA partner switching system as has been demonstrated for its CrsR-CrsA homolog in Shewanella oneidensis. Finally, it was established that HsbA, the anti-sigma factor antagonist, has a pivotal role depending on its phosphorylation state since it binds HsbR, the response regulator, when phosphorylated and FlgM, the anti-sigma factor of FliA, when non-phosphorylated. The phosphorylation state of HsbA thus drives the switch between the sessile and planktonic way of life of P. aeruginosa by driving the release or the sequestration of one or the other of these two sigma factors.
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Affiliation(s)
| | - Moly Ba
- Aix Marseille Univ, CNRS, IMM, LISM, Marseille, France
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15
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Kamaruzzaman NF, Tan LP, Mat Yazid KA, Saeed SI, Hamdan RH, Choong SS, Wong WK, Chivu A, Gibson AJ. Targeting the Bacterial Protective Armour; Challenges and Novel Strategies in the Treatment of Microbial Biofilm. MATERIALS (BASEL, SWITZERLAND) 2018; 11:E1705. [PMID: 30217006 PMCID: PMC6164881 DOI: 10.3390/ma11091705] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/07/2018] [Accepted: 09/09/2018] [Indexed: 02/07/2023]
Abstract
Infectious disease caused by pathogenic bacteria continues to be the primary challenge to humanity. Antimicrobial resistance and microbial biofilm formation in part, lead to treatment failures. The formation of biofilms by nosocomial pathogens such as Staphylococcus aureus (S. aureus), Pseudomonas aeruginosa (P. aeruginosa), and Klebsiella pneumoniae (K. pneumoniae) on medical devices and on the surfaces of infected sites bring additional hurdles to existing therapies. In this review, we discuss the challenges encountered by conventional treatment strategies in the clinic. We also provide updates on current on-going research related to the development of novel anti-biofilm technologies. We intend for this review to provide understanding to readers on the current problem in health-care settings and propose new ideas for new intervention strategies to reduce the burden related to microbial infections.
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Affiliation(s)
- Nor Fadhilah Kamaruzzaman
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa 16100, Kelantan, Malaysia.
| | - Li Peng Tan
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa 16100, Kelantan, Malaysia.
| | - Khairun Anisa Mat Yazid
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa 16100, Kelantan, Malaysia.
| | - Shamsaldeen Ibrahim Saeed
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa 16100, Kelantan, Malaysia.
| | - Ruhil Hayati Hamdan
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa 16100, Kelantan, Malaysia.
| | - Siew Shean Choong
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa 16100, Kelantan, Malaysia.
| | - Weng Kin Wong
- School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia.
| | - Alexandru Chivu
- UCL Centre for Nanotechnology and Regenerative Medicine, Division of Surgery & Interventional Science, University College London, London NW3 2PF, UK.
| | - Amanda Jane Gibson
- Royal Veterinary College, Pathobiology and Population Sciences, Hawkshead Lane, North Mymms, Hatfield AL9 7TA, UK.
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Chevalier S, Bouffartigues E, Bazire A, Tahrioui A, Duchesne R, Tortuel D, Maillot O, Clamens T, Orange N, Feuilloley MGJ, Lesouhaitier O, Dufour A, Cornelis P. Extracytoplasmic function sigma factors in Pseudomonas aeruginosa. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:706-721. [PMID: 29729420 DOI: 10.1016/j.bbagrm.2018.04.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/06/2018] [Accepted: 04/30/2018] [Indexed: 01/26/2023]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa, like all members of the genus Pseudomonas, has the capacity to thrive in very different environments, ranging from water, plant roots, to animals, including humans to whom it can cause severe infections. This remarkable adaptability is reflected in the number of transcriptional regulators, including sigma factors in this bacterium. Among those, the 19 to 21 extracytoplasmic sigma factors (ECFσ) are endowed with different regulons and functions, including the iron starvation σ (PvdS, FpvI, HasI, FecI, FecI2 and others), the cell wall stress ECFσ AlgU, SigX and SbrI, and the unorthodox σVreI involved in the expression of virulence. Recently published data show that these ECFσ have separate regulons although presenting some cross-talk. We will present evidence that these different ECFσ are involved in the expression of different phenotypes, ranging from cell-wall stress response, production of extracellular polysaccharides, formation of biofilms, to iron acquisition.
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Affiliation(s)
- Sylvie Chevalier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France.
| | - Emeline Bouffartigues
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Alexis Bazire
- IUEM, Université de Bretagne-Sud (UBL), Laboratoire de Biotechnologie et Chimie Marines EA 3884, Lorient, France
| | - Ali Tahrioui
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Rachel Duchesne
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Damien Tortuel
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Olivier Maillot
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Thomas Clamens
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Nicole Orange
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Marc G J Feuilloley
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Olivier Lesouhaitier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Alain Dufour
- IUEM, Université de Bretagne-Sud (UBL), Laboratoire de Biotechnologie et Chimie Marines EA 3884, Lorient, France
| | - Pierre Cornelis
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
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