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Hai H, Yang M, Cheng Z, Ma K, Shang F. Potential Role of SdiA in Biofilm Formation and Drug Resistance in Avian Pathogenic Escherichia coli. Animals (Basel) 2024; 14:2199. [PMID: 39123725 PMCID: PMC11311028 DOI: 10.3390/ani14152199] [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: 06/09/2024] [Revised: 07/26/2024] [Accepted: 07/27/2024] [Indexed: 08/12/2024] Open
Abstract
Avian pathogenic Escherichia coli (APEC) constitutes a significant cause of colibacillosis, a localized or systemic inflammatory disorder in avian species, resulting in considerable economic losses within the global poultry industry. SdiA (suppressor of division inhibitor) is a transcription factor recognized as a LuxR homolog in Escherichia coli, regulating various behaviors, including biofilm formation, multidrug resistance, and the secretion of virulence factors. However, the function of SdiA in APEC strains and its correlation with virulence and multidrug resistance remains unknown. This study probed into the function of SdiA by analyzing the effect of sdiA deletion on the transcription profile of an APEC strain. The microarray data revealed that SdiA upregulates 160 genes and downregulates 59 genes, exerting a particularly remarkable influence on the transcription of multiple virulence genes. A series of antibiotic sensitivity tests, biofilm formation assays, motility assays, and transcriptome analyses were performed, while a Normality test and t-test were conducted on the datasets. This research confirmed that SdiA inhibits biofilm formation by 1.9-fold (p-value < 0.01) and motility by 1.5-fold (p-value < 0.01). RT-qPCR revealed that SdiA positively regulates multidrug resistance by upregulating the expression of yafP, cbrA, and eamB. Collectively, the results of this study indicate the role of SdiA in the pathogenesis of APEC by controlling biofilm formation, motility, and multidrug resistance.
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Affiliation(s)
| | | | | | | | - Fei Shang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.H.); (M.Y.); (Z.C.); (K.M.)
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2
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Jandl B, Dighe S, Baumgartner M, Makristathis A, Gasche C, Muttenthaler M. Gastrointestinal Biofilms: Endoscopic Detection, Disease Relevance, and Therapeutic Strategies. Gastroenterology 2024:S0016-5085(24)05054-6. [PMID: 38876174 DOI: 10.1053/j.gastro.2024.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 06/16/2024]
Abstract
Gastrointestinal biofilms are matrix-enclosed, highly heterogenic and spatially organized polymicrobial communities that can cover large areas in the gastrointestinal tract. Gut microbiota dysbiosis, mucus disruption, and epithelial invasion are associated with pathogenic biofilms that have been linked to gastrointestinal disorders such as irritable bowel syndrome, inflammatory bowel diseases, gastric cancer, and colorectal cancer. Intestinal biofilms are highly prevalent in ulcerative colitis and irritable bowel syndrome patients, and most endoscopists will have observed such biofilms during colonoscopy, maybe without appreciating their biological and clinical importance. Gut biofilms have a protective extracellular matrix that renders them challenging to treat, and effective therapies are yet to be developed. This review covers gastrointestinal biofilm formation, growth, appearance and detection, biofilm architecture and signalling, human host defence mechanisms, disease and clinical relevance of biofilms, therapeutic approaches, and future perspectives. Critical knowledge gaps and open research questions regarding the biofilm's exact pathophysiological relevance and key hurdles in translating therapeutic advances into the clinic are discussed. Taken together, this review summarizes the status quo in gut biofilm research and provides perspectives and guidance for future research and therapeutic strategies.
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Affiliation(s)
- Bernhard Jandl
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria; University of Vienna, Vienna Doctoral School in Chemistry, Vienna, Austria; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia; Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Satish Dighe
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Maximillian Baumgartner
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Athanasios Makristathis
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Christoph Gasche
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria; Loha for Life, Center for Gastroenterology and Iron Deficiency, Vienna, Austria
| | - Markus Muttenthaler
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
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3
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Saifi S, Ashraf A, Hasan GM, Shamsi A, Hassan MI. Insights into the preventive actions of natural compounds against Klebsiella pneumoniae infections and drug resistance. Fitoterapia 2024; 173:105811. [PMID: 38168570 DOI: 10.1016/j.fitote.2023.105811] [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: 09/29/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/05/2024]
Abstract
Klebsiella pneumoniae is a type of Gram-negative bacteria that causes a variety of infections, including pneumonia, bloodstream infections, wound infections, and meningitis. The treatment of K. pneumoniae infection depends on the type of infection and the severity of the symptoms. Antibiotics are generally used to treat K. pneumoniae infections. However, some strains of K. pneumoniae have become resistant to antibiotics. This comprehensive review examines the potential of natural compounds as effective strategies against K. pneumonia infections. The alarming rise in antibiotic resistance underscores the urgent need for alternative therapies. This article represents current research on the effects of diverse natural compounds, highlighting their anti-microbial and antibiofilm properties against K. pneumonia. Notably, compounds such as andrographolide, artemisinin, baicalin, berberine, curcumin, epigallocatechin gallate, eugenol, mangiferin, piperine, quercetin, resveratrol, and thymol have been extensively investigated. These compounds exhibit multifaceted mechanisms, including disruption of bacterial biofilms, interference with virulence factors, and augmentation of antibiotic effectiveness. Mechanistic insights into their actions include membrane perturbation, oxidative stress induction, and altered gene expression. While promising, challenges such as limited bioavailability and varied efficacy across bacterial strains are addressed. This review further discusses the potential of natural compounds as better alternatives in combating K. pneumonia infection and emphasizes the need for continued research to harness their full therapeutic potential. As antibiotic resistance persists, these natural compounds offer a promising avenue in the fight against K. pneumonia and other multidrug-resistant pathogens.
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Affiliation(s)
- Sana Saifi
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Anam Ashraf
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia
| | - Anas Shamsi
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, United Arab Emirates
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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4
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Juszczuk-Kubiak E. Molecular Aspects of the Functioning of Pathogenic Bacteria Biofilm Based on Quorum Sensing (QS) Signal-Response System and Innovative Non-Antibiotic Strategies for Their Elimination. Int J Mol Sci 2024; 25:2655. [PMID: 38473900 DOI: 10.3390/ijms25052655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
One of the key mechanisms enabling bacterial cells to create biofilms and regulate crucial life functions in a global and highly synchronized way is a bacterial communication system called quorum sensing (QS). QS is a bacterial cell-to-cell communication process that depends on the bacterial population density and is mediated by small signalling molecules called autoinducers (AIs). In bacteria, QS controls the biofilm formation through the global regulation of gene expression involved in the extracellular polymeric matrix (EPS) synthesis, virulence factor production, stress tolerance and metabolic adaptation. Forming biofilm is one of the crucial mechanisms of bacterial antimicrobial resistance (AMR). A common feature of human pathogens is the ability to form biofilm, which poses a serious medical issue due to their high susceptibility to traditional antibiotics. Because QS is associated with virulence and biofilm formation, there is a belief that inhibition of QS activity called quorum quenching (QQ) may provide alternative therapeutic methods for treating microbial infections. This review summarises recent progress in biofilm research, focusing on the mechanisms by which biofilms, especially those formed by pathogenic bacteria, become resistant to antibiotic treatment. Subsequently, a potential alternative approach to QS inhibition highlighting innovative non-antibiotic strategies to control AMR and biofilm formation of pathogenic bacteria has been discussed.
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Affiliation(s)
- Edyta Juszczuk-Kubiak
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology-State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
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Yuasa HJ. Unusual Evolution of Cephalopod Tryptophan Indole-Lyases. J Mol Evol 2023; 91:912-921. [PMID: 38007709 DOI: 10.1007/s00239-023-10144-x] [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: 07/17/2023] [Accepted: 11/07/2023] [Indexed: 11/28/2023]
Abstract
Tryptophan indole-lyase (TIL), a pyridoxal-5-phosphate-dependent enzyme, catalyzes the hydrolysis of L-tryptophan (L-Trp) to indole and ammonium pyruvate. TIL is widely distributed among bacteria and bacterial TILs consist of a D2-symmetric homotetramer. On the other hand, TIL genes are also present in several metazoans. Cephalopods have two TILs, TILα and TILβ, which are believed to be derived from a gene duplication that occurred before octopus and squid diverged. However, both TILα and TILβ individually contain disruptive amino acid substitutions for TIL activity, and neither was active when expressed alone. When TILα and TILβ were coexpressed, however, they formed a heterotetramer that exhibited low TIL activity. The loss of TIL activity of the heterotetramer following site-directed mutagenesis strongly suggests that the active heterotetramer contains the TILα/TILβ heterodimer. Metazoan TILs generally have lower kcat values for L-Trp than those of bacterial TILs, but such low TIL activity may be rather suitable for metazoan physiology, where L-Trp is in high demand. Therefore, reduced activity may have been a less likely target for purifying selection in the evolution of cephalopod TILs. Meanwhile, the unusual evolution of cephalopod TILs may indicate the difficulty of post-gene duplication evolution of enzymes with catalytic sites contributed by multiple subunits, such as TIL.
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Affiliation(s)
- Hajime Julie Yuasa
- Laboratory of Biochemistry, Department of Chemistry and Biotechnology, Faculty of Science and Technology, National University Corporation Kochi University, Kochi, 780-8520, Japan.
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Dupont CA, Bourigault Y, Osmond T, Nier M, Barbey C, Latour X, Konto-Ghiorghi Y, Verdon J, Merieau A. Pseudomonas fluorescens MFE01 uses 1-undecene as aerial communication molecule. Front Microbiol 2023; 14:1264801. [PMID: 37908545 PMCID: PMC10614000 DOI: 10.3389/fmicb.2023.1264801] [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: 07/21/2023] [Accepted: 09/27/2023] [Indexed: 11/02/2023] Open
Abstract
Bacterial communication is a fundamental process used to synchronize gene expression and collective behavior among the bacterial population. The most studied bacterial communication system is quorum sensing, a cell density system, in which the concentration of inductors increases to a threshold level allowing detection by specific receptors. As a result, bacteria can change their behavior in a coordinated way. While in Pseudomonas quorum sensing based on the synthesis of N-acyl homoserine lactone molecules is well studied, volatile organic compounds, although considered to be communication signals in the rhizosphere, are understudied. The Pseudomonas fluorescens MFE01 strain has a very active type six secretion system that can kill some competitive bacteria. Furthermore, MFE01 emits numerous volatile organic compounds, including 1-undecene, which contributes to the aerial inhibition of Legionella pneumophila growth. Finally, MFE01 appears to be deprived of N-acyl homoserine lactone synthase. The main objective of this study was to explore the role of 1-undecene in the communication of MFE01. We constructed a mutant affected in undA gene encoding the enzyme responsible for 1-undecene synthesis to provide further insight into the role of 1-undecene in MFE01. First, we studied the impacts of this mutation both on volatile organic compounds emission, using headspace solid-phase microextraction combined with gas chromatography-mass spectrometry and on L. pneumophila long-range inhibition. Then, we analyzed influence of 1-undecene on MFE01 coordinated phenotypes, including type six secretion system activity and biofilm formation. Next, to test the ability of MFE01 to synthesize N-acyl homoserine lactones in our conditions, we investigated in silico the presence of corresponding genes across the MFE01 genome and we exposed its biofilms to an N-acyl homoserine lactone-degrading enzyme. Finally, we examined the effects of 1-undecene emission on MFE01 biofilm maturation and aerial communication using an original experimental set-up. This study demonstrated that the ΔundA mutant is impaired in biofilm maturation. An exposure of the ΔundA mutant to the volatile compounds emitted by MFE01 during the biofilm development restored the biofilm maturation process. These findings indicate that P. fluorescens MFE01 uses 1-undecene emission for aerial communication, reporting for the first time this volatile organic compound as bacterial intraspecific communication signal.
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Affiliation(s)
- Charly A. Dupont
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Yvann Bourigault
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Théo Osmond
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Maëva Nier
- Laboratoire Ecologie and Biologie des Interactions, Université de Poitiers, Poitiers, France
| | - Corinne Barbey
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Xavier Latour
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Yoan Konto-Ghiorghi
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Julien Verdon
- Laboratoire Ecologie and Biologie des Interactions, Université de Poitiers, Poitiers, France
| | - Annabelle Merieau
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
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Cui B, Guo Q, Li X, Song S, Wang M, Wang G, Yan A, Zhou J, Deng Y. A response regulator controls Acinetobacter baumannii virulence by acting as an indole receptor. PNAS NEXUS 2023; 2:pgad274. [PMID: 37649583 PMCID: PMC10465187 DOI: 10.1093/pnasnexus/pgad274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 08/18/2023] [Indexed: 09/01/2023]
Abstract
Indole is an important signal employed by many bacteria to modulate intraspecies signaling and interspecies or interkingdom communication. Our recent study revealed that indole plays a key role in regulating the physiology and virulence of Acinetobacter baumannii. However, it is not clear how A. baumannii perceives and responds to the indole signal in modulating biological functions. Here, we report that indole controls the physiology and virulence of A. baumannii through a previously uncharacterized response regulator designated as AbiR (A1S_1394), which contains a cheY-homologous receiver (REC) domain and a helix-turn-helix (HTH) DNA-binding domain. AbiR controls the same biological functions as the indole signal, and indole-deficient mutant phenotypes were rescued by in trans expression of AbiR. Intriguingly, unlike other response regulators that commonly interact with signal ligands through the REC domain, AbiR binds to indole with a high affinity via an unusual binding region, which is located between its REC and HTH domains. This interaction substantially enhances the activity of AbiR in promoter binding and in modulation of target gene expression. Taken together, our results present a widely conserved regulator that controls bacterial physiology and virulence by sensing the indole signal in a unique mechanism.
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Affiliation(s)
- Binbin Cui
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Quan Guo
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Xia Li
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Shihao Song
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Gongchang Road, Guangming District, Shenzhen 518107, China
- School of Pharmaceutical Sciences, Hainan University, Renmin Avenue, Meilan District, Haikou 570228, China
| | - Mingfang Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Gerun Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, University Road, Pok Fu Lam Estate, Central and Western District, Hong Kong 999077, China
| | - Jianuan Zhou
- Integrative Microbiology Research Center, South China Agricultural University, Wushan Road, Wushan Street, Tianhe District Guangzhou 510642, China
| | - Yinyue Deng
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Gongchang Road, Guangming District, Shenzhen 518107, China
- School of Pharmaceutical Sciences, Hainan University, Renmin Avenue, Meilan District, Haikou 570228, China
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Martínez A, Stashenko EE, Sáez RT, Zafra G, Ortiz C. Effect of Essential Oil from Lippia origanoides on the Transcriptional Expression of Genes Related to Quorum Sensing, Biofilm Formation, and Virulence of Escherichia coli and Staphylococcus aureus. Antibiotics (Basel) 2023; 12:antibiotics12050845. [PMID: 37237748 DOI: 10.3390/antibiotics12050845] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Microbial infections resistant to conventional antibiotics constitute one of the most important causes of mortality in the world. In some bacterial species, such as Escherichia coli and Staphylococcus aureus pathogens, biofilm formation can favor their antimicrobial resistance. These biofilm-forming bacteria produce a compact and protective matrix, allowing their adherence and colonization to different surfaces, and contributing to resistance, recurrence, and chronicity of the infections. Therefore, different therapeutic alternatives have been investigated to interrupt both cellular communication routes and biofilm formation. Among these, essential oils (EO) from Lippia origanoides thymol-carvacrol II chemotype (LOTC II) plants have demonstrated biological activity against different biofilm-forming pathogenic bacteria. In this work, we determined the effect of LOTC II EO on the expression of genes associated with quorum sensing (QS) communication, biofilm formation, and virulence of E. coli ATCC 25922 and S. aureus ATCC 29213. This EO was found to have high efficacy against biofilm formation, decreasing-by negative regulation-the expression of genes involved in motility (fimH), adherence and cellular aggregation (csgD), and exopolysaccharide production (pgaC) in E. coli. In addition, this effect was also determined in S. aureus where the L. origanoides EO diminished the expression of genes involved in QS communication (agrA), production of exopolysaccharides by PIA/PNG (icaA), synthesis of alpha hemolysin (hla), transcriptional regulators of the production of extracellular toxins (RNA III), QS and biofilm formation transcriptional regulators (sarA) and global regulators of biofilm formation (rbf and aur). Positive regulation was observed on the expression of genes encoding inhibitors of biofilm formation (e.g., sdiA and ariR). These findings suggest that LOTCII EO can affect biological pathways associated with QS communication, biofilm formation, and virulence of E. coli and S. aureus at subinhibitory concentrations and could be a promising candidate as a natural antibacterial alternative to conventional antibiotics.
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Affiliation(s)
- Andrés Martínez
- Grupo de Investigación en Bioquímica y Microbiología (GIBIM), Escuela de Microbiología, Facultad de Salud, Universidad Industrial de Santander, Bucaramanga 680002, Colombia
| | - Elena E Stashenko
- Escuela de Química, Centro de Cromatografía y Espectrometría de Masas (CROM-MASS), Universidad Industrial de Santander, Bucaramanga 680002, Colombia
| | - Rodrigo Torres Sáez
- Grupo de Investigación en Bioquímica y Microbiología (GIBIM), Escuela de Microbiología, Facultad de Salud, Universidad Industrial de Santander, Bucaramanga 680002, Colombia
| | - German Zafra
- Grupo de Investigación en Bioquímica y Microbiología (GIBIM), Escuela de Microbiología, Facultad de Salud, Universidad Industrial de Santander, Bucaramanga 680002, Colombia
| | - Claudia Ortiz
- Grupo de Investigación en Bioquímica y Microbiología (GIBIM), Escuela de Microbiología, Facultad de Salud, Universidad Industrial de Santander, Bucaramanga 680002, Colombia
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9
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Dominelli N, Regaiolo A, Willy L, Heermann R. Interkingdom Signaling of the Insect Pathogen Photorhabdus luminescens with Plants Via the LuxR solo SdiA. Microorganisms 2023; 11:microorganisms11040890. [PMID: 37110313 PMCID: PMC10143992 DOI: 10.3390/microorganisms11040890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
In bacteria, group-coordinated behavior such as biofilm formation or virulence are often mediated via cell–cell communication, a process referred to as quorum sensing (QS). The canonical QS system of Gram-negative bacteria uses N-acyl homoserine lactones (AHLs) as communication molecules, which are produced by LuxI-type synthases and sensed by cognate LuxR-type receptors. These receptors act as transcriptional regulators controlling the expression of specific genes. Some bacteria harbor LuxR-type receptors lacking a cognate LuxI-type synthases, designated as LuxR solos. Among many other LuxR solos, the entomopathogenic enteric bacterium Photorhabdus luminescens harbors a SdiA-like LuxR solo containing an AHL signal-binding domain, for which a respective signal molecule and target genes have not been identified yet. Here we performed SPR analysis to demonstrate that SdiA acts as a bidirectional regulator of transcription, tightly controlling its own expression and the adjacent PluDJC_01670 (aidA) gene in P. luminescens, a gene supposed to be involved in the colonization of eukaryotes. Via qPCR we could further determine that in sdiA deletion mutant strains, aidA is upregulated, indicating that SdiA negatively affects expression of aidA. Furthermore, the ΔsdiA deletion mutant exhibited differences in biofilm formation and motility compared with the wild-type. Finally, using nanoDSF analysis we could identify putative binding ability of SdiA towards diverse AHLs, but also to plant-derived signals, modulating the DNA-binding capacity of SdiA, suggesting that this LuxR solo acts as an important player in interkingdom signaling between P. luminescens and plants.
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10
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Yuasa HJ. Metazoan tryptophan indole-lyase: Are they still active? Comp Biochem Physiol B Biochem Mol Biol 2023; 263:110801. [PMID: 36228898 DOI: 10.1016/j.cbpb.2022.110801] [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: 09/05/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
Tryptophan indole-lyase (TIL), also known as tryptophanase, is a pyridoxal-5'-phosphate dependent bacterial enzyme that catalyzes the reversible hydrolytic cleavage of l-tryptophan (l-Trp) to indole and ammonium pyruvate. TIL is also found in some metazoans, and they may have been acquired by horizontal gene transfer. In this study, two metazoans, Nematostella vectensis (starlet sea anemone) and Bradysia coprophila (fungus gnat) TILs were bacterially expressed and characterized. The kcat values of metazoan TILs were low, < 1/200 of the kcat of Escherichia coli TIL. By contrast, metazoan TILs showed lower Km values than the TILs of common bacteria, indicating that their affinity for l-Trp is higher than that of bacterial TILs. Analysis of a series of chimeric enzymes based on B. coprophila and bacterial TILs revealed that the low Km value of B. coprophila TIL is not accidental due to the substitution of a single residue, but is due to the cooperative effect of multiple residues. This suggests that high affinity for l-Trp was positively selected during the molecular evolution of metazoan TIL. This is the first report that metazoan TILs have low but obvious activity.
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Affiliation(s)
- Hajime Julie Yuasa
- Laboratory of Biochemistry, Department of Chemistry and Biotechnology, Faculty of Science and Technology, National University Corporation Kochi University, Kochi 780-8520, Japan.
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11
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Sun R, Yu P, Zuo P, Villagrán D, Mathieu J, Alvarez PJJ. Biofilm Control in Flow-Through Systems Using Polyvalent Phages Delivered by Peptide-Modified M13 Coliphages with Enhanced Polysaccharide Affinity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:17177-17187. [PMID: 36413403 DOI: 10.1021/acs.est.2c06561] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Eradication of biofilms that may harbor pathogens in water distribution systems is an elusive goal due to limited penetration of residual disinfectants. Here, we explore the use of engineered filamentous coliphage M13 for enhanced biofilm affinity and precise delivery of lytic polyvalent phages (i.e., broad-host-range phages lysing multiple host strains after infection). To promote biofilm attachment, we modified the M13 major coat protein (pVIII) by inserting a peptide sequence with high affinity for Pseudomonas aeruginosa (P. aeruginosa) extracellular polysaccharides (commonly present on the surface of biofilms in natural and engineered systems). Additionally, we engineered the M13 tail fiber protein (pIII) to contain a peptide sequence capable of binding a specific polyvalent lytic phage. The modified M13 had 102- and 5-fold higher affinity for P. aeruginosa-dominated mixed-species biofilms than wildtype M13 and unconjugated polyvalent phage, respectively. When applied to a simulated water distribution system, the resulting phage conjugates achieved targeted phage delivery to the biofilm and were more effective than polyvalent phages alone in reducing live bacterial biomass (84 vs 34%) and biofilm surface coverage (81 vs 22%). Biofilm regrowth was also mitigated as high phage concentrations induced residual bacteria to downregulate genes associated with quorum sensing and extracellular polymeric substance secretion. Overall, we demonstrate that engineered M13 can enable more accurate delivery of polyvalent phages to biofilms in flow-through systems for enhanced biofilm control.
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Affiliation(s)
- Ruonan Sun
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Pengxiao Zuo
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Dino Villagrán
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
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12
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Shi X, Zarkan A. Bacterial survivors: evaluating the mechanisms of antibiotic persistence. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748698 DOI: 10.1099/mic.0.001266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacteria withstand antibiotic onslaughts by employing a variety of strategies, one of which is persistence. Persistence occurs in a bacterial population where a subpopulation of cells (persisters) survives antibiotic treatment and can regrow in a drug-free environment. Persisters may cause the recalcitrance of infectious diseases and can be a stepping stone to antibiotic resistance, so understanding persistence mechanisms is critical for therapeutic applications. However, current understanding of persistence is pervaded by paradoxes that stymie research progress, and many aspects of this cellular state remain elusive. In this review, we summarize the putative persister mechanisms, including toxin-antitoxin modules, quorum sensing, indole signalling and epigenetics, as well as the reasons behind the inconsistent body of evidence. We highlight present limitations in the field and underscore a clinical context that is frequently neglected, in the hope of supporting future researchers in examining clinically important persister mechanisms.
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Affiliation(s)
- Xiaoyi Shi
- Cambridge Centre for International Research, Cambridge CB4 0PZ, UK
| | - Ashraf Zarkan
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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13
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Song S, Wood TK. Manipulating indole symbiont signalling. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:691-696. [PMID: 35667868 DOI: 10.1111/1758-2229.13100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Sooyeon Song
- Department of Animal Science, Jeonbuk National University, Jeonju-si, Jeollabuk-do, Republic of Korea
- Agricultural Convergence Technology, Jeonbuk National University, Jeonju-si, Jeollabuk-do, Republic of Korea
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
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14
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Quorum Sensing Orchestrates Antibiotic Drug Resistance, Biofilm Formation, and Motility in Escherichia coli and Quorum Quenching Activities of Plant-derived Natural Products: A Review. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.3.52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Quorum sensing (QS) is a type of cell-to-cell communication that is influenced by an increase in signaling molecules known as autoinducers, which is correlated to the increase in the density of microbial communities. In this review, we aim to discuss and provide updates on the different signaling molecules used by Escherichia coli, such as acyl-homoserine lactone (AHL), autoinducer-2 (AI-2), and indole to influence key phenotypes such as antibiotic drug resistance, biofilm formation, and motility during quorum sensing. Based on the literature, E. coli signaling molecules have different functions during cell-to-cell communication such that the increase in AHL and indole was found to cause the modulation of antibiotic resistance and inhibition of biofilm formation and motility. Meanwhile, AI-2 is known to modulate biofilm formation, antibiotic resistance, and motility. On the other hand, in the existing literature, we found that various plants possess phytochemicals that can be used to alter QS and its downstream key phenotypes such as biofilm formation, swimming and swarming motility, and genes related to motility, curli and AI-2 production. However, the exact physiological and molecular mechanisms of these natural compounds are still understudied. Understanding the mechanisms of those phytochemicals during QS are therefore highly recommended to conduct as a necessary step for future scholars to develop drugs that target the actions of QS-signaling molecules and receptors linked to antibiotic resistance, biofilm formation, and motility without putting bacteria under stress, thereby preventing the development of drug resistance.
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15
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Xiao Y, Zou H, Li J, Song T, Lv W, Wang W, Wang Z, Tao S. Impact of quorum sensing signaling molecules in gram-negative bacteria on host cells: current understanding and future perspectives. Gut Microbes 2022; 14:2039048. [PMID: 35188058 PMCID: PMC8865250 DOI: 10.1080/19490976.2022.2039048] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Quorum sensing is a molecular signaling-based communication mechanism in prokaryotes. In the basic mode, signaling molecules released by certain bacteria are sensed by intracellular receptors or membrane-bound receptors of other members in the community, leading to the collective isogenic signaling molecule synthesis and synchronized activities. This regulation is important for the symbiosis of the bacterium with the host, as well as virulence and biofilm formation. Notably, quorum sensing signaling molecules are not only able to control microbial community behavior but can likewise regulate the physiological status of host cells. Here, we provide a comprehensive review of the importance of quorum sensing signaling molecules in gram-negative bacteria in regulating host cell function and gut health, and suggest possible opportunities for application in combating human and animal diseases by blocking the pathways through which quorum sensing signaling molecules exert their functions.
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Affiliation(s)
- Yingping Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Huicong Zou
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jingjing Li
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tongxing Song
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wentao Lv
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wen Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhenyu Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shiyu Tao
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China,CONTACT Shiyu TaoCollege of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070China
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16
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Veetilvalappil VV, Manuel A, Aranjani JM, Tawale R, Koteshwara A. Pathogenic arsenal of Pseudomonas aeruginosa: an update on virulence factors. Future Microbiol 2022; 17:465-481. [PMID: 35289684 DOI: 10.2217/fmb-2021-0158] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The emergence of Pseudomonas aeruginosa as a potential threat in persistent infections can be attributed to the plethora of virulence factors expressed by it. This review discusses the various virulence factors that help this pathogen to establish an infection and regulatory systems controlling these virulence factors. Cell-associated virulence factors such as flagella, type IV pili and non-pilus adhesins have been reviewed. Extracellular virulence factors have also been explained. Quorum-sensing systems present in P. aeruginosa play a cardinal role in regulating the expression of virulence factors. The identification of novel virulence factors in hypervirulent strains indicate that the expression of virulence is dynamic and constantly evolving. An understanding of this is critical for the better clinical management of infections.
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Affiliation(s)
- Vimal V Veetilvalappil
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Atulya Manuel
- Central Frozen Semen Production and Training Institute, Bengaluru, Karnataka, 560088, India
| | - Jesil M Aranjani
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Roshan Tawale
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Ananthamurthy Koteshwara
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
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17
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Li H, Xie R, Xu X, Liao X, Guo J, Fang Y, Fang Z, Huang J. Static Magnetic Field Inhibits Growth of Escherichia coli Colonies via Restriction of Carbon Source Utilization. Cells 2022; 11:cells11050827. [PMID: 35269449 PMCID: PMC8909705 DOI: 10.3390/cells11050827] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
Magnetobiological effects on growth and virulence have been widely reported in Escherichia coli (E. coli). However, published results are quite varied and sometimes conflicting because the underlying mechanism remains unknown. Here, we reported that the application of 250 mT static magnetic field (SMF) significantly reduces the diameter of E. coli colony-forming units (CFUs) but has no impact on the number of CFUs. Transcriptomic analysis revealed that the inhibitory effect of SMF is attributed to differentially expressed genes (DEGs) primarily involved in carbon source utilization. Consistently, the addition of glycolate or glyoxylate to the culture media successfully restores the bacterial phenotype in SMF, and knockout mutants lacking glycolate oxidase are no longer sensitive to SMF. These results suggest that SMF treatment results in a decrease in glycolate oxidase activity. In addition, metabolomic assay showed that long-chain fatty acids (LCFA) accumulate while phosphatidylglycerol and middle-chain fatty acids decrease in the SMF-treated bacteria, suggesting that SMF inhibits LCFA degradation. Based on the published evidence together with ours derived from this study, we propose a model showing that free radicals generated by LCFA degradation are the primary target of SMF action, which triggers the bacterial oxidative stress response and ultimately leads to growth inhibition.
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Affiliation(s)
- Haodong Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Runnan Xie
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Xiang Xu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Xingru Liao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Jiaxin Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Yanwen Fang
- Heye Health Industrial Research Institute, Zhejiang Heye Health Technology, Anji, Huzhou 313300, China; (Y.F.); (Z.F.)
| | - Zhicai Fang
- Heye Health Industrial Research Institute, Zhejiang Heye Health Technology, Anji, Huzhou 313300, China; (Y.F.); (Z.F.)
| | - Jirong Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
- Correspondence:
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18
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Bhowmik P, Rajagopal S, Hmar RV, Singh P, Saxena P, Amar P, Thomas T, Ravishankar R, Nagaraj S, Katagihallimath N, Sarangapani RK, Ramachandran V, Datta S. Validated In Silico Model for Biofilm Formation in Escherichia coli. ACS Synth Biol 2022; 11:713-731. [PMID: 35025506 DOI: 10.1021/acssynbio.1c00445] [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] [Indexed: 11/29/2022]
Abstract
Using Escherichia coli as the representative biofilm former, we report here the development of an in silico model built by simulating events that transform a free-living bacterial entity into self-encased multicellular biofilms. Published literature on ∼300 genes associated with pathways involved in biofilm formation was curated, static maps were created, and suitably interconnected with their respective metabolites using ordinary differential equations. Precise interplay of genetic networks that regulate the transitory switching of bacterial growth pattern in response to environmental changes and the resultant multicomponent synthesis of the extracellular matrix were appropriately represented. Subsequently, the in silico model was analyzed by simulating time-dependent changes in the concentration of components by using the R and python environment. The model was validated by simulating and verifying the impact of key gene knockouts (KOs) and systematic knockdowns on biofilm formation, thus ensuring the outcomes were comparable with the reported literature. Similarly, specific gene KOs in laboratory and pathogenic E. coli were constructed and assessed. MiaA, YdeO, and YgiV were found to be crucial in biofilm development. Furthermore, qRT-PCR confirmed the elevation of expression in biofilm-forming clinical isolates. Findings reported in this study offer opportunities for identifying biofilm inhibitors with applications in multiple industries. The application of this model can be extended to the health care sector specifically to develop novel adjunct therapies that prevent biofilms in medical implants and reduce emergence of biofilm-associated resistant polymicrobial-chronic infections. The in silico framework reported here is open source and accessible for further enhancements.
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Affiliation(s)
- Purnendu Bhowmik
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka 560064, India
| | - Sreenath Rajagopal
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Rothangamawi Victoria Hmar
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Purnima Singh
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Pragya Saxena
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Prakruthi Amar
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Teby Thomas
- St. John’s Research Institute, Bengaluru, Karnataka 560034, India
| | - Rajani Ravishankar
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Savitha Nagaraj
- St. John’s Medical College, Bengaluru, Karnataka 560034, India
| | - Nainesh Katagihallimath
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka 560064, India
| | - Ramanujan Kadambi Sarangapani
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Vasanthi Ramachandran
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka 560064, India
| | - Santanu Datta
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
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Beneficial biofilms: A mini-review of strategies to enhance biofilm formation for biotechnological applications. Appl Environ Microbiol 2021; 88:e0199421. [PMID: 34851721 DOI: 10.1128/aem.01994-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The capacity of bacteria to form biofilms is an important trait for their survival and persistence. Biofilms occur naturally in soil and aquatic environments, are associated with animals ranging from insects to humans and are also found in built environments. They are typically encountered as a challenge in healthcare, food industry, and water supply ecosystems. In contrast, they are known to play a key role in the industrial production of commercially valuable products, environmental remediation processes, and in microbe-catalysed electrochemical systems for energy and resource recovery from wastewater. While there are many recent articles on biofilm control and removal, review articles on promoting biofilm growth for biotechnological applications are unavailable. Biofilm formation is a tightly regulated response to perturbations in the external environment. The multi-stage process, mediated by an assortment of proteins and signaling systems, involves the attachment of bacterial cells to a surface followed by their aggregation in a matrix of extracellular polymeric substances. Biofilms can be promoted by altering the external environment in a controlled manner, supplying molecules that trigger the aggregation of cells and engineering genes associated with biofilm development. This mini-review synthesizes findings from studies that have described such strategies and highlights areas needing research attention.
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20
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Escherichia coli small molecule metabolism at the host-microorganism interface. Nat Chem Biol 2021; 17:1016-1026. [PMID: 34552219 DOI: 10.1038/s41589-021-00807-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022]
Abstract
Escherichia coli are a common component of the human microbiota, and isolates exhibit probiotic, commensal and pathogenic roles in the host. E. coli members often use diverse small molecule chemistry to regulate intrabacterial, intermicrobial and host-bacterial interactions. While E. coli are considered to be a well-studied model organism in biology, much of their chemical arsenal has only more recently been defined, and much remains to be explored. Here we describe chemical signaling systems in E. coli in the context of the broader field of metabolism at the host-bacteria interface and the role of this signaling in disease modulation.
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21
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Sathiyamoorthi E, Faleye OS, Lee JH, Raj V, Lee J. Antibacterial and Antibiofilm Activities of Chloroindoles Against Vibrio parahaemolyticus. Front Microbiol 2021; 12:714371. [PMID: 34408739 PMCID: PMC8365150 DOI: 10.3389/fmicb.2021.714371] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/13/2021] [Indexed: 01/05/2023] Open
Abstract
Vibrio parahaemolyticus is a food-borne pathogen recognized as the prominent cause of seafood-borne gastroenteritis globally, necessitating novel therapeutic strategies. This study examined the antimicrobial and antivirulence properties of indole and 16 halogenated indoles on V. parahaemolyticus. Among them, 4-chloroindole, 7-chloroindole, 4-iodoindole, and 7-iodoindole effectively inhibited planktonic cell growth, biofilm formation, bacterial motility, fimbrial activity, hydrophobicity, protease activity, and indole production. Specifically, 4-chloroindole at 20 μg/mL inhibited more than 80% of biofilm formation with a minimum inhibitory concentration (MIC) of 50 μg/mL against V. parahaemolyticus and Vibrio harveyi. In contrast, 7-chloroindole inhibited biofilm formation without affecting planktonic cell growth with a MIC of 200 μg/mL. Both chlorinated indoles caused visible damage to the cell membrane, and 4-chloroindole at 100 μg/mL had a bactericidal effect on V. parahaemolyticus within 30 min treatment, which is superior to the effect of tetracycline at the same dose. The quantitative structure-activity relationship (QSAR) analyses revealed that chloro and bromo at positions 4 or 5 of the indole are essential for eradicating the growth of V. parahaemolyticus. These results suggest that halogenated indoles have potential use in antimicrobial and antivirulence strategies against Vibrio species.
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Affiliation(s)
| | | | | | | | - Jintae Lee
- School of Chemical Engineering, Yeungnam University, Gyeongsan, South Korea
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22
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Functionalized Chitosan Nanomaterials: A Jammer for Quorum Sensing. Polymers (Basel) 2021; 13:polym13152533. [PMID: 34372136 PMCID: PMC8348235 DOI: 10.3390/polym13152533] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 12/02/2022] Open
Abstract
The biggest challenge in the present-day healthcare scenario is the rapid emergence and spread of antimicrobial resistance due to the rampant use of antibiotics in daily therapeutics. Such drug resistance is associated with the enhancement of microbial virulence and the acquisition of the ability to evade the host’s immune response under the shelter of a biofilm. Quorum sensing (QS) is the mechanism by which the microbial colonies in a biofilm modulate and intercept communication without direct interaction. Hence, the eradication of biofilms through hindering this communication will lead to the successful management of drug resistance and may be a novel target for antimicrobial chemotherapy. Chitosan shows microbicidal activities by acting electrostatically with its positively charged amino groups, which interact with anionic moieties on microbial species, causing enhanced membrane permeability and eventual cell death. Therefore, nanoparticles (NPs) prepared with chitosan possess a positive surface charge and mucoadhesive properties that can adhere to microbial mucus membranes and release their drug load in a constant release manner. As the success in therapeutics depends on the targeted delivery of drugs, chitosan nanomaterial, which displays low toxicity, can be safely used for eradicating a biofilm through attenuating the quorum sensing (QS). Since the anti-biofilm potential of chitosan and its nano-derivatives are reported for various microorganisms, these can be used as attractive tools for combating chronic infections and for the preparation of functionalized nanomaterials for different medical devices, such as orthodontic appliances. This mini-review focuses on the mechanism of the downregulation of quorum sensing using functionalized chitosan nanomaterials and the future prospects of its applications.
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Pacheco T, Gomes AÉI, Siqueira NMG, Assoni L, Darrieux M, Venter H, Ferraz LFC. SdiA, a Quorum-Sensing Regulator, Suppresses Fimbriae Expression, Biofilm Formation, and Quorum-Sensing Signaling Molecules Production in Klebsiella pneumoniae. Front Microbiol 2021; 12:597735. [PMID: 34234747 PMCID: PMC8255378 DOI: 10.3389/fmicb.2021.597735] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 04/26/2021] [Indexed: 12/24/2022] Open
Abstract
Klebsiella pneumoniae is a Gram-negative pathogen that has become a worldwide concern due to the emergence of multidrug-resistant isolates responsible for various invasive infectious diseases. Biofilm formation constitutes a major virulence factor for K. pneumoniae and relies on the expression of fimbrial adhesins and aggregation of bacterial cells on biotic or abiotic surfaces in a coordinated manner. During biofilm aggregation, bacterial cells communicate with each other through inter- or intra-species interactions mediated by signallng molecules, called autoinducers, in a mechanism known as quorum sensing (QS). In most Gram-negative bacteria, intra-species communication typically involves the LuxI/LuxR system: LuxI synthase produces N-acyl homoserine lactones (AHLs) as autoinducers and the LuxR transcription factor is their cognate receptor. However, K. pneumoniae does not produce AHL but encodes SdiA, an orphan LuxR-type receptor that responds to exogenous AHL molecules produced by other bacterial species. While SdiA regulates several cellular processes and the expression of virulence factors in many pathogens, the role of this regulator in K. pneumoniae remains unknown. In this study, we describe the characterization of sdiA mutant strain of K. pneumoniae. The sdiA mutant strain has increased biofilm formation, which correlates with the increased expression of type 1 fimbriae, thus revealing a repressive role of SdiA in fimbriae expression and bacterial cell adherence and aggregation. On the other hand, SdiA acts as a transcriptional activator of cell division machinery assembly in the septum, since cells lacking SdiA regulator exhibited a filamentary shape rather than the typical rod shape. We also show that K. pneumoniae cells lacking SdiA regulator present constant production of QS autoinducers at maximum levels, suggesting a putative role for SdiA in the regulation of AI-2 production. Taken together, our results demonstrate that SdiA regulates cell division and the expression of virulence factors such as fimbriae expression, biofilm formation, and production of QS autoinducers in K. pneumoniae.
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Affiliation(s)
- Thaisy Pacheco
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Ana Érika Inácio Gomes
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | | | - Lucas Assoni
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Michelle Darrieux
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Henrietta Venter
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Lúcio Fábio Caldas Ferraz
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
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Yu J, Jia M, Feng Y. The cytidine repressor regulates the survival of Pantoea agglomerans YS19 under oxidative stress and sulfur starvation conditions. J GEN APPL MICROBIOL 2021; 67:59-66. [PMID: 33518552 DOI: 10.2323/jgam.2020.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Pantoea agglomerans YS19 is a dominant endophytic bacterium isolated from rice, which is capable of promoting host plant growth by nitrogen-fixing and phytohormone secreting. We previously found that the cytidine repressor (CytR) protein conducts the regulation of indole signal in YS19. Here, we compared the whole-cell protein of the wild type YS19 and the ΔcytR mutant and subsequently identified one differential protein as alkyl hydroperoxide reductase subunit C related to oxidative stress and sulfur starvation tolerance. It was tested that cytR had a positive effect on the survival of YS19 under the oxidative stress and sulfur starvation conditions and this effect was inhibited by indole. To further understand the functional mode of indole in this regulation, we cloned the cytR promoter region (PcytR) of YS19 and tested the effect of indole on PcytR using gfp as a reporter gene. It was found that PcytR can sense indole and significantly inhibit the expression of the downstream gene. This study provided a deeper understanding of the multiple function of cytR and expanded a new research direction of how indole participates in gene regulation.
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Affiliation(s)
- Jiajia Yu
- School of Life Science, Beijing Institute of Technology
| | - Mengqi Jia
- School of Life Science, Beijing Institute of Technology
| | - Yongjun Feng
- School of Life Science, Beijing Institute of Technology
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Cao Y, Li L, Zhang Y, Liu F, Xiao X, Li X, Yu Y. SdiA plays a crucial role in stress tolerance of C. sakazakii CICC 21544. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111189] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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26
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Wood TK. Concerns with computational protein engineering programmes IPRO and OptMAVEn and metabolic pathway engineering programme optStoic. Open Biol 2021; 11:200173. [PMID: 33529550 PMCID: PMC8061685 DOI: 10.1098/rsob.200173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It has become customary in engineering to require a modelling component in research endeavours. In addition, as the code for these models becomes more byzantine in complexity, it is difficult for reviewers and readers to discern their value and understand the underlying code. This opinion piece summarizes the negative experience of the author with the IPRO and OptMAVEn computational protein engineering models as well as problems with the optStoic metabolic pathway model. In our hands, these models often fail to predict reliable ways to engineer proteins and metabolic pathways.
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Affiliation(s)
- Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802-4400, USA
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Mukherjee M, Cao B. Engineering controllable biofilms for biotechnological applications. Microb Biotechnol 2021; 14:74-78. [PMID: 33249757 PMCID: PMC7888450 DOI: 10.1111/1751-7915.13715] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 11/30/2022] Open
Affiliation(s)
- Manisha Mukherjee
- Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingapore637551Singapore
- School of Civil and Environmental EngineeringNanyang Technological UniversitySingapore639798Singapore
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingapore637551Singapore
- School of Civil and Environmental EngineeringNanyang Technological UniversitySingapore639798Singapore
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28
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Lau YY, How KY, Yin WF, Chan KG. Functional characterization of quorum sensing LuxR-type transcriptional regulator, EasR in Enterobacter asburiae strain L1. PeerJ 2020; 8:e10068. [PMID: 33150063 PMCID: PMC7585371 DOI: 10.7717/peerj.10068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 09/08/2020] [Indexed: 01/17/2023] Open
Abstract
Over the past decades, Enterobacter spp. have been identified as challenging and important pathogens. The emergence of multidrug-resistant Enterobacteria especially those that produce Klebsiella pneumoniae carbapenemase has been a very worrying health crisis. Although efforts have been made to unravel the complex mechanisms that contribute to the pathogenicity of different Enterobacter spp., there is very little information associated with AHL-type QS mechanism in Enterobacter spp. Signaling via N-acyl homoserine lactone (AHL) is the most common quorum sensing (QS) mechanism utilized by Proteobacteria. A typical AHL-based QS system involves two key players: a luxI gene homolog to synthesize AHLs and a luxR gene homolog, an AHL-dependent transcriptional regulator. These signaling molecules enable inter-species and intra-species interaction in response to external stimuli according to population density. In our recent study, we reported the genome of AHL-producing bacterium, Enterobacter asburiae strain L1. Whole genome sequencing and in silico analysis revealed the presence of a pair of luxI/R genes responsible for AHL-type QS, designated as easI/R, in strain L1. In a QS system, a LuxR transcriptional protein detects and responds to the concentration of a specific AHL controlling gene expression. In E. asburiae strain L1, EasR protein binds to its cognate AHLs, N-butanoyl homoserine lactone (C4-HSL) and N–hexanoyl homoserine lactone (C6-HSL), modulating the expression of targeted genes. In this current work, we have cloned the 693 bp luxR homolog of strain L1 for further characterization. The functionality and specificity of EasR protein in response to different AHL signaling molecules to activate gene transcription were tested and validated with β-galactosidase assays. Higher β-galactosidase activities were detected for cells harboring EasR, indicating EasR is a functional transcriptional regulator. This is the first report documenting the cloning and characterization of transcriptional regulator, luxR homolog of E. asburiae.
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Affiliation(s)
- Yin Yin Lau
- International Genome Centre, Jiangsu University, Zhenjiang, China.,Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Malaysia
| | - Kah Yan How
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Malaysia
| | - Kok-Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang, China.,Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Malaysia
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Role of Toxin-Antitoxin-Regulated Persister Population and Indole in Bacterial Heat Tolerance. Appl Environ Microbiol 2020; 86:AEM.00935-20. [PMID: 32503909 DOI: 10.1128/aem.00935-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/28/2020] [Indexed: 01/30/2023] Open
Abstract
YafQ is an endoribonuclease toxin that degrades target gene transcripts such as that of tnaA, a gene encoding tryptophanase to synthesize indole from tryptophan. DinJ is the cognate antitoxin of YafQ, and the YafQ-DinJ system was reported to regulate persister formation by controlling indole production in Escherichia coli In this study, we investigated the role of YafQ-DinJ, indole production, and persister population in bacterial heat tolerance. yafQ (ΔyafQ), dinJ (ΔdinJ), and tnaA (ΔtnaA) single-gene knockout mutants showed approximately 10-fold higher heat tolerance than wild-type (WT) E. coli BW25113. Persister fractions of all mutants were slightly larger than that of the WT. Interestingly, these persister cells showed an approximately 100-fold higher heat tolerance than normal cells, but there was no difference among the persister cells of all mutants and the WT in terms of heat tolerance. Indole and its derivatives promoted a drastic reduction of bacterial heat tolerance by just 10 min of pretreatment, which is not sufficient to affect persister formation before heat treatment. Surprisingly, indole and its derivatives also reduced the heat tolerance of persister cells. Among the tested derivatives, 5-iodoindole exhibited the strongest effect on both normal and persister cells.IMPORTANCE Our study demonstrated that a small persister population exhibits significantly higher heat tolerance than normal cells and that this small fraction contributes to the heat tolerance of the total bacterial population. This study also demonstrated that indole, known to inhibit persister formation, and its derivatives are very promising candidates to reduce the heat tolerance of not only normal bacterial cells but also persister cells.
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Song S, Wood TK. Combatting Persister Cells With Substituted Indoles. Front Microbiol 2020; 11:1565. [PMID: 32733426 PMCID: PMC7358577 DOI: 10.3389/fmicb.2020.01565] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022] Open
Abstract
Given that a subpopulation of most bacterial cells becomes dormant due to stress, and that the resting cells of pathogens can revive and reconstitute infections, it is imperative to find methods to treat dormant cells to eradicate infections. The dormant bacteria that are not spores or cysts are known as persister cells. Remarkably, in contrast to the original report that incorrectly indicated indole increases persistence, a large number of indole-related compounds have been found in the last few years that kill persister cells. Hence, in this review, along with a summary of recent results related to persister cell formation and resuscitation, we focus on the ability of indole and substituted indoles to combat the persister cells of both pathogens and non-pathogens.
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Affiliation(s)
- Sooyeon Song
- Department of Animal Science, Jeonbuk National University, Jeonju, South Korea
| | - Thomas K. Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, United States
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Local and Universal Action: The Paradoxes of Indole Signalling in Bacteria. Trends Microbiol 2020; 28:566-577. [PMID: 32544443 DOI: 10.1016/j.tim.2020.02.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/05/2020] [Accepted: 02/25/2020] [Indexed: 02/06/2023]
Abstract
Indole is a signalling molecule produced by many bacterial species and involved in intraspecies, interspecies, and interkingdom signalling. Despite the increasing volume of research published in this area, many aspects of indole signalling remain enigmatic. There is disagreement over the mechanism of indole import and export and no clearly defined target through which its effects are exerted. Progress is hindered further by the confused and sometimes contradictory body of indole research literature. We explore the reasons behind this lack of consistency and speculate whether the discovery of a new, pulse mode of indole signalling, together with a move away from the idea of a conventional protein target, might help to overcome these problems and enable the field to move forward.
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32
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Wang J, Li G, Yin H, An T. Bacterial response mechanism during biofilm growth on different metal material substrates: EPS characteristics, oxidative stress and molecular regulatory network analysis. ENVIRONMENTAL RESEARCH 2020; 185:109451. [PMID: 32251912 DOI: 10.1016/j.envres.2020.109451] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 02/07/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Overwhelming growth of bacterial biofilms on different metal-based pipeline materials are intractable and pose a serious threat to public health when tap water flows though these pipelines. Indeed, the underlying mechanism of biofilm growth on the surface of different pipeline materials deserves detailed exploration to provide subsequent implementation strategies for biofilm control. Thus, in this study, how bacteria response to their encounters was explored, when they inhabit different metal-based pipeline substrates. Results revealed that bacteria proliferated when they grew on stainless steel (SS) and titanium sheet (Ti), quickly developing into bacterial biofilms. In contrast, the abundance of bacteria on copper (Cu) and nickel foam (Ni) substates decreased sharply by 4-5 logs within 24 h. The morphological shrinkage and shortening of bacterial cells, as well as a sudden 64-fold increase of carbohydrate content in extracellular polymeric substances (EPS), were observed on Cu substrate. Furthermore, generation of reactive oxygen species and fluctuation of enzymatic activity demonstrated the destruction of redox equilibrium in bacteria. Bacteria cultured on Cu substrate showed the strongest response, followed by Ni, SS and Ti. The oxidative stress increased quickly during the growth of bacterial biofilm, and almost all tested metal transporter-related genes were upregulated by 2-11 folds on Cu, which were higher than on other substrates (1-2 folds for SS and Ti, 2-9 folds for Ni). Finally, these behaviors were compared under the biofilm regulatory molecular network. This work may facilitate better understanding different response mechanisms during bacterial biofilm colonization on metal-based pipelines and provide implications for subsequent biofilm control.
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Affiliation(s)
- Jiaping Wang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Guiying Li
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Hongliang Yin
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Taicheng An
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China.
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33
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Fang K, Park OJ, Hong SH. Controlling biofilms using synthetic biology approaches. Biotechnol Adv 2020; 40:107518. [PMID: 31953206 PMCID: PMC7125041 DOI: 10.1016/j.biotechadv.2020.107518] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 01/09/2020] [Accepted: 01/11/2020] [Indexed: 12/22/2022]
Abstract
Bacterial biofilms are formed by the complex but ordered regulation of intra- or inter-cellular communication, environmentally responsive gene expression, and secretion of extracellular polymeric substances. Given the robust nature of biofilms due to the non-growing nature of biofilm bacteria and the physical barrier provided by the extracellular matrix, eradicating biofilms is a very difficult task to accomplish with conventional antibiotic or disinfectant treatments. Synthetic biology holds substantial promise for controlling biofilms by improving and expanding existing biological tools, introducing novel functions to the system, and re-conceptualizing gene regulation. This review summarizes synthetic biology approaches used to eradicate biofilms via protein engineering of biofilm-related enzymes, utilization of synthetic genetic circuits, and the development of functional living agents. Synthetic biology also enables beneficial applications of biofilms through the production of biomaterials and patterning biofilms with specific temporal and spatial structures. Advances in synthetic biology will add novel biofilm functionalities for future therapeutic, biomanufacturing, and environmental applications.
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Affiliation(s)
- Kuili Fang
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Oh-Jin Park
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA; Department of Biological and Chemical Engineering, Yanbian University of Science and Technology, Yanji, Jilin, People's Republic of China
| | - Seok Hoon Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA.
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Maddela NR, Meng F. Discrepant roles of a quorum quenching bacterium (Rhodococcus sp. BH4) in growing dual-species biofilms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 713:136402. [PMID: 31955076 DOI: 10.1016/j.scitotenv.2019.136402] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/22/2019] [Accepted: 12/27/2019] [Indexed: 06/10/2023]
Abstract
Quorum quenching (QQ) is a promising alternative method for biofilm control. However, a largely unexplored issue is the mechanism through which QQ bacteria interact with biofilm-forming bacteria. Here, we explore inter-species interactions during biofilm development (using 96-well polystyrene plates in a static incubator) between the QQ bacterium Rhodococcus sp. BH4 and sludge bacteria. Experimental results revealed that strain BH4 provoked both competitive (76%) and cooperative (24%) interactions (P < 0.05) in dual-species biofilms after 24 h of incubation (mature biofilm), implying that signal destruction by strain BH4 was strain-dependent. Besides hike in the biofilm biomass (~21%), amount of extracellular polymeric substances (EPS) (25-30 times) and particle size (3.5 times) in the Serratia sp. JSB1 biofilm were increased by str. BH4. This suggests that strain BH4 may only have quenching effects against certain bacteria, and that such effects are overlooked at the community level. Taken together, present results imply that in a given biofilm community, not all QS-bacteria interact similarly with Rhodococcus sp. BH4, either because QS-bacteria are tolerant of strain BH4 or QS-bacteria have more than one mechanism for biofilm development. Overall, the QQ-strategy alone seems ineffective at controlling biofilm development, although it may be used in combination with other strategies.
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Affiliation(s)
- Naga Raju Maddela
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, People's Republic of China; Instituto de Investigación, Universidad Técnica de Manabí, Portoviejo 130105, Ecuador; Facultad de Ciencias de la Salud, Universidad Técnica de Manabí, Portoviejo 130105, Ecuador; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, People's Republic of China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, People's Republic of China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, People's Republic of China.
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35
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Interspecies and Intraspecies Signals Synergistically Regulate Lysobacter enzymogenes Twitching Motility. Appl Environ Microbiol 2019; 85:AEM.01742-19. [PMID: 31540995 DOI: 10.1128/aem.01742-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/18/2019] [Indexed: 12/24/2022] Open
Abstract
The twitching motility of bacteria is closely related to environmental adaptability and pathogenic behaviors. Lysobacter is a good genus in which to study twitching motility because of the complex social activities and distinct movement patterns of its members. Regardless, the mechanism that induces twitching motility is largely unknown. In this study, we found that the interspecies signal indole caused Lysobacter to have irregular, random twitching motility with significantly enhanced speed. Deletion of qseC or qseB from the two-component system for indole signaling perception resulted in the disappearance of rapid, random movements and significantly decreased twitching activity. Indole-induced, rapid, random twitching was achieved through upregulation of expression of gene cluster pilE1-pilY11-pilX1-pilW1-pilV1-fimT1 In addition, under conditions of extremely low bacterial density, individual Lysobacter cells grew and divided in a stable manner in situ without any movement. The intraspecies quorum-sensing signaling factor 13-methyltetradecanoic acid, designated L. enzymogenes diffusible signaling factor (LeDSF), was essential for Lysobacter to produce twitching motility through indirect regulation of gene clusters pilM-pilN-pilO-pilP-pilQ and pilS1-pilR-pilA-pilB-pilC These results demonstrate that the motility of Lysobacter is induced and regulated by indole and LeDSF, which reveals a novel theory for future studies of the mechanisms of bacterial twitching activities.IMPORTANCE The mechanism underlying bacterial twitching motility is an important research area because it is closely related to social and pathogenic behaviors. The mechanism mediating cell-to-cell perception of twitching motility is largely unknown. Using Lysobacter as a model, we found in this study that the interspecies signal indole caused Lysobacter to exhibit irregular, random twitching motility via activation of gene cluster pilE1-pilY11-pilX1-pilW1-pilV1-fimT1 In addition, population-dependent behavior induced by 13-methyltetradecanoic acid, a quorum-sensing signaling molecule designated LeDSF, was involved in twitching motility by indirectly regulating gene clusters pilM-pilN-pilO-pilP-pilQ and pilS1-pilR-pilA-pilB-pilC The results demonstrate that the twitching motility of Lysobacter is regulated by these two signaling molecules, offering novel clues for exploring the mechanisms of twitching motility and population-dependent behaviors of bacteria.
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Zheng J, Liu Q, Xia Y, Bai L, Feng Y. Pantoea agglomerans YS19 poly(A) polymerase I gene possesses the indole-sensing sequence in the promoter region. FEMS Microbiol Lett 2019; 366:5538762. [PMID: 31344226 DOI: 10.1093/femsle/fnz166] [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: 10/18/2018] [Accepted: 07/23/2019] [Indexed: 11/13/2022] Open
Abstract
Pantoea agglomerans YS19 is a predominant diazotrophic endophyte with multiple growth-promoting effects on its host plant that was isolated from rice. Indole is confirmed to induce many changes of physiological and biochemical characteristics in bacteria. Although YS19 cannot produce indole, it can sense indole in the environment and be regulated by indole. Here, using gfp as a reporter gene, we constructed a series of recombinant plasmids containing the promoter region of the poly(A) polymerase I gene (pcnB) fused with gfp, and compared the green fluorescence intensity at different concentrations of exogenous indole by a flow cytometer. In this research, we confirmed that exogenous indole significantly inhibited the expression of pcnB by its promoter; the regulation sequence sensitive to indole in the promoter region of the pcnB gene (In-pcnB) was between -129 and -88 bp. In-pcnB is widely distributed and strictly conserved in the same genus. These results suggest novel roles of In-pcnB in P. agglomerans YS19, showing its special relation to the indole regulatory pathway.
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Affiliation(s)
- Jing Zheng
- School of Life Science, Beijing Institute of Technology, 5# Zhongguancun Nandajie, Beijing 100081, People's Republic of China
| | - Qi Liu
- School of Life Science, Beijing Institute of Technology, 5# Zhongguancun Nandajie, Beijing 100081, People's Republic of China
| | - Yifan Xia
- School of Life Science, Beijing Institute of Technology, 5# Zhongguancun Nandajie, Beijing 100081, People's Republic of China
| | - Lijuan Bai
- School of Life Science, Beijing Institute of Technology, 5# Zhongguancun Nandajie, Beijing 100081, People's Republic of China
| | - Yongjun Feng
- School of Life Science, Beijing Institute of Technology, 5# Zhongguancun Nandajie, Beijing 100081, People's Republic of China
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Pyruvate-depleting conditions induce biofilm dispersion and enhance the efficacy of antibiotics in killing biofilms in vitro and in vivo. Sci Rep 2019; 9:3763. [PMID: 30842579 PMCID: PMC6403282 DOI: 10.1038/s41598-019-40378-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/14/2019] [Indexed: 01/09/2023] Open
Abstract
The formation of biofilms is a developmental process initiated by planktonic cells transitioning to the surface, which comes full circle when cells disperse from the biofilm and transition to the planktonic mode of growth. Considering that pyruvate has been previously demonstrated to be required for the formation of P. aeruginosa biofilms, we asked whether pyruvate likewise contributes to the maintenance of the biofilm structure, with depletion of pyruvate resulting in dispersion. Here, we demonstrate that the enzymatic depletion of pyruvate coincided with the dispersion of established biofilms by S. aureus and laboratory and clinical P. aeruginosa isolates. The dispersion response was dependent on pyruvate fermentation pathway components but independent of proteins previously described to contribute to P. aeruginosa biofilm dispersion. Using porcine second-degree burn wounds infected with P. aeruginosa biofilm cells, we furthermore demonstrated that pyruvate depletion resulted in a reduction of biofilm biomass in vivo. Pyruvate-depleting conditions enhanced the efficacy of tobramycin killing of the resident wound biofilms by up to 5-logs. Our findings strongly suggest the management of pyruvate availability to be a promising strategy to combat biofilm-related infections by two principal pathogens associated with wound and cystic fibrosis lung infections.
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38
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Chatterjee R, Shreenivas MM, Sunil R, Chakravortty D. Enteropathogens: Tuning Their Gene Expression for Hassle-Free Survival. Front Microbiol 2019; 9:3303. [PMID: 30687282 PMCID: PMC6338047 DOI: 10.3389/fmicb.2018.03303] [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: 09/26/2018] [Accepted: 12/19/2018] [Indexed: 12/27/2022] Open
Abstract
Enteropathogenic bacteria have been the cause of the majority of foodborne illnesses. Much of the research has been focused on elucidating the mechanisms by which these pathogens evade the host immune system. One of the ways in which they achieve the successful establishment of a niche in the gut microenvironment and survive is by a chain of elegantly regulated gene expression patterns. Studies have shown that this process is very elaborate and is also regulated by several factors. Pathogens like, enteropathogenic Escherichia coli (EPEC), Salmonella Typhimurium, Shigellaflexneri, Yersinia sp. have been seen to employ various regulated gene expression strategies. These include toxin-antitoxin systems, quorum sensing systems, expression controlled by nucleoid-associated proteins (NAPs), several regulons and operons specific to these pathogens. In the following review, we have tried to discuss the common gene regulatory systems of enteropathogenic bacteria as well as pathogen-specific regulatory mechanisms.
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Affiliation(s)
- Ritika Chatterjee
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India.,Division of Biological Sciences, Indian Institute of Science, Bengaluru, India
| | - Meghanashree M Shreenivas
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India.,Division of Biological Sciences, Indian Institute of Science, Bengaluru, India.,Undergraduate Studies, Indian Institute of Science, Bengaluru, India
| | - Rohith Sunil
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India.,Division of Biological Sciences, Indian Institute of Science, Bengaluru, India.,Undergraduate Studies, Indian Institute of Science, Bengaluru, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India.,Division of Biological Sciences, Indian Institute of Science, Bengaluru, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
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Jin X, Lee YJ, Hong SH. Canavalia ensiformis-derived lectin inhibits biofilm formation of enterohemorrhagic Escherichia coli and Listeria monocytogenes. J Appl Microbiol 2018; 126:300-310. [PMID: 30240117 DOI: 10.1111/jam.14108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 09/02/2018] [Accepted: 09/10/2018] [Indexed: 12/18/2022]
Abstract
AIM A lectin Concanavalin A (ConA) derived from Canavalia ensiformis (jack bean) exhibits high-binding affinity to carbohydrates on bacterial cell surfaces. The objective of this study was to inhibit the biofilm formation of the foodborne pathogens enterohemorrhagic Escherichia coli and Listeria monocytogenes using ConA prepared by a membrane-based extraction method. METHODS AND RESULTS ConA was extracted using a simple and inexpensive membrane method instead of a chromatography approach. The extracted ConA was effective in inhibiting biofilms of E. coli by 30-fold and L. monocytogenes by 140-fold. In addition, ConA decreased the swimming motility of enterohemorrhagic E. coli EDL933 (EHEC) by 37%, resulting in low biofilm formation, as ConA binding to the bacterial cell surfaces might cause a reduced capability to adhere due to low cellular motility. We confirmed that the extracted ConA contains active components at less than 10 kDa as well as ConA multimers (>30 kDa) that repress EHEC biofilms. Additionally, noncell-based mannose reduced the activity of ConA in inhibiting biofilms. CONCLUSIONS ConA extracted using the membrane-based method is active in inhibiting the biofilm formation by E. coli and L. monocytogenes via the mannose-binding affinity of ConA. SIGNIFICANCE AND IMPACT OF THE STUDY ConA can be used as a promising anti-adherent and antibiofilm agent in inhibiting biofilm formation by enterohemorrhagic E. coli and L. monocytogenes. The membrane-based extraction approach may be applied for the economic production of biologically active lectins.
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Affiliation(s)
- X Jin
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Y J Lee
- Department of Nutrition and Food Science, Texas A&M University, College Station, TX, USA
| | - S H Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, USA
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Coordinated Hibernation of Transcriptional and Translational Apparatus during Growth Transition of Escherichia coli to Stationary Phase. mSystems 2018; 3:mSystems00057-18. [PMID: 30225374 PMCID: PMC6134199 DOI: 10.1128/msystems.00057-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/06/2018] [Indexed: 12/14/2022] Open
Abstract
During the growth transition of E. coli from exponential phase to stationary, the genome expression pattern is altered markedly. For this alteration, the transcription apparatus is altered by binding of anti-sigma factor Rsd to the RpoD sigma factor for sigma factor replacement, while the translation machinery is modulated by binding of RMF to 70S ribosome to form inactive ribosome dimer. Using the PS-TF screening system, a number of TFs were found to bind to both the rsd and rmf promoters, of which the regulatory roles of 5 representative TFs (one repressor ArcA and the four activators McbR, RcdA, SdiA, and SlyA) were analyzed in detail. The results altogether indicated the involvement of a common set of TFs, each sensing a specific environmental condition, in coordinated hibernation of the transcriptional and translational apparatus for adaptation and survival under stress conditions. In the process of Escherichia coli K-12 growth from exponential phase to stationary, marked alteration takes place in the pattern of overall genome expression through modulation of both parts of the transcriptional and translational apparatus. In transcription, the sigma subunit with promoter recognition properties is replaced from the growth-related factor RpoD by the stationary-phase-specific factor RpoS. The unused RpoD is stored by binding with the anti-sigma factor Rsd. In translation, the functional 70S ribosome is converted to inactive 100S dimers through binding with the ribosome modulation factor (RMF). Up to the present time, the regulatory mechanisms of expression of these two critical proteins, Rsd and RMF, have remained totally unsolved. In this study, attempts were made to identify the whole set of transcription factors involved in transcription regulation of the rsd and rmf genes using the newly developed promoter-specific transcription factor (PS-TF) screening system. In the first screening, 74 candidate TFs with binding activity to both of the rsd and rmf promoters were selected from a total of 194 purified TFs. After 6 cycles of screening, we selected 5 stress response TFs, ArcA, McbR, RcdA, SdiA, and SlyA, for detailed analysis in vitro and in vivo of their regulatory roles. Results indicated that both rsd and rmf promoters are repressed by ArcA and activated by McbR, RcdA, SdiA, and SlyA. We propose the involvement of a number of TFs in simultaneous and coordinated regulation of the transcriptional and translational apparatus. By using genomic SELEX (gSELEX) screening, each of the five TFs was found to regulate not only the rsd and rmf genes but also a variety of genes for growth and survival. IMPORTANCE During the growth transition of E. coli from exponential phase to stationary, the genome expression pattern is altered markedly. For this alteration, the transcription apparatus is altered by binding of anti-sigma factor Rsd to the RpoD sigma factor for sigma factor replacement, while the translation machinery is modulated by binding of RMF to 70S ribosome to form inactive ribosome dimer. Using the PS-TF screening system, a number of TFs were found to bind to both the rsd and rmf promoters, of which the regulatory roles of 5 representative TFs (one repressor ArcA and the four activators McbR, RcdA, SdiA, and SlyA) were analyzed in detail. The results altogether indicated the involvement of a common set of TFs, each sensing a specific environmental condition, in coordinated hibernation of the transcriptional and translational apparatus for adaptation and survival under stress conditions.
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Fructose furoic acid ester: An effective quorum sensing inhibitor against uropathogenic Escherichia coli. Bioorg Chem 2018; 79:310-318. [PMID: 29800818 DOI: 10.1016/j.bioorg.2018.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/05/2018] [Accepted: 05/14/2018] [Indexed: 12/12/2022]
Abstract
Uropathogenic Escherichia coli (UPEC) are the most common cause of UTI, accounting for more than 90% infections in the normal and unobstructed urinary tracts. Multi-drug resistance (MDR) is an emerging threat to the mankind and hence, there is an urge to develop alternative therapies. Targeting quorum sensing (QS), a cell-cell communication process regulates various biofilm and virulence factors would be a most promising alternate which curbs the pathogenesis without killing the bacteria, unlike antibiotics. SdiA, a quorum regulator is well-known to control the behavioural changes of UPEC in establishing biofilm and virulence. Therefore, we have hypothesized that the SdiA-selective inhibitors derived from the plant, Melia dubia using the molecular docking would be a remarkable therapeutic candidate to down regulate the UPEC biofilm and virulence phenotypes. In this study, we have designed, synthesized and characterized the fructose-furoic acid ester by NMR and ESI-MS. In vitro studies revealed that the QSI-MD selectively inhibits UPEC adherence and confocal laser scanning microscopy (CLSM) analysis showed the effectiveness of QSI-MD to inhibit the UPEC biofilm. Genetic studies using qRT-PCR revealed the down-regulation of quorum sensing regulated genes (fimA, csgA, espA). Based on the findings, we could propose that the QSI-MD could possibly act through SdiA and show target-specific inhibition of biofilm and virulence. It is notable that more than 70 bacterial species execute their communication through the SdiA homologues (LuxIR system). Hence, the QSI-MD could be further developed as a broad-spectrum anti-infective drug.
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García-Martínez J, Maldonado RD, Guzmán NM, Mojica FJM. The CRISPR conundrum: evolve and maybe die, or survive and risk stagnation. MICROBIAL CELL 2018; 5:262-268. [PMID: 29850463 PMCID: PMC5972030 DOI: 10.15698/mic2018.06.634] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
CRISPR-Cas represents a prokaryotic defense mechanism against invading genetic elements. Although there is a diversity of CRISPR-Cas systems, they all share similar, essential traits. In general, a CRISPR-Cas system consists of one or more groups of DNA repeats named CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), regularly separated by unique sequences referred to as spacers, and a set of functionally associated cas (CRISPR associated) genes typically located next to one of the repeat arrays. The origin of spacers is in many cases unknown but, when ascertained, they usually match foreign genetic molecules. The proteins encoded by some of the cas genes are in charge of the incorporation of new spacers upon entry of a genetic element. Other Cas proteins participate in generating CRISPR-spacer RNAs and perform the task of destroying nucleic acid molecules carrying sequences similar to the spacer. In this way, CRISPR-Cas provides protection against genetic intruders that could substantially affect the cell viability, thus acting as an adaptive immune system. However, this defensive action also hampers the acquisition of potentially beneficial, horizontally transferred genes, undermining evolution. Here we cover how the model bacterium Escherichia coli deals with CRISPR-Cas to tackle this major dilemma, evolution versus survival.
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Affiliation(s)
- Jesús García-Martínez
- Departamento de Fisiología, Genética y Microbiología. Universidad de Alicante, Campus de San Vicente, 03690 San Vicente del Raspeig (Alicante), Spain
| | - Rafael D Maldonado
- Departamento de Fisiología, Genética y Microbiología. Universidad de Alicante, Campus de San Vicente, 03690 San Vicente del Raspeig (Alicante), Spain
| | - Noemí M Guzmán
- Departamento de Fisiología, Genética y Microbiología. Universidad de Alicante, Campus de San Vicente, 03690 San Vicente del Raspeig (Alicante), Spain
| | - Francisco J M Mojica
- Departamento de Fisiología, Genética y Microbiología. Universidad de Alicante, Campus de San Vicente, 03690 San Vicente del Raspeig (Alicante), Spain.,I.M.E.M. Ramón Margalef. Universidad de Alicante, Campus de San Vicente, 03690 San Vicente del Raspeig (Alicante), Spain
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Culler HF, Couto SCF, Higa JS, Ruiz RM, Yang MJ, Bueris V, Franzolin MR, Sircili MP. Role of SdiA on Biofilm Formation by Atypical Enteropathogenic Escherichia coli. Genes (Basel) 2018; 9:genes9050253. [PMID: 29762495 PMCID: PMC5977193 DOI: 10.3390/genes9050253] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 02/19/2018] [Accepted: 02/21/2018] [Indexed: 01/11/2023] Open
Abstract
Atypical enteropathogenic Escherichia coli are capable to form biofilm on biotic and abiotic surfaces, regardless of the adherence pattern displayed. Several E. coli mechanisms are regulated by Quorum sensing (QS), including virulence factors and biofilm formation. Quorum sensing is a signaling system that confers bacteria with the ability to respond to chemical molecules known as autoinducers. Suppressor of division inhibitor (SdiA) is a QS receptor present in atypical enteropathogenic E.coli (aEPEC) that detects acyl homoserine lactone (AHL) type autoinducers. However, these bacteria do not encode an AHL synthase, but they are capable of sensing AHL molecules produced by other species, establishing an inter-species bacterial communication. In this study, we performed experiments to evaluate pellicle, ring-like structure and biofilm formation on wild type, sdiA mutants and complemented strains. We also evaluated the transcription of genes involved in different stages of biofilm formation, such as bcsA, csgA, csgD, fliC and fimA. The sdiA mutants were capable of forming thicker biofilm structures and showed increased motility when compared to wild type and complemented strains. Moreover, they also showed denser pellicles and ring-like structures. Quantitative real-time PCR (qRT-PCR) analysis demonstrated increased csgA, csgD and fliC transcription on mutant strains. Biofilm formation, as well as csgD, csgA and fimA transcription decreased on wild type strains by the addition of AHL. These results indicate that SdiA participates on the regulation of these phenotypes in aEPEC and that AHL addition enhances the repressor effect of this receptor on the transcription of biofilm and motility related genes.
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Affiliation(s)
- Hebert F Culler
- Laboratory of Genetics, Butantan Institute, São Paulo 05503-900, Brazil.
| | - Samuel C F Couto
- Laboratory of Genetics, Butantan Institute, São Paulo 05503-900, Brazil.
| | - Juliana S Higa
- Laboratory of Genetics, Butantan Institute, São Paulo 05503-900, Brazil.
| | - Renato M Ruiz
- Laboratory of Genetics, Butantan Institute, São Paulo 05503-900, Brazil.
| | - Min J Yang
- Laboratory of Genetics, Butantan Institute, São Paulo 05503-900, Brazil.
| | - Vanessa Bueris
- Laboratory of Genetics, Butantan Institute, São Paulo 05503-900, Brazil.
| | - Marcia R Franzolin
- Laboratory of Bacteriology, Butantan Institute, São Paulo 05503-900, Brazil.
| | - Marcelo P Sircili
- Laboratory of Genetics, Butantan Institute, São Paulo 05503-900, Brazil.
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Indole-Induced Reversion of Intrinsic Multiantibiotic Resistance in Lysobacter enzymogenes. Appl Environ Microbiol 2017. [PMID: 28625984 DOI: 10.1128/aem.00995-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Lysobacter species are a group of environmental bacteria that are emerging as a new source of antibiotics. One characteristic of Lysobacter is intrinsic resistance to multiple antibiotics, which had not been studied. To understand the resistance mechanism, we tested the effect of blocking two-component regulatory systems (TCSs) on the antibiotic resistance of Lysobacter enzymogenes, a prolific producer of antibiotics. Upon treatment with LED209, an inhibitor of the widespread TCS QseC/QseB, L. enzymogenes produced a large amount of an unknown metabolite that was barely detectable in the untreated culture. Subsequent structural elucidation by nuclear magnetic resonance (NMR) unexpectedly revealed that the metabolite was indole. Indole production was also markedly induced by adrenaline, a known modulator of QseC/QseB. Next, we identified two TCS genes, L. enzymogenesqseC (Le-qseC) and Le-qseB, in L. enzymogenes and found that mutations of Le-qseC and Le-qseB also led to a dramatic increase in indole production. We then chemically synthesized a fluorescent indole probe that could label the cells. While the Le-qseB (cytoplasmic response regulator) mutant was clearly labeled by the probe, the Le-qseC (membrane sensor) mutant was not labeled. It was reported previously that indole can enhance antibiotic resistance in bacteria. Therefore, we tested if the dramatic increase in the level of indole production in L. enzymogenes upon blocking of Le-qseC and Le-qseB would lead to enhanced antibiotic resistance. Surprisingly, we found that indole caused the intrinsically multiantibiotic-resistant bacterium L. enzymogenes to become susceptible. Point mutations at conserved amino acids in Le-QseC also led to antibiotic susceptibility. Because indole is known as an interspecies signal, these findings may have implications.IMPORTANCE The environmental bacterium Lysobacter is a new source of antibiotic compounds and exhibits intrinsic antibiotic resistance. Here, we found that the inactivation of a two-component regulatory system (TCS) by an inhibitor or by gene deletion led to a remarkable increase in the level of production of a metabolite in L. enzymogenes, and this metabolite was identified to be indole. We chemically synthesized a fluorescent indole probe and found that it could label the wild type and a mutant of the TCS cytoplasmic response regulator but not a mutant of the TCS membrane sensor. Indole treatment caused the intrinsically multidrug-resistant bacterium L. enzymogenes to be susceptible to antibiotics. Mutations of the TCS sensor also led to antibiotic susceptibility. Because indole is known as an interspecies signal between gut microbiota and mammalian hosts, the observation that indole could render intrinsically resistant L. enzymogenes susceptible to common antibiotics may have implications.
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Bhattacharjee A, Khan M, Kleiman M, Hochbaum AI. Effects of Growth Surface Topography on Bacterial Signaling in Coculture Biofilms. ACS APPLIED MATERIALS & INTERFACES 2017; 9:18531-18539. [PMID: 28485146 DOI: 10.1021/acsami.7b04223] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacteria form interface-associated communities called biofilms, often comprising multiple species. Biofilms can be detrimental or beneficial in medical, industrial, and technological settings, and their stability and function are determined by interspecies communication via specific chemical signaling or metabolite exchange. The deterministic control of biofilm development, behavior, and properties remains an unmet challenge, limiting our ability to inhibit the formation of detrimental biofilms in biomedical settings and promote the growth of beneficial biofilms in biotechnology applications. Here, we describe the development of growth surfaces that promote the growth of commensal Escherichia coli instead of the opportunistic pathogen Pseudomonas aeruginosa. Periodically patterned growth surfaces induced robust morphological changes in surface-associated E. coli biofilms and influenced the antibiotic susceptibilities of E. coli and P. aeruginosa biofilms. Changes in the biofilm architecture resulted in the accumulation of a metabolite, indole, which controls the competition dynamics between the two species. Our results show that the surface on which a biofilm grows has important implications for species colonization, growth, and persistence when exposed to antibiotics.
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Affiliation(s)
| | - Mughees Khan
- Wyss Institute for Biologically Inspired Engineering, Harvard University , Cambridge, Massachusetts 02138, United States
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Rossi E, Cimdins A, Lüthje P, Brauner A, Sjöling Å, Landini P, Römling U. "It's a gut feeling" - Escherichia coli biofilm formation in the gastrointestinal tract environment. Crit Rev Microbiol 2017; 44:1-30. [PMID: 28485690 DOI: 10.1080/1040841x.2017.1303660] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Escherichia coli can commonly be found, either as a commensal, probiotic or a pathogen, in the human gastrointestinal (GI) tract. Biofilm formation and its regulation is surprisingly variable, although distinct regulatory pattern of red, dry and rough (rdar) biofilm formation arise in certain pathovars and even clones. In the GI tract, environmental conditions, signals from the host and from commensal bacteria contribute to shape E. coli biofilm formation within the multi-faceted multicellular communities in a complex and integrated fashion. Although some major regulatory networks, adhesion factors and extracellular matrix components constituting E. coli biofilms have been recognized, these processes have mainly been characterized in vitro and in the context of interaction of E. coli strains with intestinal epithelial cells. However, direct observation of E. coli cells in situ, and the vast number of genes encoding surface appendages on the core or accessory genome of E. coli suggests the complexity of the biofilm process to be far from being fully understood. In this review, we summarize biofilm formation mechanisms of commensal, probiotic and pathogenic E. coli in the context of the gastrointestinal tract.
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Affiliation(s)
- Elio Rossi
- a Department of Biosciences , Università degli Studi di Milano , Milan , Italy.,b Novo Nordisk Center for Biosustainabiliy , Technical University of Denmark , Kgs. Lyngby , Denmark
| | - Annika Cimdins
- c Department of Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Stockholm , Sweden.,d Institute of Hygiene, University of Münster , Münster , Germany
| | - Petra Lüthje
- c Department of Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Stockholm , Sweden.,e Division of Clinical Microbiology, Department of Laboratory Medicine , Karolinska Institutet and Karolinska University Hospital Huddinge , Stockholm , Sweden
| | - Annelie Brauner
- c Department of Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Stockholm , Sweden
| | - Åsa Sjöling
- c Department of Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Stockholm , Sweden
| | - Paolo Landini
- a Department of Biosciences , Università degli Studi di Milano , Milan , Italy
| | - Ute Römling
- c Department of Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Stockholm , Sweden
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Yang Q, Pande GSJ, Wang Z, Lin B, Rubin RA, Vora GJ, Defoirdt T. Indole signalling and (micro)algal auxins decrease the virulence of Vibrio campbellii, a major pathogen of aquatic organisms. Environ Microbiol 2017; 19:1987-2004. [PMID: 28251783 DOI: 10.1111/1462-2920.13714] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/25/2017] [Indexed: 12/23/2022]
Abstract
Vibrios belonging to the Harveyi clade are major pathogens of marine vertebrates and invertebrates, causing major losses in wild and cultured organisms. Despite their significant impact, the pathogenicity mechanisms of these bacteria are not yet completely understood. In this study, the impact of indole signalling on the virulence of Vibrio campbellii was investigated. Elevated indole levels significantly decreased motility, biofilm formation, exopolysaccharide production and virulence to crustacean hosts. Indole furthermore inhibited the three-channel quorum sensing system of V. campbellii, a regulatory mechanism that is required for full virulence of the pathogen. Further, indole signalling was found to interact with the stress sigma factor RpoS. Together with the observations that energy-consuming processes (motility and bioluminescence) are downregulated, and microarray-based transcriptomics demonstrating that indole decreases the expression of genes involved in energy and amino acid metabolism, the data suggest that indole is a starvation signal in V. campbellii. Finally, it was found that the auxins indole-3-acetic acid and indole-3-acetamide, which were produced by various (micro)algae sharing the aquatic environment with V. campbellii, have a similar effect as observed for indole. Auxins might, therefore, have a significant impact on the interactions between vibrios, (micro)algae and higher organisms, with major ecological and practical implications.
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Affiliation(s)
- Qian Yang
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University, Gent, Belgium
| | | | - Zheng Wang
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Baochuan Lin
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Robert A Rubin
- Mathematics Department, Whittier College, Whittier, CA, USA
| | - Gary J Vora
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Tom Defoirdt
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University, Gent, Belgium.,Center for Microbial Ecology and Technology (cmet), Ghent University, Gent, Belgium
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Gart EV, Suchodolski JS, Welsh TH, Alaniz RC, Randel RD, Lawhon SD. Salmonella Typhimurium and Multidirectional Communication in the Gut. Front Microbiol 2016; 7:1827. [PMID: 27920756 PMCID: PMC5118420 DOI: 10.3389/fmicb.2016.01827] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 10/31/2016] [Indexed: 12/20/2022] Open
Abstract
The mammalian digestive tract is home to trillions of microbes, including bacteria, archaea, protozoa, fungi, and viruses. In monogastric mammals the stomach and small intestine harbor diverse bacterial populations but are typically less populated than the colon. The gut bacterial community (microbiota hereafter) varies widely among different host species and individuals within a species. It is influenced by season of the year, age of the host, stress and disease. Ideally, the host and microbiota benefit each other. The host provides nutrients to the microbiota and the microbiota assists the host with digestion and nutrient metabolism. The resident microbiota competes with pathogens for space and nutrients and, through this competition, protects the host in a phenomenon called colonization resistance. The microbiota participates in development of the host immune system, particularly regulation of autoimmunity and mucosal immune response. The microbiota also shapes gut–brain communication and host responses to stress; and, indeed, the microbiota is a newly recognized endocrine organ within mammalian hosts. Salmonella enterica serovar Typhimurium (S. Typhimurium hereafter) is a food-borne pathogen which adapts to and alters the gastrointestinal (GI) environment. In the GI tract, S. Typhimurium competes with the microbiota for nutrients and overcomes colonization resistance to establish infection. To do this, S. Typhimurium uses multiple defense mechanisms to resist environmental stressors, like the acidic pH of the stomach, and virulence mechanisms which allow it to invade the intestinal epithelium and disseminate throughout the host. To coordinate gene expression and disrupt signaling within the microbiota and between host and microbiota, S. Typhimurium employs its own chemical signaling and may regulate host hormone metabolism. This review will discuss the multidirectional interaction between S. Typhimurium, host and microbiota as well as mechanisms that allow S. Typhimurium to succeed in the gut.
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Affiliation(s)
- Elena V Gart
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station TX, USA
| | - Jan S Suchodolski
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Texas A&M University, College Station TX, USA
| | - Thomas H Welsh
- Department of Animal Science, College of Agriculture and Life Sciences, Texas A&M University, College Station TX, USA
| | - Robert C Alaniz
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station TX, USA
| | | | - Sara D Lawhon
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station TX, USA
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Effect of small chain N acyl homoserine lactone quorum sensing signals on biofilms of food-borne pathogens. Journal of Food Science and Technology 2016; 53:3609-3614. [PMID: 27777468 DOI: 10.1007/s13197-016-2346-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 08/26/2016] [Accepted: 09/08/2016] [Indexed: 01/17/2023]
Abstract
Quorum sensing or cell to cell communication which includes inter- and intra-cellular communication has been implicated in the production of virulence factor and formation of biofilm in food-borne pathogens. In the present study, the effect of quorum sensing signals on the biofilms of food-borne pathogens has been elucidated. N-butryl homoserine lactone and N-hexanoyl homoserine lactone belonging to acyl homoserine lactone (AHL) family of signaling molecules were investigated for their effect on the biofilm formation (attachment and exopolymeric substance production) in the food-borne pathogens Escherichia coli, Salmonella enterica serovar Typhimurium and Vibrio parahemolyticus. The signaling molecules at a concentration of 1 µM were capable of increasing biofilm formation in all the tested pathogens. There was an increase in the attachment of the bacterial cells and biomass as observed by microtiter plate assay and exopolymeric substances production in the biofilms in presence of the AHLs. Further, it needs to be elucidated if the effect of AHLS on the biofilms of E. coli and S. enterica serovar Typhimurium is SdiA dependent.
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50
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Almeida FAD, Pinto UM, Vanetti MCD. Novel insights from molecular docking of SdiA from Salmonella Enteritidis and Escherichia coli with quorum sensing and quorum quenching molecules. Microb Pathog 2016; 99:178-190. [PMID: 27565088 DOI: 10.1016/j.micpath.2016.08.024] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/04/2016] [Accepted: 08/22/2016] [Indexed: 12/11/2022]
Abstract
Quorum sensing is a cell-to-cell communication mechanism leading to differential gene expression in response to high population density. The autoinducer-1 (AI-1) type quorum sensing system is incomplete in Escherichia coli and Salmonella due to the lack of the AI-1 synthase (LuxI homolog) responsible for acyl homoserine lactone (AHL) synthesis. However, these bacteria encode the AHL receptor SdiA (a LuxR homolog) leading to gene regulation in response to AI-1 produced by other bacteria. This study aimed to model the SdiA protein of Salmonella enterica serovar Enteritidis PT4 578 based on three crystallized SdiA structures from Enterohemorrhagic E. coli (EHEC) with different ligands. Molecular docking of these predicted structures with AHLs, furanones and 1-octanoyl-rac-glycerol were also performed. The available EHEC SdiA structures provided good prototypes for modeling SdiA from Salmonella. The molecular docking of these proteins showed that residues Y63, W67, Y71, D80 and S134 are common binding sites for different quorum modulating signals, besides being conserved among other LuxR type proteins. We also show that AHLs with twelve carbons presented better binding affinity to SdiA than AHLs with smaller side chains in our docking analysis, regardless of the protein structures used. Interestingly, the conformational changes provided by AHL binding resulted in structural models with increased affinities to brominated furanones. These results suggest that the use of brominated furanones to inhibit phenotypes controlled by quorum sensing in Salmonella and EHEC may present a good strategy since these inhibitors seem to specifically compete with AHLs for binding to SdiA in both pathogens.
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Affiliation(s)
- Felipe Alves de Almeida
- Department of Microbiology, Laboratory of Food Microbiology, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Uelinton Manoel Pinto
- Food Research Center, Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Maria Cristina Dantas Vanetti
- Department of Microbiology, Laboratory of Food Microbiology, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
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