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Imam S, Kaperak CJ, Hozain AE, Qin H, Nguyen CT, Sudhindra P, Jeevanandam V, Landon E. Native Aortic Valve Endocarditis Caused by Scopulariopsis Species: Case Report, Considerations for Management, and Review of Literature. Open Forum Infect Dis 2024; 11:ofae323. [PMID: 38966852 PMCID: PMC11222977 DOI: 10.1093/ofid/ofae323] [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: 04/08/2024] [Accepted: 06/11/2024] [Indexed: 07/06/2024] Open
Abstract
We present the first case of native aortic valve endocarditis caused by Scopulariopsis. Intraoperative images and videos from valve replacement surgery illustrate the severity of fungal endocarditis. This case demonstrates the aggressive presentation of left-sided fungal endocarditis, highlights challenges with treating highly resistant fungi, and considers the potential utility of olorofim.
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Affiliation(s)
- Sabrina Imam
- Section of Infectious Diseases and Global Health, University of Chicago Medicine, Chicago, Illinois, USA
| | - Christopher J Kaperak
- Section of Infectious Diseases and Global Health, University of Chicago Medicine, Chicago, Illinois, USA
| | - Ahmed E Hozain
- Section of Cardiac Surgery, Department of Surgery, University of Chicago Medicine, Chicago, Illinois, USA
| | - Hecong Qin
- Pritzker School of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Cynthia T Nguyen
- Department of Pharmacy, University of Chicago Medicine, Chicago, Illinois, USA
| | - Praveen Sudhindra
- Infectious Diseases and Critical Care Medicine, Carle Health Methodist Hospital, Peoria, Illinois, USA
| | - Valluvan Jeevanandam
- Section of Cardiac Surgery, Department of Surgery, University of Chicago Medicine, Chicago, Illinois, USA
| | - Emily Landon
- Section of Infectious Diseases and Global Health, University of Chicago Medicine, Chicago, Illinois, USA
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2
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Chen Y, Liu F, Sha A, Xu M, Rao Z, Zhang X. Deciphering styrene oxide tolerance mechanisms in Gluconobacter oxydans mutant strain. BIORESOURCE TECHNOLOGY 2024; 401:130674. [PMID: 38642663 DOI: 10.1016/j.biortech.2024.130674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/21/2024] [Accepted: 04/05/2024] [Indexed: 04/22/2024]
Abstract
Chemical production wastewater contains large amounts of organic solvents (OSs), which pose a significant threat to the environment. In this study, a 10 g·L-1 styrene oxide tolerant strain with broad-spectrum OSs tolerance was obtained via adaptive laboratory evolution. The mechanisms underlying the high OS tolerance of tolerant strain were investigated by integrating physiological, multi-omics, and genetic engineering analyses. Physiological changes are one of the main factors responsible for the high OS tolerance in mutant strains. Moreover, the P-type ATPase GOX_RS04415 and the LysR family transcriptional regulator GOX_RS04700 were also verified as critical genes for styrene oxide tolerance. The tolerance mechanisms of OSs can be used in biocatalytic chassis cell factories to synthesize compounds and degrade environmental pollutants. This study provides new insights into the mechanisms underlying the toxicological response to OS stress and offers potential targets for enhancing the solvent tolerance of G. oxydans.
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Affiliation(s)
- Yan Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Fei Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Aobo Sha
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China.
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3
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Ravishankar S, Baldelli V, Angeletti C, Raffaelli N, Landini P, Rossi E. Fluoropyrimidines affect de novo pyrimidine synthesis impairing biofilm formation in Escherichia coli. Biofilm 2024; 7:100180. [PMID: 38370152 PMCID: PMC10869245 DOI: 10.1016/j.bioflm.2024.100180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/20/2024] Open
Abstract
Antivirulence agents are considered a promising strategy to treat bacterial infections. Fluoropyrimidines possess antivirulence and antibiofilm activity against Gram-negative bacteria; however, their mechanism of action is yet unknown. Consistent with their known antibiofilm activity, fluoropyrimidines, particularly 5-fluorocytosine (5-FC), impair curli-dependent surface adhesion by Escherichia coli MG1655 via downregulation of curli fimbriae gene transcription. Curli inhibition requires fluoropyrimidine conversion into fluoronucleotides and is not mediated by c-di-GMP or the ymg-rcs envelope stress response axis, previously suggested as the target of fluorouracil antibiofilm activity in E. coli. In contrast, 5-FC hampered the transcription of curli activators RpoS and stimulated the expression of Fis, a curli repressor affected by nucleotide availability. This last observation suggested a possible perturbation of the de novo pyrimidine biosynthesis by 5-FC: indeed, exposure to 5-FC resulted in a ca. 2-fold reduction of UMP intracellular levels while not affecting ATP. Consistently, expression of the de novo pyrimidine biosynthesis genes carB and pyrB was upregulated in the presence of 5-FC. Our results suggest that the antibiofilm activity of fluoropyrimidines is mediated, at least in part, by perturbation of the pyrimidine nucleotide pool. We screened a genome library in search of additional determinants able to counteract the effects of 5-FC. We found that a DNA fragment encoding the unknown protein D8B36_18,480 and the N-terminal domain of the penicillin-binding protein 1b (PBP1b), involved in peptidoglycan synthesis, could restore curli production in the presence of 5-FC. Deletion of the PBP1b-encoding gene mrcB, induced csgBAC transcription, while overexpression of the gene encoding the D8B36_18,480 protein obliterated its expression, possibly as part of a coordinated response in curli regulation with PBP1b. While the two proteins do not appear to be direct targets of 5-FC, their involvement in curli regulation suggests a connection between peptidoglycan biosynthesis and curli production, which might become even more relevant upon pyrimidine starvation and reduced availability of UDP-sugars needed in cell wall biosynthesis. Overall, our findings link the antibiofilm activity of fluoropyrimidines to the redirection of at least two global regulators (RpoS, Fis) by induction of pyrimidine starvation. This highlights the importance of the de novo pyrimidines biosynthesis pathway in controlling virulence mechanisms in different bacteria and makes the pathway a potential target for antivirulence strategies.
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Affiliation(s)
| | | | - Carlo Angeletti
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Italy
| | - Nadia Raffaelli
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Italy
| | - Paolo Landini
- Department of Biosciences, University of Milan, Milan, Italy
| | - Elio Rossi
- Department of Biosciences, University of Milan, Milan, Italy
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4
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Hernandez DM, Marzouk M, Cole M, Fortoul MC, Kethireddy SR, Contractor R, Islam H, Moulder T, Kalifa AR, Meneses EM, Mendoza MB, Thomas R, Masud S, Pubien S, Milanes P, Diaz-Tang G, Lopatkin AJ, Smith RP. Purine and pyrimidine synthesis differently affect the strength of the inoculum effect for aminoglycoside and β-lactam antibiotics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588696. [PMID: 38645041 PMCID: PMC11030397 DOI: 10.1101/2024.04.09.588696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The inoculum effect has been observed for nearly all antibiotics and bacterial species. However, explanations accounting for its occurrence and strength are lacking. We previously found that growth productivity, which captures the relationship between [ATP] and growth, can account for the strength of the inoculum effect for bactericidal antibiotics. However, the molecular pathway(s) underlying this relationship, and therefore determining the inoculum effect, remain undiscovered. We show that nucleotide synthesis can determine the relationship between [ATP] and growth, and thus the strength of inoculum effect in an antibiotic class-dependent manner. Specifically, and separate from activity through the tricarboxylic acid cycle, we find that transcriptional activity of genes involved in purine and pyrimidine synthesis can predict the strength of the inoculum effect for β-lactam and aminoglycosides antibiotics, respectively. Our work highlights the antibiotic class-specific effect of purine and pyrimidine synthesis on the severity of the inoculum effect and paves the way for intervention strategies to reduce the inoculum effect in the clinic.
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Affiliation(s)
- Daniella M. Hernandez
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Melissa Marzouk
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Madeline Cole
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Marla C. Fortoul
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Saipranavi Reddy Kethireddy
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Rehan Contractor
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Habibul Islam
- Department of Chemical Engineering, University of Rochester; Rochester, NY 14627; USA
| | - Trent Moulder
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Ariane R. Kalifa
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Estefania Marin Meneses
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Maximiliano Barbosa Mendoza
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Ruth Thomas
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Saad Masud
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Sheena Pubien
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Patricia Milanes
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Gabriela Diaz-Tang
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Allison J. Lopatkin
- Department of Chemical Engineering, University of Rochester; Rochester, NY 14627; USA
- Department of Microbiology and Immunology, University of Rochester Medical Center; Rochester, NY 14627; USA
- Department of Biomedical Engineering, University of Rochester Medical Center; Rochester, NY 14627; USA
| | - Robert P. Smith
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
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5
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Yin Y, Yu H, Wang X, Hu Q, Liu Z, Luo D, Yang X. Cytoophidia: a conserved yet promising mode of enzyme regulation in nucleotide metabolism. Mol Biol Rep 2024; 51:245. [PMID: 38300325 DOI: 10.1007/s11033-024-09208-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024]
Abstract
Nucleotide biosynthesis encompasses both de novo and salvage synthesis pathways, each characterized by significant material and procedural distinctions. Despite these differences, cells with elevated nucleotide demands exhibit a preference for the more intricate de novo synthesis pathway, intricately linked to modes of enzyme regulation. In this study, we primarily scrutinize the biological importance of a conserved yet promising mode of enzyme regulation in nucleotide metabolism-cytoophidia. Cytoophidia, comprising cytidine triphosphate synthase or inosine monophosphate dehydrogenase, is explored across diverse biological models, including yeasts, Drosophila, mice, and human cancer cell lines. Additionally, we delineate potential biomedical applications of cytoophidia. As our understanding of cytoophidia deepens, the roles of enzyme compartmentalization and polymerization in various biochemical processes will unveil, promising profound impacts on both research and the treatment of metabolism-related diseases.
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Affiliation(s)
- Yue Yin
- School of Queen Mary, Jiangxi Medical College, Nanchang University, Jiangxi, China
| | - Huanhuan Yu
- First School of Clinical Medicine, Jiangxi Medical College, Nanchang University, Jiangxi, China
| | - Xinyi Wang
- Thyroid Surgery Center, West China Hospital of Sichuan University, Chengdu, China
| | - Qiaohao Hu
- The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Jiangxi, China
| | - Zhuoqi Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Jiangxi Medical College, Nanchang University, Jiangxi, China
| | - Daya Luo
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Jiangxi Medical College, Nanchang University, Jiangxi, China.
| | - Xiaohong Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Jiangxi Medical College, Nanchang University, Jiangxi, China.
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Wang LL, Yin ZY, Xu Y, Deng MY, Zhang KM, Wang Q, Chen RP, Yu L. Responses of Bacillus sp. under Cu(II) stress in relation to extracellular polymeric substances and functional gene expression level. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27589-8. [PMID: 37195605 DOI: 10.1007/s11356-023-27589-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/08/2023] [Indexed: 05/18/2023]
Abstract
The production and composition of extracellular polymeric substances (EPS), as well as the EPS-related functional resistance genes and metabolic levels of Bacillus sp. under Cu(II) stress, were investigated. EPS production increased by 2.73 ± 0.29 times compared to the control when the strain was treated with 30 mg L-1 Cu(II). Specifically, the polysaccharide (PS) content in EPS increased by 2.26 ± 0.28 g CDW-1 and the PN/PS (protein/polysaccharide) ratio value increased by 3.18 ± 0.33 times under 30 mg L-1 Cu(II) compared to the control. The increased EPS secretion and higher PN/PS ratio in EPS strengthened the cells' ability to resist the toxic effect of Cu(II). Differential expression of functional genes under Cu(II) stress was revealed by Gene Ontology pathway enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. The enriched genes were most obviously upregulated in the UMP biosynthesis pathway, the pyrimidine metabolism pathway, and the TCS metabolism pathway. This indicates an enhancement of EPS regulation-related metabolic levels and their role as a defense mechanism for cells to adapt to Cu(II) stress. Additionally, seven copper resistance genes were upregulated while three were downregulated. The upregulated genes were related to the heavy metal resistance, while downregulated genes were related to cell differentiation, indicating that the strain had initiated an obvious resistance to Cu(II) despite its severe cell toxicity. These results provided a basis for promoting EPS-regulated associated functional genes and the application of gene-regulated bacteria in heavy metal-containing wastewater treatment.
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Affiliation(s)
- Ling-Ling Wang
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Zheng-Yan Yin
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Yun Xu
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Miao-Yu Deng
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Kai-Ming Zhang
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Quan Wang
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Rong-Ping Chen
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Lei Yu
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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7
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Guillín Y, Cáceres M, Stashenko EE, Hidalgo W, Ortiz C. Untargeted Metabolomics for Unraveling the Metabolic Changes in Planktonic and Sessile Cells of Salmonella Enteritidis ATCC 13076 after Treatment with Lippia origanoides Essential Oil. Antibiotics (Basel) 2023; 12:antibiotics12050899. [PMID: 37237802 DOI: 10.3390/antibiotics12050899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/03/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Nontyphoidal Salmonella species are one of the main bacterial causes of foodborne diseases, causing a public health problem. In addition, the ability to form biofilms, multiresistance to traditional drugs, and the absence of effective therapies against these microorganisms are some of the principal reasons for the increase in bacterial diseases. In this study, the anti-biofilm activity of twenty essential oils (EOs) on Salmonella enterica serovar Enteritidis ATCC 13076 was evaluated, as well as the metabolic changes caused by Lippia origanoides thymol chemotype EO (LOT-II) on planktonic and sessile cells. The anti-biofilm effect was evaluated by the crystal violet staining method, and cell viability was evaluated through the XTT method. The effect of EOs was observed by scanning electron microscopy (SEM) analysis. Untargeted metabolomics analyses were conducted to determine the effect of LOT-II EO on the cellular metabolome. LOT-II EO inhibited S. Enteritidis biofilm formation by more than 60%, without decreasing metabolic activity. Metabolic profile analysis identified changes in the modulation of metabolites in planktonic and sessile cells after LOT-II EO treatment. These changes showed alterations in different metabolic pathways, mainly in central carbon metabolism and nucleotide and amino acid metabolism. Finally, the possible mechanism of action of L. origanoides EO is proposed based on a metabolomics approach. Further studies are required to advance at the molecular level on the cellular targets affected by EOs, which are promising natural products for developing new therapeutic agents against Salmonella sp. strains.
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Affiliation(s)
- Yuliany Guillín
- Escuela de Biología, Universidad Industrial de Santander, Bucaramanga 680002, Colombia
| | - Marlon Cáceres
- Escuela de Medicina, Universidad Industrial de Santander, Bucaramanga 680002, Colombia
| | - Elena E Stashenko
- Center for Chromatography and Mass Spectrometry CROM-MASS, School of Chemistry, Universidad Industrial de Santander, Bucaramanga 680002, Colombia
| | - William Hidalgo
- Escuela de Química, Universidad Industrial de Santander, Bucaramanga 680002, Colombia
| | - Claudia Ortiz
- Escuela de Microbiología y Bioanálisis, Universidad Industrial de Santander, Bucaramanga 680002, Colombia
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8
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Comprehensive Study of Components and Antimicrobial Properties of Essential Oil Extracted from Carum carvi L. Seeds. Antibiotics (Basel) 2023; 12:antibiotics12030591. [PMID: 36978458 PMCID: PMC10045241 DOI: 10.3390/antibiotics12030591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/27/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Carum carvi L. belongs to the Apiaceae family and is widely used as a vegetable, food spice, preservative, and herbal medicine. This study investigated the impact of essential oil extracted from Carum carvi L. seeds (CEO) on methicillin-resistant Staphylococcus aureus (MRSA) and its possible action mechanism. The dominant chemical components of CEO determined by GC-MS were carvone and limonene. It was observed that CEO had a considerable inhibitory effect against the growth of planktonic bacteria and biofilm in MRSA cells. Untargeted metabolomics based on GC-Q-TOF-MS was used to analyze the possible mechanism of the interaction of MRSA with CEO. It was determined that there were 63 different metabolites based on fold change values greater than 1.5 or less than 1.5, p < 0.05, VIP > 1, which demonstrated amino acid metabolism in MRSA was significantly affected by CEO. In conclusion, CEO has a potent antimicrobial property and has promising potential for use in food and drugs.
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Lozano-Terol G, Gallego-Jara J, Sola-Martínez RA, Ortega Á, Martínez Vivancos A, Cánovas Díaz M, de Diego Puente T. Regulation of the pyrimidine biosynthetic pathway by lysine acetylation of E. coli OPRTase. FEBS J 2023; 290:442-464. [PMID: 35989594 PMCID: PMC10087573 DOI: 10.1111/febs.16598] [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: 02/21/2022] [Revised: 07/01/2022] [Accepted: 08/19/2022] [Indexed: 02/05/2023]
Abstract
The de novo pyrimidine biosynthesis pathway is an important route due to the relevance of its products, its implications in health and its conservation among organisms. Here, we investigated the regulation by lysine acetylation of this pathway. To this aim, intracellular and extracellular metabolites of the route were quantified, revealing a possible blockage of the pathway by acetylation of the OPRTase enzyme (orotate phosphoribosyltransferase). Chemical acetylation of OPRTase by acetyl-P involved a decrease in enzymatic activity. To test the effect of acetylation in this enzyme, K26 and K103 residues were selected to generate site-specific acetylated proteins. Several differences were observed in kinetic parameters, emphasizing that the kcat of these mutants showed a strong decrease of 300 and 150-fold for OPRTase-103AcK and 19 and 6.3-fold for OPRTase-26AcK, for forward and reverse reactions. In vivo studies suggested acetylation of this enzyme by a nonenzymatic acetyl-P-dependent mechanism and a reversion of this process by the CobB deacetylase. A complementation assay of a deficient strain in the pyrE gene with OPRTase-26AcK and OPRTase-103AcK was performed, and curli formation, stoichiometric parameters and orotate excretion were measured. Complementation with acetylated enzymes entailed a profile very similar to that of the ∆pyrE strain, especially in the case of complementation with OPRTase-103AcK. These results suggest regulation of the de novo pyrimidine biosynthesis pathway by lysine acetylation of OPRTase in Escherichia coli. This finding is of great relevance due to the essential role of this route and the OPRTase enzyme as a target for antimicrobial, antiviral and cancer treatments.
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Affiliation(s)
- Gema Lozano-Terol
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Rosa Alba Sola-Martínez
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Adrián Martínez Vivancos
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
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10
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Hou B, Wang CY, Li SW, Zhou LJ, Che YL, Chen QY. Effects of Toxin-Antitoxin System HicAB on Biofilm Formation by Extraintestinal Pathogenic E. coli. Curr Microbiol 2022; 80:50. [PMID: 36542185 DOI: 10.1007/s00284-022-03138-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022]
Abstract
The type II toxin-antitoxin (T-A) HicAB system is abundant in several bacteria and archaea, such as Escherichia coli, Burkholderia Pseudomallei, Yersinia pestis, Pseudomonas aeruginosa, and Streptococcus pneumoniae. This system engages in stress response, virulence, and bacterial persistence. This study showed that the biofilm-forming ability of the hicAB deletion mutant was significantly decreased to moderate ability compared to the extra-intestinal pathogenic Escherichia coli (ExPEC) parent strain and the complemented strain, which are strong biofilm producers. Congo red assay showed that the hicAB mutant maintained the ability to form curli fimbriae. Using RNA-seq and comparative real-time quantitative RT-PCR, we observed the difference in gene expression between the hicAB mutant and the parent strain, which was associated with biofilm formation. Our data indicate that the HicAB type II T-A system has a key role in biofilm formation by ExPEC, which may be associated with outer membrane protein (OMP) gene expression. Collectively, our results indicate that the hicAB type II T-A system is involved in ExPEC biofilm formation.
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Affiliation(s)
- Bo Hou
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Animal Disease Control Technology Development Center, Fujian Academy of Agricultural Sciences, No. 104 Xindian Town, Fuzhou, 350013, Fujian, China.
| | - Chen-Yan Wang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Animal Disease Control Technology Development Center, Fujian Academy of Agricultural Sciences, No. 104 Xindian Town, Fuzhou, 350013, Fujian, China
| | - Shao-Wen Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Lun-Jiang Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Animal Disease Control Technology Development Center, Fujian Academy of Agricultural Sciences, No. 104 Xindian Town, Fuzhou, 350013, Fujian, China.
| | - Yong-Liang Che
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Animal Disease Control Technology Development Center, Fujian Academy of Agricultural Sciences, No. 104 Xindian Town, Fuzhou, 350013, Fujian, China
| | - Qiu-Yong Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Animal Disease Control Technology Development Center, Fujian Academy of Agricultural Sciences, No. 104 Xindian Town, Fuzhou, 350013, Fujian, China
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11
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Sung K, Park M, Chon J, Kweon O, Khan SA, Shen A, Paredes A. Concentration-Dependent Global Quantitative Proteome Response of Staphylococcus epidermidis RP62A Biofilms to Subinhibitory Tigecycline. Cells 2022; 11:3488. [PMID: 36359886 PMCID: PMC9655631 DOI: 10.3390/cells11213488] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 07/21/2023] Open
Abstract
Staphylococcus epidermidis is a leading cause of biofilm-associated infections on implanted medical devices. During the treatment of an infection, bacterial cells inside biofilms may be exposed to sublethal concentrations of the antimicrobial agents. In the present study, the effect of subinhibitory concentrations of tigecycline (TC) on biofilms formed by S. epidermidis strain RP62A was investigated using a quantitative global proteomic technique. Sublethal concentrations of TC [1/8 (T1) and 1/4 minimum inhibitory concentration (MIC) (T2)] promoted biofilm production in strain RP62A, but 1/2 MIC TC (T3) significantly inhibited biofilm production. Overall, 413, 429, and 518 proteins were differentially expressed in biofilms grown with 1/8 (T1), 1/4 (T2), and 1/2 (T3) MIC of TC, respectively. As the TC concentration increased, the number of induced proteins in each Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway increased. The TC concentration dependence of the proteome response highlights the diverse mechanisms of adaptive responses in strain RP62A biofilms. In both COG and KEGG functional analyses, most upregulated proteins belong to the metabolism pathway, suggesting that it may play an important role in the defense of strain RP62A biofilm cells against TC stress. Sub-MIC TC treatment of strain RP62A biofilms led to significant changes of protein expression related to biofilm formation, antimicrobial resistance, virulence, quorum sensing, ABC transporters, protein export, purine/pyrimidine biosynthesis, ribosomes, and essential proteins. Interestingly, in addition to tetracycline resistance, proteins involved in resistance of various antibiotics, including aminoglycosides, antimicrobial peptides, β-lactams, erythromycin, fluoroquinolones, fusidic acid, glycopeptides, lipopeptides, mupirocin, rifampicin and trimethoprim were differentially expressed. Our study demonstrates that global protein expression profiling of biofilm cells to antibiotic pressure may improve our understanding of the mechanisms of antibiotic resistance in biofilms.
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Affiliation(s)
- Kidon Sung
- Division of Microbiology, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
| | - Miseon Park
- Division of Microbiology, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
| | - Jungwhan Chon
- Companion Animal Health, Inje University, Gimhae 50834, Korea
| | - Ohgew Kweon
- Division of Microbiology, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
| | - Saeed A. Khan
- Division of Microbiology, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
| | - Andrew Shen
- Division of Neurotoxicology, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
| | - Angel Paredes
- Office of Scientific Coordination, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
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12
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Revealing novel synergistic defense and acid tolerant performance of Escherichia coli in response to organic acid stimulation. Appl Microbiol Biotechnol 2022; 106:7577-7594. [DOI: 10.1007/s00253-022-12241-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
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13
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The Effect of E. coli Uridine-Cytidine Kinase Gene Deletion on Cytidine Synthesis and Transcriptome Analysis. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8110586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cytidine is an antiviral and anticancer drug intermediate, its primary method of manufacture being fermentation. Uridine-cytidine kinase (UCK) catalyzes the reverse process of phosphorylation of cytidine to produce cytidylic acid, which influences cytidine accumulation in the Escherichia coli cytidine biosynthesis pathway. The cytidine-producing strain E. coli NXBG-11 was used as the starting strain in this work; the udk gene coding UCK was knocked out of the chromosomal genome using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology. The mutant strain E. coli NXBG-12 was obtained; its transcriptomics were studied to see how udk gene deletion affected cytidine synthesis and cell-wide transcription. The mutant strain E. coli NXBG-12 generated 1.28 times more cytidine than the original strain E. coli NXBG-11 after 40 h of shake-flask fermentation at 37 °C. The udk gene was knocked out, and transcriptome analysis showed that there were 1168 differentially expressed genes between the mutant and original strains, 559 upregulated genes and 609 downregulated genes. It was primarily shown that udk gene knockout has a positive impact on the cytidine synthesis network because genes involved in cytidine synthesis were significantly upregulated (p < 0.05) and genes related to the cytidine precursor PRPP and cofactor NADPH were upregulated in the PPP and TCA pathways. These results principally demonstrate that udk gene deletion has a favorable impact on the cytidine synthesis network. The continual improvement of cytidine synthesis and metasynthesis is made possible by this information, which is also useful for further converting microorganisms that produce cytidine.
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14
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Liu Y, Su S, Yu M, Zhai D, Hou Y, Zhao H, Ma X, Jia M, Xue X, Li M. Pyrancoumarin derivative LP4C targeting of pyrimidine de novo synthesis pathway inhibits MRSA biofilm and virulence. Front Pharmacol 2022; 13:959736. [PMID: 36147327 PMCID: PMC9486200 DOI: 10.3389/fphar.2022.959736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/03/2022] [Indexed: 11/28/2022] Open
Abstract
Staphylococcus aureus poses a serious public health threat because of its multidrug resistance and biofilm formation ability. Hence, developing novel anti-biofilm agents and finding targets are needed to mitigate the proliferation of drug-resistant pathogens. In our previous study, we showed that the pyrancoumarin derivative 2-amino-4-(2,6-dichlorophenyl)-3-cyano-5-oxo-4H, 5H- pyrano [3,2c] chromene (LP4C) can destroy the biofilm of methicillin-resistant S. aureus (MRSA) in vitro and in vivo. Here, we further explored the possible mechanism of LP4C as a potential anti-biofilm drug. We found that LP4C inhibits the expression of enzymes involved in the de novo pyrimidine pathway and attenuates the virulence of MRSA USA300 strain without affecting the agr or luxS quorum sensing system. The molecular docking results indicated that LP4C forms interactions with the key amino acid residues of pyrR protein, which functions as the important regulator of bacterial pyrimidine synthesis. These findings reveal that pyrancoumarin derivative LP4C inhibits MRSA biofilm formation and targeting pyrimidine de novo synthesis pathway.
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Affiliation(s)
- Yongsheng Liu
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medical of the State Administration of Traditional Chinese Medicine, School of Pharmacy, The Fourth Military Medical University, Xi’an, China
| | - Shan Su
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medical of the State Administration of Traditional Chinese Medicine, School of Pharmacy, The Fourth Military Medical University, Xi’an, China
| | - Moxi Yu
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medical of the State Administration of Traditional Chinese Medicine, School of Pharmacy, The Fourth Military Medical University, Xi’an, China
| | - Dongshen Zhai
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medical of the State Administration of Traditional Chinese Medicine, School of Pharmacy, The Fourth Military Medical University, Xi’an, China
| | - Yachen Hou
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medical of the State Administration of Traditional Chinese Medicine, School of Pharmacy, The Fourth Military Medical University, Xi’an, China
| | - Hui Zhao
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medical of the State Administration of Traditional Chinese Medicine, School of Pharmacy, The Fourth Military Medical University, Xi’an, China
| | - Xue Ma
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medical of the State Administration of Traditional Chinese Medicine, School of Pharmacy, The Fourth Military Medical University, Xi’an, China
| | - Min Jia
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medical of the State Administration of Traditional Chinese Medicine, School of Pharmacy, The Fourth Military Medical University, Xi’an, China
| | - Xiaoyan Xue
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medical of the State Administration of Traditional Chinese Medicine, School of Pharmacy, The Fourth Military Medical University, Xi’an, China
- *Correspondence: Mingkai Li, ; Xiaoyan Xue,
| | - Mingkai Li
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medical of the State Administration of Traditional Chinese Medicine, School of Pharmacy, The Fourth Military Medical University, Xi’an, China
- Precision Pharmacy and Drug Development Center, The Fourth Military Medical University, Xi’an, China
- *Correspondence: Mingkai Li, ; Xiaoyan Xue,
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15
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Xu N, Li L, Chen F. Construction of gene modification system with highly efficient and markerless for Monascus ruber M7. Front Microbiol 2022; 13:952323. [PMID: 35979480 PMCID: PMC9376451 DOI: 10.3389/fmicb.2022.952323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022] Open
Abstract
Monascus spp. are traditional medicinal and edible filamentous fungi in China, and can produce various secondary metabolites, such as Monascus pigments (MPs) and citrinin (CIT). Genetic modification methods, such as gene knock-out, complementation, and overexpression, have been used extensively to investigate the function of related genes in Monascus spp.. However, the resistance selection genes that can have been used for genetic modification in Monascus spp. are limited, and the gene replacement frequency (GRF) is usually <5%. Therefore, we are committed to construct a highly efficient gene editing system without resistance selection marker gene. In this study, using M. ruber M7 as the starting strain, we successfully constructed a so-called markerlessly and highly genetic modification system including the mutants ΔmrpyrGΔmrlig4 and ΔmrpyrGΔmrlig4::mrpyrG, in which we used the endogenous gene mrpyrG from M. ruber M7 instead of the resistance marker gene as the screening marker, and simultaneously deleted mrlig4 related to non-homologous end joining in M. ruber M7. Then, the morphology, the growth rate, the production of MPs and CIT of the mutants were analyzed. And the results show that the mutant strains have normal mycelia, cleistothecia and conidia on PDA+Uridine(U) plate, the biomass of each mutant is also no different from M. ruber M7. However, the U addition also has a certain effect on the orange and red pigments yield of M. ruber M7, which needs our further study. Finally, we applied the system to delete multiple genes from M. ruber M7 separately or continuously without any resistance marker gene, and found that the average GRF of ΔmrpyrGΔmrlig4 was about 18 times of that of M. ruber M7. The markerlessly and highly genetic modification system constructed in current study not only will be used for multi-gene simultaneous modification in Monascus spp., and also lays a foundation for investigating the effects of multi-genes modification on Monascus spp..
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Affiliation(s)
- Na Xu
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Li Li
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, Hubei Engineering University, Xiaogan, China
- College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - Fusheng Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Fusheng Chen
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16
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Inactivation of the Pyrimidine Biosynthesis pyrD Gene Negatively Affects Biofilm Formation and Virulence Determinants in the Crohn’s Disease-Associated Adherent Invasive Escherichia coli LF82 Strain. Microorganisms 2022; 10:microorganisms10030537. [PMID: 35336113 PMCID: PMC8956108 DOI: 10.3390/microorganisms10030537] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/17/2022] [Accepted: 02/26/2022] [Indexed: 01/07/2023] Open
Abstract
In Crohn’s disease (CD) patients, the adherent-invasive Escherichia coli (AIEC) pathovar contributes to the chronic inflammation typical of the disease via its ability to invade gut epithelial cells and to survive in macrophages. We show that, in the AIEC strain LF82, inactivation of the pyrD gene, encoding dihydroorotate dehydrogenase (DHOD), an enzyme of the de novo pyrimidine biosynthetic pathway, completely abolished its ability of to grow in a macrophage environment-mimicking culture medium. In addition, pyrD inactivation reduced flagellar motility and strongly affected biofilm formation by downregulating transcription of both type 1 fimbriae and curli subunit genes. Thus, the pyrD gene appears to be essential for several cellular processes involved in AIEC virulence. Interestingly, vidofludimus (VF), a DHOD inhibitor, has been proposed as an effective drug in CD treatment. Despite displaying a potentially similar binding mode for both human and E. coli DHOD in computational molecular docking experiments, VF showed no activity on either growth or virulence-related processes in LF82. Altogether, our results suggest that the crucial role played by the pyrD gene in AIEC virulence, and the presence of structural differences between E. coli and human DHOD allowing for the design of specific inhibitors, make E. coli DHOD a promising target for therapeutical strategies aiming at counteracting chronic inflammation in CD by acting selectively on its bacterial triggers.
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17
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Wang TY, Guo R, Hu LL, Liu JJ, Lu HT. Mass Spectrometry-Based Targeted Metabolomics Revealed the Regulatory Roles of Magnesium on Biofilm Formation in Escherichia coli by Targeting Functional Metabolites. JOURNAL OF ANALYSIS AND TESTING 2022. [DOI: 10.1007/s41664-021-00208-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Duggal Y, Kurasz JE, Fontaine BM, Marotta NJ, Chauhan SS, Karls AC, Weinert EE. Cellular Effects of 2',3'-Cyclic Nucleotide Monophosphates in Gram-Negative Bacteria. J Bacteriol 2022; 204:e0020821. [PMID: 34662237 PMCID: PMC8765455 DOI: 10.1128/jb.00208-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022] Open
Abstract
Organismal adaptations to environmental stimuli are governed by intracellular signaling molecules such as nucleotide second messengers. Recent studies have identified functional roles for the noncanonical 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) in both eukaryotes and prokaryotes. In Escherichia coli, 2',3'-cNMPs are produced by RNase I-catalyzed RNA degradation, and these cyclic nucleotides modulate biofilm formation through unknown mechanisms. The present work dissects cellular processes in E. coli and Salmonella enterica serovar Typhimurium that are modulated by 2',3'-cNMPs through the development of cell-permeable 2',3'-cNMP analogs and a 2',3'-cyclic nucleotide phosphodiesterase. Utilization of these chemical and enzymatic tools, in conjunction with phenotypic and transcriptomic investigations, identified pathways regulated by 2',3'-cNMPs, including flagellar motility and biofilm formation, and by oligoribonucleotides with 3'-terminal 2',3'-cyclic phosphates, including responses to cellular stress. Furthermore, interrogation of metabolomic and organismal databases has identified 2',3'-cNMPs in numerous organisms and homologs of the E. coli metabolic proteins that are involved in key eukaryotic pathways. Thus, the present work provides key insights into the roles of these understudied facets of nucleotide metabolism and signaling in prokaryotic physiology and suggest broad roles for 2',3'-cNMPs among bacteria and eukaryotes. IMPORTANCE Bacteria adapt to environmental challenges by producing intracellular signaling molecules that control downstream pathways and alter cellular processes for survival. Nucleotide second messengers serve to transduce extracellular signals and regulate a wide array of intracellular pathways. Recently, 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) were identified as contributing to the regulation of cellular pathways in eukaryotes and prokaryotes. In this study, we define previously unknown cell processes that are affected by fluctuating 2',3'-cNMP levels or RNA oligomers with 2',3'-cyclic phosphate termini in E. coli and Salmonella Typhimurium, providing a framework for studying novel signaling networks in prokaryotes. Furthermore, we utilize metabolomics databases to identify additional prokaryotic and eukaryotic species that generate 2',3'-cNMPs as a resource for future studies.
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Affiliation(s)
- Yashasvika Duggal
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA
| | | | | | - Nick J. Marotta
- Molecular, Cellular and Integrative Biosciences Program, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Shikha S. Chauhan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Anna C. Karls
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Emily E. Weinert
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
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19
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Chen Q, Yang X, Meng Q, Zhao L, Yuan Y, Chi W, He L, Shi K, Liu S. Integrative multiomics analysis of the acid stress response of Oenococcus oeni mutants at different growth stages. Food Microbiol 2021; 102:103905. [PMID: 34809937 DOI: 10.1016/j.fm.2021.103905] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Acid stress is one of the most important environmental stresses that adversely affect the growth of lactic acid bacteria (LAB), such as Oenococcus oeni which was isolated from grape-berries and mainly used in wine fermentation. The aim of this paper is to comprehensively characterize the mechanisms of acid stress regulation in O. oeni and to provide a viable theoretical basis for breed and improvement of existing LAB. METHOD First, six O. oeni mutants with acid-sensitive (strains b2, a1, c2) and acid-tolerant (strains b1, a3, c1) phenotypes were screened from three wild-type O. oeni, and then their genome (sequencing), transcriptome and metabolome (LC-MS/MS) were examined. RESULTS A total of 459 genes were identified with one or more intragenic single nucleotide polymorphisms (SNPs) in these mutants, and were extensively involved in metabolism and cellular functions with a high mutation rates in purine (46%) and pyrimidine (48%) metabolic pathways. There were 210 mutated genes that cause significant changes in expression levels. In addition, 446 differentially accumulated metabolites were detected, and they were consistently detected at relatively high levels in the acid-tolerant O. oeni mutant. The levels of intracellular differentially expressed genes and differential metabolites changed with increasing culture time. CONCLUSION The integrative pathways analysis showed that the intracellular response associated with acid regulation differed significantly between acid-sensitive and acid-tolerant O. oeni mutants, and also changed at different growth stages.
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Affiliation(s)
- Qiling Chen
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Xiangke Yang
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; Henan University of Animal Husbandry and Economy, Zhenzhou, Henan, China
| | - Qiang Meng
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Lili Zhao
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuxin Yuan
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Wei Chi
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ling He
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Kan Shi
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station of, Northwest A&F University, Yongning, Ningxia, 750104, China.
| | - Shuwen Liu
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station of, Northwest A&F University, Yongning, Ningxia, 750104, China.
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20
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Holden ER, Yasir M, Turner AK, Wain J, Charles IG, Webber MA. Massively parallel transposon mutagenesis identifies temporally essential genes for biofilm formation in Escherichia coli. Microb Genom 2021; 7. [PMID: 34783647 PMCID: PMC8743551 DOI: 10.1099/mgen.0.000673] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Biofilms complete a life cycle where cells aggregate, grow and produce a structured community before dispersing to colonize new environments. Progression through this life cycle requires temporally controlled gene expression to maximize fitness at each stage. Previous studies have largely focused on identifying genes essential for the formation of a mature biofilm; here, we present an insight into the genes involved at different stages of biofilm formation. We used TraDIS-Xpress, a massively parallel transposon mutagenesis approach using transposon-located promoters to assay the impact of disruption or altered expression of all genes in the genome on biofilm formation. We identified 48 genes that affected the fitness of cells growing in a biofilm, including genes with known roles and those not previously implicated in biofilm formation. Regulation of type 1 fimbriae and motility were important at all time points, adhesion and motility were important for the early biofilm, whereas matrix production and purine biosynthesis were only important as the biofilm matured. We found strong temporal contributions to biofilm fitness for some genes, including some where expression changed between being beneficial or detrimental depending on the stage at which they are expressed, including dksA and dsbA. Novel genes implicated in biofilm formation included zapE and truA involved in cell division, maoP in chromosome organization, and yigZ and ykgJ of unknown function. This work provides new insights into the requirements for successful biofilm formation through the biofilm life cycle and demonstrates the importance of understanding expression and fitness through time.
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Affiliation(s)
- Emma R Holden
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK
| | - Muhammad Yasir
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK
| | - A Keith Turner
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK
| | - John Wain
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK.,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Ian G Charles
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK.,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK.,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
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21
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Cheng F, Mo Y, Chen K, Shang X, Yang Z, Hao B, Shang R, Liang J, Liu Y. Integration of metabolomics and transcriptomics indicates changes in MRSA exposed to terpinen-4-ol. BMC Microbiol 2021; 21:305. [PMID: 34736405 PMCID: PMC8566654 DOI: 10.1186/s12866-021-02348-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 10/08/2021] [Indexed: 12/15/2022] Open
Abstract
Background This study investigated the effects of terpinen-4-ol on methicillin-resistant Staphylococcus aureus (MRSA) and its biofilm, and the possible mechanisms governing this effect. Results We observed that terpinen-4-ol has good antibacterial activity and inhibits the formation of MRSA biofilm. The MIC and MBC values for terpinen-4-ol against S. aureus were 0.08% ~ 0.32%. And terpinen-4-ol at 0.32% could kill all bacteria and clear all biofilms. Untargeted metabolomic and transcriptomic analyses showed that terpinen-4-ol strongly inhibited DNA and RNA biosynthesis in MRSA at 2 h after treatment by affecting genes and metabolites related to purine and pyrimidine metabolic pathways. Some differential genes which play important roles in DNA synthesis and the production of eDNA from biofilm exposed to terpinen-4-ol was also significantly decreased compared with that of the control. Conclusions Terpinen-4-ol has good antibacterial activity and significantly inhibits the formation of MRSA biofilm by inhibiting purine and pyrimidine metabolism.
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Affiliation(s)
- Feng Cheng
- Key Laboratory of New Animal Drug Project, Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, 730050, Lanzhou, People's Republic of China
| | - Yanan Mo
- Key Laboratory of New Animal Drug Project, Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, 730050, Lanzhou, People's Republic of China
| | - Keyuan Chen
- Key Laboratory of New Animal Drug Project, Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, 730050, Lanzhou, People's Republic of China
| | - Xiaofei Shang
- Key Laboratory of New Animal Drug Project, Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, 730050, Lanzhou, People's Republic of China
| | - Zhen Yang
- Key Laboratory of New Animal Drug Project, Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, 730050, Lanzhou, People's Republic of China
| | - Baocheng Hao
- Key Laboratory of New Animal Drug Project, Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, 730050, Lanzhou, People's Republic of China
| | - Ruofeng Shang
- Key Laboratory of New Animal Drug Project, Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, 730050, Lanzhou, People's Republic of China
| | | | - Yu Liu
- Key Laboratory of New Animal Drug Project, Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, 730050, Lanzhou, People's Republic of China.
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22
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Genome-Scale Metabolic Models and Machine Learning Reveal Genetic Determinants of Antibiotic Resistance in Escherichia coli and Unravel the Underlying Metabolic Adaptation Mechanisms. mSystems 2021; 6:e0091320. [PMID: 34342537 PMCID: PMC8409726 DOI: 10.1128/msystems.00913-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Antimicrobial resistance (AMR) is becoming one of the largest threats to public health worldwide, with the opportunistic pathogen Escherichia coli playing a major role in the AMR global health crisis. Unravelling the complex interplay between drug resistance and metabolic rewiring is key to understand the ability of bacteria to adapt to new treatments and to the development of new effective solutions to combat resistant infections. We developed a computational pipeline that combines machine learning with genome-scale metabolic models (GSMs) to elucidate the systemic relationships between genetic determinants of resistance and metabolism beyond annotated drug resistance genes. Our approach was used to identify genetic determinants of 12 AMR profiles for the opportunistic pathogenic bacterium E. coli. Then, to interpret the large number of identified genetic determinants, we applied a constraint-based approach using the GSM to predict the effects of genetic changes on growth, metabolite yields, and reaction fluxes. Our computational platform leads to multiple results. First, our approach corroborates 225 known AMR-conferring genes, 35 of which are known for the specific antibiotic. Second, integration with the GSM predicted 20 top-ranked genetic determinants (including accA, metK, fabD, fabG, murG, lptG, mraY, folP, and glmM) essential for growth, while a further 17 top-ranked genetic determinants linked AMR to auxotrophic behavior. Third, clusters of AMR-conferring genes affecting similar metabolic processes are revealed, which strongly suggested that metabolic adaptations in cell wall, energy, iron and nucleotide metabolism are associated with AMR. The computational solution can be used to study other human and animal pathogens. IMPORTANCEEscherichia coli is a major public health concern given its increasing level of antibiotic resistance worldwide and extraordinary capacity to acquire and spread resistance via horizontal gene transfer with surrounding species and via mutations in its existing genome. E. coli also exhibits a large amount of metabolic pathway redundancy, which promotes resistance via metabolic adaptability. In this study, we developed a computational approach that integrates machine learning with metabolic modeling to understand the correlation between AMR and metabolic adaptation mechanisms in this model bacterium. Using our approach, we identified AMR genetic determinants associated with cell wall modifications for increased permeability, virulence factor manipulation of host immunity, reduction of oxidative stress toxicity, and changes to energy metabolism. Unravelling the complex interplay between antibiotic resistance and metabolic rewiring may open new opportunities to understand the ability of E. coli, and potentially of other human and animal pathogens, to adapt to new treatments.
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Vasicek EM, O'Neal L, Parsek MR, Fitch J, White P, Gunn JS. L-Arabinose Transport and Metabolism in Salmonella Influences Biofilm Formation. Front Cell Infect Microbiol 2021; 11:698146. [PMID: 34368016 PMCID: PMC8341724 DOI: 10.3389/fcimb.2021.698146] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/21/2021] [Indexed: 11/28/2022] Open
Abstract
L-arabinose inducible promoters are commonly used in gene expression analysis. However, nutrient source and availability also play a role in biofilm formation; therefore, L-arabinose metabolism could impact biofilm development. In this study we examined the impact of L-arabinose on Salmonella enterica serovar Typhimurium (S. Typhimurium) biofilm formation. Using mutants impaired for the transport and metabolism of L-arabinose, we showed that L-arabinose metabolism negatively impacts S. Typhimurium biofilm formation in vitro. When L-arabinose metabolism is abrogated, biofilm formation returned to baseline levels. However, without the ability to import extracellular L-arabinose, biofilm formation significantly increased. Using RNA-Seq we identified several gene families involved in these different phenotypes including curli expression, amino acid synthesis, and L-arabinose metabolism. Several individual candidate genes were tested for their involvement in the L-arabinose-mediated biofilm phenotypes, but most played no significant role. Interestingly, in the presence of L-arabinose the diguanylate cyclase gene adrA was downregulated in wild type S. Typhimurium. Meanwhile cyaA, encoding an adenylate cyclase, was downregulated in an L-arabinose transport mutant. Using an IPTG-inducible plasmid to deplete c-di-GMP via vieA expression, we were able to abolish the increased biofilm phenotype seen in the transport mutant. However, the mechanism by which the L-arabinose import mutant forms significantly larger biofilms remains to be determined. Regardless, these data suggest that L-arabinose metabolism influences intracellular c-di-GMP levels and therefore biofilm formation. These findings are important when considering the use of an L-arabinose inducible promoter in biofilm conditions.
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Affiliation(s)
- Erin M Vasicek
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Lindsey O'Neal
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - James Fitch
- The Institute for Genomic Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
| | - Peter White
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States.,The Institute for Genomic Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
| | - John S Gunn
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
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24
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Kirchhoff L, Dittmer S, Weisner AK, Buer J, Rath PM, Steinmann J. Antibiofilm activity of antifungal drugs, including the novel drug olorofim, against Lomentospora prolificans. J Antimicrob Chemother 2021; 75:2133-2140. [PMID: 32386411 DOI: 10.1093/jac/dkaa157] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/12/2020] [Accepted: 03/23/2020] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Patients with immunodeficiency or cystic fibrosis frequently suffer from respiratory fungal infections. In particular, biofilm-associated fungi cause refractory infection manifestations, linked to increased resistance to anti-infective agents. One emerging filamentous fungus is Lomentospora prolificans. Here, the biofilm-formation capabilities of L. prolificans isolates were investigated and the susceptibility of biofilms to various antifungal agents was analysed. METHODS Biofilm formation of L. prolificans (n = 11) was estimated by crystal violet stain and antibiofilm activity was additionally determined via detection of metabolically active biofilm using an XTT assay. Amphotericin B, micafungin, voriconazole and olorofim were compared with regard to their antibiofilm effects when added prior to adhesion, after adhesion and on mature and preformed fungal biofilms. Imaging via confocal laser scanning microscopy was carried out to demonstrate the effect of drug treatment on the fungal biofilm. RESULTS Antibiofilm activities of the tested antifungal agents were shown to be most effective on adherent cells whilst mature biofilm was the most resistant. The most promising antibiofilm effects were detected with voriconazole and olorofim. Olorofim showed an average minimum biofilm eradication concentration (MBEC) of 0.06 mg/L, when added prior to and after adhesion. The MBECs of voriconazole were ≤4 mg/L. On mature biofilm the MBECs of olorofim and voriconazole were higher than the previously determined MICs against planktonic cultures. In contrast, amphotericin B and especially micafungin did not exhibit sufficient antibiofilm activity against L. prolificans. CONCLUSIONS To our knowledge, this is the first study demonstrating the antibiofilm potential of olorofim against the human pathogenic fungus L. prolificans.
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Affiliation(s)
- Lisa Kirchhoff
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Silke Dittmer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ann-Kathrin Weisner
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Joerg Steinmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Klinikum Nürnberg, Paracelsus Medical University, Nuremberg, Germany
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25
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Gray J, Chandry PS, Kaur M, Kocharunchitt C, Fanning S, Bowman JP, Fox EM. Colonisation dynamics of Listeria monocytogenes strains isolated from food production environments. Sci Rep 2021; 11:12195. [PMID: 34108547 PMCID: PMC8190317 DOI: 10.1038/s41598-021-91503-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/06/2021] [Indexed: 12/19/2022] Open
Abstract
Listeria monocytogenes is a ubiquitous bacterium capable of colonising and persisting within food production environments (FPEs) for many years, even decades. This ability to colonise, survive and persist within the FPEs can result in food product cross-contamination, including vulnerable products such as ready to eat food items. Various environmental and genetic elements are purported to be involved, with the ability to form biofilms being an important factor. In this study we examined various mechanisms which can influence colonisation in FPEs. The ability of isolates (n = 52) to attach and grow in biofilm was assessed, distinguishing slower biofilm formers from isolates forming biofilm more rapidly. These isolates were further assessed to determine if growth rate, exopolymeric substance production and/or the agr signalling propeptide influenced these dynamics and could promote persistence in conditions reflective of FPE. Despite no strong association with the above factors to a rapid colonisation phenotype, the global transcriptome suggested transport, energy production and metabolism genes were widely upregulated during the initial colonisation stages under nutrient limited conditions. However, the upregulation of the metabolism systems varied between isolates supporting the idea that L. monocytogenes ability to colonise the FPEs is strain-specific.
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Affiliation(s)
- Jessica Gray
- CSIRO Agriculture and Food, Werribee, VIC, Australia. .,Food Safety Centre, Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Hobart, TAS, Australia.
| | | | - Mandeep Kaur
- Biosciences and Food Technology, School of Science, RMIT University, Melbourne, VIC, Australia
| | - Chawalit Kocharunchitt
- Food Safety Centre, Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Hobart, TAS, Australia
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, D04 N2E5, Ireland.,Institute for Global Food Security, Queen's University Belfast, Chlorine Gardens, Belfast, BT5 6AG, UK
| | - John P Bowman
- Food Safety Centre, Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Hobart, TAS, Australia
| | - Edward M Fox
- CSIRO Agriculture and Food, Werribee, VIC, Australia. .,Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK.
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26
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Gough EK, Edens TJ, Geum HM, Baharmand I, Gill SK, Robertson RC, Mutasa K, Ntozini R, Smith LE, Chasekwa B, Majo FD, Tavengwa NV, Mutasa B, Francis F, Carr L, Tome J, Stoltzfus RJ, Moulton LH, Prendergast AJ, Humphrey JH, Manges AR, Team SHINET. Maternal fecal microbiome predicts gestational age, birth weight and neonatal growth in rural Zimbabwe. EBioMedicine 2021; 68:103421. [PMID: 34139432 PMCID: PMC8217692 DOI: 10.1016/j.ebiom.2021.103421] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Preterm birth and low birth weight (LBW) affect one in ten and one in seven livebirths, respectively, primarily in low-income and middle-income countries (LMIC) and are major predictors of poor child health outcomes. However, both have been recalcitrant to public health intervention. The maternal intestinal microbiome may undergo substantial changes during pregnancy and may influence fetal and neonatal health in LMIC populations. METHODS Within a subgroup of 207 mothers and infants enrolled in the SHINE trial in rural Zimbabwe, we performed shotgun metagenomics on 351 fecal specimens provided during pregnancy and at 1-month post-partum to investigate the relationship between the pregnancy gut microbiome and infant gestational age, birth weight, 1-month length-, and weight-for-age z-scores using extreme gradient boosting machines. FINDINGS Pregnancy gut microbiome taxa and metabolic functions predicted birth weight and WAZ at 1 month more accurately than gestational age and LAZ. Blastoscystis sp, Brachyspira sp and Treponeme carriage were high compared to Western populations. Resistant starch-degraders were important predictors of birth outcomes. Microbiome capacity for environmental sensing, vitamin B metabolism, and signalling predicted increased infant birth weight and neonatal growth; while functions involved in biofilm formation in response to nutrient starvation predicted reduced birth weight and growth. INTERPRETATION The pregnancy gut microbiome in rural Zimbabwe is characterized by resistant starch-degraders and may be an important metabolic target to improve birth weight. FUNDING Bill and Melinda Gates Foundation, UK Department for International Development, Wellcome Trust, Swiss Agency for Development and Cooperation, US National Institutes of Health, and UNICEF.
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Affiliation(s)
- Ethan K. Gough
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Thaddeus J. Edens
- Devil's Staircase Consulting, West Vancouver, British Columbia, Canada
| | - Hyun Min Geum
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Iman Baharmand
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Sandeep K. Gill
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | | | - Kuda Mutasa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Robert Ntozini
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Laura E Smith
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
- Department of Population Medicine and Diagnostics, Cornell University, Ithaca, NY, USA
| | - Bernard Chasekwa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Florence D. Majo
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Naume V. Tavengwa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Batsirai Mutasa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Freddy Francis
- Department of Experimental Medicine, University of British Columbia, Canada
| | - Lynnea Carr
- Department of Microbiology and Immunology, University of British Columbia, Canada
| | - Joice Tome
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | | | - Lawrence H. Moulton
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew J. Prendergast
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Blizard Institute, Queen Mary University of London, London, UK
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Jean H. Humphrey
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Blizard Institute, Queen Mary University of London, London, UK
| | - Amee R. Manges
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - SHINE Trial Team
- Members of the SHINE Trial team who are not named authors are listed in https://academic.oup.com/cid/article/61/suppl_7/S685/358186
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27
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Blaschke U, Skiebe E, Wilharm G. Novel Genes Required for Surface-Associated Motility in Acinetobacter baumannii. Curr Microbiol 2021; 78:1509-1528. [PMID: 33666749 PMCID: PMC7997844 DOI: 10.1007/s00284-021-02407-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 02/10/2021] [Indexed: 01/28/2023]
Abstract
Acinetobacter baumannii is an opportunistic and increasingly multi-drug resistant human pathogen rated as a critical priority one pathogen for the development of new antibiotics by the WHO in 2017. Despite the lack of flagella, A. baumannii can move along wet surfaces in two different ways: via twitching motility and surface-associated motility. While twitching motility is known to depend on type IV pili, the mechanism of surface-associated motility is poorly understood. In this study, we established a library of 30 A. baumannii ATCC® 17978™ mutants that displayed deficiency in surface-associated motility. By making use of natural competence, we also introduced these mutations into strain 29D2 to differentiate strain-specific versus species-specific effects of mutations. Mutated genes were associated with purine/pyrimidine/folate biosynthesis (e.g. purH, purF, purM, purE), alarmone/stress metabolism (e.g. Ap4A hydrolase), RNA modification/regulation (e.g. methionyl-tRNA synthetase), outer membrane proteins (e.g. ompA), and genes involved in natural competence (comEC). All tested mutants originally identified as motility-deficient in strain ATCC® 17978™ also displayed a motility-deficient phenotype in 29D2. By contrast, further comparative characterization of the mutant sets of both strains regarding pellicle biofilm formation, antibiotic resistance, and virulence in the Galleria mellonella infection model revealed numerous strain-specific mutant phenotypes. Our studies highlight the need for comparative analyses to characterize gene functions in A. baumannii and for further studies on the mechanisms underlying surface-associated motility.
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Affiliation(s)
- Ulrike Blaschke
- Robert Koch Institute, Project group P2, Burgstr. 37, 38855, Wernigerode, Germany.
| | - Evelyn Skiebe
- Robert Koch Institute, Project group P2, Burgstr. 37, 38855, Wernigerode, Germany
| | - Gottfried Wilharm
- Robert Koch Institute, Project group P2, Burgstr. 37, 38855, Wernigerode, Germany.
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28
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Orellana CA, Zaragoza NE, Licona-Cassani C, Palfreyman RW, Cowie N, Moonen G, Moutafis G, Power J, Nielsen LK, Marcellin E. Time-course transcriptomics reveals that amino acids catabolism plays a key role in toxinogenesis and morphology in Clostridium tetani. ACTA ACUST UNITED AC 2020; 47:1059-1073. [DOI: 10.1007/s10295-020-02330-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 11/02/2020] [Indexed: 10/23/2022]
Abstract
Abstract
Tetanus is a fatal disease caused by Clostridium tetani infections. To prevent infections, a toxoid vaccine, developed almost a century ago, is routinely used in humans and animals. The vaccine is listed in the World Health Organisation list of Essential Medicines and can be produced and administered very cheaply in the developing world for less than one US Dollar per dose. Recent developments in both analytical tools and frameworks for systems biology provide industry with an opportunity to gain a deeper understanding of the parameters that determine C. tetani virulence and physiological behaviour in bioreactors. Here, we compared a traditional fermentation process with a fermentation medium supplemented with five heavily consumed amino acids. The experiment demonstrated that amino acid catabolism plays a key role in the virulence of C. tetani. The addition of the five amino acids favoured growth, decreased toxin production and changed C. tetani morphology. Using time-course transcriptomics, we created a “fermentation map”, which shows that the tetanus toxin transcriptional regulator BotR, P21 and the tetanus toxin gene was downregulated. Moreover, this in-depth analysis revealed potential genes that might be involved in C. tetani virulence regulation. We observed differential expression of genes related to cell separation, surface/cell adhesion, pyrimidine biosynthesis and salvage, flagellar motility, and prophage genes. Overall, the fermentation map shows that, mediated by free amino acid concentrations, virulence in C. tetani is regulated at the transcriptional level and affects a plethora of metabolic functions.
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Affiliation(s)
- Camila A Orellana
- grid.1003.2 0000 0000 9320 7537 Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland 4072 Brisbane QLD Australia
- grid.7870.8 0000 0001 2157 0406 Department of Chemical and Bioprocess Engineering, School of Engineering Pontificia Universidad Católica de Chile Santiago Chile
| | - Nicolas E Zaragoza
- grid.1003.2 0000 0000 9320 7537 Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland 4072 Brisbane QLD Australia
| | - Cuauhtemoc Licona-Cassani
- grid.1003.2 0000 0000 9320 7537 Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland 4072 Brisbane QLD Australia
- grid.419886.a 0000 0001 2203 4701 Centro de Biotecnología FEMSA Tecnológico de Monterrey Nuevo León Mexico
| | - Robin W Palfreyman
- grid.1003.2 0000 0000 9320 7537 Metabolomics Australia The University of Queensland 4072 Brisbane QLD Australia
| | - Nicholas Cowie
- grid.1003.2 0000 0000 9320 7537 Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland 4072 Brisbane QLD Australia
| | - Glenn Moonen
- Zoetis. 45 Poplar Road 3052 Parkville VIC Australia
| | | | - John Power
- Zoetis. 45 Poplar Road 3052 Parkville VIC Australia
| | - Lars K Nielsen
- grid.1003.2 0000 0000 9320 7537 Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland 4072 Brisbane QLD Australia
- grid.1003.2 0000 0000 9320 7537 Metabolomics Australia The University of Queensland 4072 Brisbane QLD Australia
- grid.5170.3 0000 0001 2181 8870 The Novo Nordisk Foundation Centre for Biosustainability Technical University of Denmark Kgs. Lyngby Denmark
| | - Esteban Marcellin
- grid.1003.2 0000 0000 9320 7537 Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland 4072 Brisbane QLD Australia
- grid.1003.2 0000 0000 9320 7537 Metabolomics Australia The University of Queensland 4072 Brisbane QLD Australia
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29
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Cepas V, Ballén V, Gabasa Y, Ramírez M, López Y, Soto SM. Transposon Insertion in the purL Gene Induces Biofilm Depletion in Escherichia coli ATCC 25922. Pathogens 2020; 9:pathogens9090774. [PMID: 32971800 PMCID: PMC7558270 DOI: 10.3390/pathogens9090774] [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: 08/07/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 12/20/2022] Open
Abstract
Current Escherichia coli antibiofilm treatments comprise a combination of antibiotics commonly used against planktonic cells, leading to treatment failure. A better understanding of the genes involved in biofilm formation could facilitate the development of efficient and specific new antibiofilm treatments. A total of 2578 E. coli mutants were generated by transposon insertion, of which 536 were analysed in this study. After sequencing, Tn263 mutant, classified as low biofilm-former (LF) compared to the wild-type (wt) strain (ATCC 25922), showed an interruption in the purL gene, involved in the de novo purine biosynthesis pathway. To elucidate the role of purL in biofilm formation, a knockout was generated showing reduced production of curli fibres, leading to an impaired biofilm formation. These conditions were restored by complementation of the strain or addition of exogenous inosine. Proteomic and transcriptional analyses were performed to characterise the differences caused by purL alterations. Thirteen proteins were altered compared to wt. The corresponding genes were analysed by qRT-PCR not only in the Tn263 and wt, but also in clinical strains with different biofilm activity. Overall, this study suggests that purL is essential for biofilm formation in E. coli and can be considered as a potential antibiofilm target.
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30
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Rai AK, Panda M, Das AK, Rahman T, Das R, Das K, Sarma A, Kataki AC, Chattopadhyay I. Dysbiosis of salivary microbiome and cytokines influence oral squamous cell carcinoma through inflammation. Arch Microbiol 2020; 203:137-152. [PMID: 32783067 DOI: 10.1007/s00203-020-02011-w] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/23/2020] [Accepted: 08/03/2020] [Indexed: 01/10/2023]
Abstract
Advanced combinatorial treatments of surgery, chemotherapy, and radiotherapy do not have any effect on the enhancement of a 5-year survival rate of oral squamous cell carcinoma (OSCC). The discovery of early diagnostic non-invasive biomarkers is required to improve the survival rate of OSCC patients. Recently, it has been reported that oral microbiome has a significant contribution to the development of OSCC. Oral microbiome induces inflammatory response through the production of cytokines and chemokines that enhances tumor cell proliferation and survival. The study aims to develop saliva-based oral microbiome and cytokine biomarker panel that screen OSCC patients based on the level of the microbiome and cytokine differences. We compared the oral microbiome signatures and cytokine level in the saliva of OSCC patients and healthy individuals by 16S rRNA gene sequencing targeting the V3/V4 region using the MiSeq platform and cytokine assay, respectively. The higher abundance of Prevotella melaninogenica, Fusobacterium sp., Veillonella parvula, Porphyromonas endodontalis, Prevotella pallens, Dialister, Streptococcus anginosus, Prevotella nigrescens, Campylobacter ureolyticus, Prevotella nanceiensis, Peptostreptococcus anaerobius and significant elevation of IL-8, IL-6, TNF-α, GM-CSF, and IFN-γ in the saliva of patients having OSCC. Oncobacteria such as S. anginosus, V. parvula, P. endodontalis, and P. anaerobius may contribute to the development of OSCC by increasing inflammation via increased expression of inflammatory cytokines such as IL-6, IL-8, TNF-α, IFN-γ, and GM-CSF. These oncobacteria and cytokines panels could potentially be used as a non-invasive biomarker in clinical practice for more efficient screening and early detection of OSCC patients.
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Affiliation(s)
- Avdhesh Kumar Rai
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 16, India
| | - Madhusmita Panda
- Department of Life Sciences, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610101, India
| | - Ashok Kumar Das
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 16, India
| | - Tashnin Rahman
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 16, India
| | - Rajjyoti Das
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 16, India
| | - Kishore Das
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 16, India
| | - Anupam Sarma
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 16, India
| | - Amal Ch Kataki
- Dr. B. Borooah Cancer Institute, A. K. Azad Road, Gopinath Nagar, Guwahati, Assam, 16, India
| | - Indranil Chattopadhyay
- Department of Life Sciences, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610101, India.
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31
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Duggal Y, Fontaine BM, Dailey DM, Ning G, Weinert EE. RNase I Modulates Escherichia coli Motility, Metabolism, and Resistance. ACS Chem Biol 2020; 15:1996-2004. [PMID: 32551492 DOI: 10.1021/acschembio.0c00390] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacteria are constantly adapting to their environment by sensing extracellular factors that trigger production of intracellular signaling molecules, known as second messengers. Recently, 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) were identified in Escherichia coli and have emerged as possible novel signaling molecules. 2',3'-cNMPs are produced through endonucleolytic cleavage of short RNAs by the T2 endoribonuclease, RNase I; however, the physiological roles of RNase I remain unclear. Our transcriptomic analysis suggests that RNase I is involved in modulating numerous cellular processes, including nucleotide metabolism, motility, acid sensitivity, metal homeostasis, and outer membrane morphology. Through a combination of deletion strain and inhibitor studies, we demonstrate that RNase I plays a previously unknown role in E. coli stress resistance by affecting pathways that are part of the defense mechanisms employed by bacteria when introduced to external threats, including antibiotics. Thus, this work provides insight into the emerging roles of RNase I in bacterial signaling and physiology and highlights the potential of RNase I as a target for antibacterial adjuvants.
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Affiliation(s)
- Yashasvika Duggal
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Benjamin M. Fontaine
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Deanna M. Dailey
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Gang Ning
- Microscopy Facility, Huck Institute of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Emily E. Weinert
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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32
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Characterization and transcriptomic basis of biofilm formation by Lactobacillus plantarum J26 isolated from traditional fermented dairy products. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109333] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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33
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Yang K, Li Z. Multistep construction of metabolically engineered Escherichia coli for enhanced cytidine biosynthesis. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2019.107433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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34
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Capo F, Wilson A, Di Cara F. The Intestine of Drosophila melanogaster: An Emerging Versatile Model System to Study Intestinal Epithelial Homeostasis and Host-Microbial Interactions in Humans. Microorganisms 2019; 7:microorganisms7090336. [PMID: 31505811 PMCID: PMC6780840 DOI: 10.3390/microorganisms7090336] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/16/2019] [Accepted: 09/03/2019] [Indexed: 12/31/2022] Open
Abstract
In all metazoans, the intestinal tract is an essential organ to integrate nutritional signaling, hormonal cues and immunometabolic networks. The dysregulation of intestinal epithelium functions can impact organism physiology and, in humans, leads to devastating and complex diseases, such as inflammatory bowel diseases, intestinal cancers, and obesity. Two decades ago, the discovery of an immune response in the intestine of the genetic model system, Drosophila melanogaster, sparked interest in using this model organism to dissect the mechanisms that govern gut (patho) physiology in humans. In 2007, the finding of the intestinal stem cell lineage, followed by the development of tools available for its manipulation in vivo, helped to elucidate the structural organization and functions of the fly intestine and its similarity with mammalian gastrointestinal systems. To date, studies of the Drosophila gut have already helped to shed light on a broad range of biological questions regarding stem cells and their niches, interorgan communication, immunity and immunometabolism, making the Drosophila a promising model organism for human enteric studies. This review summarizes our current knowledge of the structure and functions of the Drosophila melanogaster intestine, asserting its validity as an emerging model system to study gut physiology, regeneration, immune defenses and host-microbiota interactions.
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Affiliation(s)
- Florence Capo
- Department of Microbiology and Immunology, IWK Research Centre, Dalhousie University, 5850/5980 University Avenue, Halifax, NS B3K 6R8, Canada.
| | - Alexa Wilson
- Department of Microbiology and Immunology, IWK Research Centre, Dalhousie University, 5850/5980 University Avenue, Halifax, NS B3K 6R8, Canada.
| | - Francesca Di Cara
- Department of Microbiology and Immunology, IWK Research Centre, Dalhousie University, 5850/5980 University Avenue, Halifax, NS B3K 6R8, Canada.
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35
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Bottagisio M, Soggiu A, Piras C, Bidossi A, Greco V, Pieroni L, Bonizzi L, Roncada P, Lovati AB. Proteomic Analysis Reveals a Biofilm-Like Behavior of Planktonic Aggregates of Staphylococcus epidermidis Grown Under Environmental Pressure/Stress. Front Microbiol 2019; 10:1909. [PMID: 31551940 PMCID: PMC6743020 DOI: 10.3389/fmicb.2019.01909] [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: 02/05/2019] [Accepted: 08/05/2019] [Indexed: 01/14/2023] Open
Abstract
Prosthetic joint replacement failure has a huge impact on quality of life and hospitalization costs. A leading cause of prosthetic joint infection is bacteria-forming biofilm on the surface of orthopedic devices. Staphylococcus epidermidis is an emergent, low-virulence pathogen implicated in chronic infections, barely indistinguishable from aseptic loosening when embedded in a mature matrix. The literature on the behavior of quiescent S. epidermidis in mature biofilms is scarce. To fill this gap, we performed comparative analysis of the whole proteomic profiles of two methicillin-resistant S. epidermidis strains growing in planktonic and in sessile form to investigate the molecular mechanisms underlying biofilm stability. After 72-h culture of biofilm-forming S. epidermidis, overexpression of proteins involved in the synthesis of nucleoside triphosphate and polysaccharides was observed, whereas planktonic bacteria expressed proteins linked to stress and anaerobic growth. Cytological analysis was performed to determine why planktonic bacteria unexpectedly expressed proteins typical of sessile culture. Images evidenced that prolonged culture under vigorous agitation can create a stressful growing environment that triggers microorganism aggregation in a biofilm-like matrix as a mechanism to survive harsh conditions. The choice of a unique late time point provided an important clue for future investigations into the biofilm-like behavior of planktonic cells. Our preliminary results may inform comparative proteomic strategies in the study of mature bacterial biofilm. Finally, there is an increasing number of studies on the aggregation of free-floating bacteria embedded in an extracellular matrix, prompting the need to gain further insight into this mode of bacterial growth.
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Affiliation(s)
- Marta Bottagisio
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Clinical Chemistry and Microbiology, Milan, Italy
| | - Alessio Soggiu
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
| | - Cristian Piras
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
| | - Alessandro Bidossi
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Clinical Chemistry and Microbiology, Milan, Italy
| | - Viviana Greco
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore Roma, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Luisa Pieroni
- Proteomics and Metabonomics Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Luigi Bonizzi
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
| | - Paola Roncada
- Department of Health Sciences, Università degli Studi "Magna Græcia", Catanzaro, Italy
| | - Arianna B Lovati
- IRCCS Istituto Ortopedico Galeazzi, Cell and Tissue Engineering Laboratory, Milan, Italy
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Fontaine BM, Duggal Y, Weinert EE. Exploring the Links between Nucleotide Signaling and Quorum Sensing Pathways in Regulating Bacterial Virulence. ACS Infect Dis 2018; 4:1645-1655. [PMID: 30381948 DOI: 10.1021/acsinfecdis.8b00255] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The survival of all organisms depends on implementation of appropriate phenotypic responses upon perception of relevant environmental stimuli. Sensory inputs are propagated via interconnected biochemical and/or electrical cascades mediated by diverse signaling molecules, including gases, metal cations, lipids, peptides, and nucleotides. These networks often comprise second messenger signaling systems in which a ligand (the primary messenger) binds to an extracellular receptor, thereby altering the intracellular concentration of a second messenger molecule which ultimately modulates gene expression through interaction with various effectors. The identification of intersections of these signaling pathways, such as nucleotide second messengers and quorum sensing, provides new insights into the mechanisms by which bacteria use multiple inputs to regulate cellular metabolism and phenotypes. Further investigations of the overlap between bacterial signaling pathways may yield new targets and methods to control bacterial behavior, such as biofilm formation and virulence.
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Affiliation(s)
- Benjamin M. Fontaine
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Yashasvika Duggal
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Emily E. Weinert
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
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37
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Di Sante L, Pugnaloni A, Biavasco F, Giovanetti E, Vignaroli C. Multicellular behavior of environmental Escherichia coli isolates grown under nutrient-poor and low-temperature conditions. Microbiol Res 2018; 210:43-50. [DOI: 10.1016/j.micres.2018.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/20/2018] [Accepted: 03/10/2018] [Indexed: 11/26/2022]
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38
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Fontaine BM, Martin KS, Garcia-Rodriguez JM, Jung C, Briggs L, Southwell JE, Jia X, Weinert EE. RNase I regulates Escherichia coli 2',3'-cyclic nucleotide monophosphate levels and biofilm formation. Biochem J 2018; 475:1491-1506. [PMID: 29555843 PMCID: PMC6452634 DOI: 10.1042/bcj20170906] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/13/2018] [Accepted: 03/16/2018] [Indexed: 12/15/2022]
Abstract
Regulation of nucleotide and nucleoside concentrations is critical for faithful DNA replication, transcription, and translation in all organisms, and has been linked to bacterial biofilm formation. Unusual 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) recently were quantified in mammalian systems, and previous reports have linked these nucleotides to cellular stress and damage in eukaryotes, suggesting an intriguing connection with nucleotide/nucleoside pools and/or cyclic nucleotide signaling. This work reports the first quantification of 2',3'-cNMPs in Escherichia coli and demonstrates that 2',3'-cNMP levels in E. coli are generated specifically from RNase I-catalyzed RNA degradation, presumably as part of a previously unidentified nucleotide salvage pathway. Furthermore, RNase I and 2',3'-cNMP levels are demonstrated to play an important role in controlling biofilm formation. This work identifies a physiological role for cytoplasmic RNase I and constitutes the first progress toward elucidating the biological functions of bacterial 2',3'-cNMPs.
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Affiliation(s)
- Benjamin M. Fontaine
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Kevin S. Martin
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | | | - Claire Jung
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Laura Briggs
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Jessica E. Southwell
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Xin Jia
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Emily E. Weinert
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
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39
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Nagar SD, Aggarwal B, Joon S, Bhatnagar R, Bhatnagar S. A Network Biology Approach to Decipher Stress Response in Bacteria Using Escherichia coli As a Model. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 20:310-24. [PMID: 27195968 DOI: 10.1089/omi.2016.0028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The development of drug-resistant pathogenic bacteria poses challenges to global health for their treatment and control. In this context, stress response enables bacterial populations to survive extreme perturbations in the environment but remains poorly understood. Specific modules are activated for unique stressors with few recognized global regulators. The phenomenon of cross-stress protection strongly suggests the presence of central proteins that control the diverse stress responses. In this work, Escherichia coli was used to model the bacterial stress response. A Protein-Protein Interaction Network was generated by integrating differentially expressed genes in eight stress conditions of pH, temperature, and antibiotics with relevant gene ontology terms. Topological analysis identified 24 central proteins. The well-documented role of 16 central proteins in stress indicates central control of the response, while the remaining eight proteins may have a novel role in stress response. Cluster analysis of the generated network implicated RNA binding, flagellar assembly, ABC transporters, and DNA repair as important processes during response to stress. Pathway analysis showed crosstalk of Two Component Systems with metabolic processes, oxidative phosphorylation, and ABC transporters. The results were further validated by analysis of an independent cross-stress protection dataset. This study also reports on the ways in which bacterial stress response can progress to biofilm formation. In conclusion, we suggest that drug targets or pathways disrupting bacterial stress responses can potentially be exploited to combat antibiotic tolerance and multidrug resistance in the future.
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Affiliation(s)
- Shashwat Deepali Nagar
- 1 Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology , New Delhi, India
| | - Bhavye Aggarwal
- 1 Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology , New Delhi, India
| | - Shikha Joon
- 1 Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology , New Delhi, India .,2 Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University , New Delhi, India
| | - Rakesh Bhatnagar
- 2 Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University , New Delhi, India
| | - Sonika Bhatnagar
- 1 Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology , New Delhi, India
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40
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Carvalho SM, Kloosterman TG, Manzoor I, Caldas J, Vinga S, Martinussen J, Saraiva LM, Kuipers OP, Neves AR. Interplay Between Capsule Expression and Uracil Metabolism in Streptococcus pneumoniae D39. Front Microbiol 2018; 9:321. [PMID: 29599757 PMCID: PMC5863508 DOI: 10.3389/fmicb.2018.00321] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/09/2018] [Indexed: 11/13/2022] Open
Abstract
Pyrimidine nucleotides play an important role in the biosynthesis of activated nucleotide sugars (NDP-sugars). NDP-sugars are the precursors of structural polysaccharides in bacteria, including capsule, which is a major virulence factor of the human pathogen S. pneumoniae. In this work, we identified a spontaneous non-reversible mutant of strain D39 that displayed a non-producing capsule phenotype. Whole-genome sequencing analysis of this mutant revealed several non-synonymous single base modifications, including in genes of the de novo synthesis of pyrimidines and in the -10 box of capsule operon promoter (Pcps). By directed mutagenesis we showed that the point mutation in Pcps was solely responsible for the drastic decrease in capsule expression. We also demonstrated that D39 subjected to uracil deprivation shows increased biomass and decreased Pcps activity and capsule amounts. Importantly, Pcps expression is further decreased by mutating the first gene of the de novo synthesis of pyrimidines, carA. In contrast, the absence of uracil from the culture medium showed no effect on the spontaneous mutant strain. Co-cultivation of the wild-type and the mutant strain indicated a competitive advantage of the spontaneous mutant (non-producing capsule) in medium devoid of uracil. We propose a model in that uracil may act as a signal for the production of different capsule amounts in S. pneumoniae.
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Affiliation(s)
- Sandra M Carvalho
- Instituto de Tecnologia Química e Biológica NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Tomas G Kloosterman
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Irfan Manzoor
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - José Caldas
- Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal
| | - Susana Vinga
- IDMEC, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Jan Martinussen
- DTU Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lígia M Saraiva
- Instituto de Tecnologia Química e Biológica NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Ana R Neves
- Instituto de Tecnologia Química e Biológica NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
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41
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The Production of Curli Amyloid Fibers Is Deeply Integrated into the Biology of Escherichia coli. Biomolecules 2017; 7:biom7040075. [PMID: 29088115 PMCID: PMC5745457 DOI: 10.3390/biom7040075] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/13/2017] [Accepted: 10/23/2017] [Indexed: 12/29/2022] Open
Abstract
Curli amyloid fibers are the major protein component of the extracellular matrix produced by Enterobacteriaceae during biofilm formation. Curli are required for proper biofilm development and environmental persistence by Escherichia coli. Here, we present a complete and vetted genetic analysis of functional amyloid fiber biogenesis. The Keio collection of single gene deletions was screened on Congo red indicator plates to identify E. coli mutants that had defective amyloid production. We discovered that more than three hundred gene products modulated curli production. These genes were involved in fundamental cellular processes such as regulation, environmental sensing, respiration, metabolism, cell envelope biogenesis, transport, and protein turnover. The alternative sigma factors, σS and σE, had opposing roles in curli production. Mutations that induced the σE or Cpx stress response systems had reduced curli production, while mutant strains with increased σS levels had increased curli production. Mutations in metabolic pathways, including gluconeogenesis and the biosynthesis of lipopolysaccharide (LPS), produced less curli. Regulation of the master biofilm regulator, CsgD, was diverse, and the screen revealed several proteins and small RNAs (sRNA) that regulate csgD messenger RNA (mRNA) levels. Using previously published studies, we found minimal overlap between the genes affecting curli biogenesis and genes known to impact swimming or swarming motility, underlying the distinction between motile and sessile lifestyles. Collectively, the diversity and number of elements required suggest curli production is part of a highly regulated and complex developmental pathway in E. coli.
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42
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Yang HJ, Bogomolnaya L, McClelland M, Andrews-Polymenis H. De novo pyrimidine synthesis is necessary for intestinal colonization of Salmonella Typhimurium in chicks. PLoS One 2017; 12:e0183751. [PMID: 29040285 PMCID: PMC5644981 DOI: 10.1371/journal.pone.0183751] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/10/2017] [Indexed: 11/18/2022] Open
Abstract
pyrE (STM3733) encodes orotate phosphoribosyltransferase (OPRTase; EC 2.4.2.10), the fifth enzyme of the de novo pyrimidine biosynthetic pathway. We identified a ΔpyrE mutant as under selection in screening of a Salmonella mutant library in 4-day old chicks. Here, we confirm that a ΔpyrE mutant colonizes 4-day old chicks poorly in competitive infection with isogenic wild type, and that the ability of this mutant to colonize chicks could be restored by providing a copy of pyrE in trans. We further show that our ΔpyrE mutant grows poorly in nutrient poor conditions in vitro, and that the ability of this mutant to grow is restored, both in vitro and in chicks, when precursors to the pyrimidine salvage pathway were provided. This finding suggests that the environment in the chick intestine during our infections lacks sufficient precursors of the pyrimidine salvage pathway to support Salmonella growth. Finally, we show that the colonization defect of a ΔpyrE mutant during infection occurs in to chicks, but not in CBA/J mice or ligated ileal loops in calves. Our data suggest that de novo pyrimidine synthesis is necessary for colonization of Salmonella Typhimurium in the chick, and that the salvage pathway is not used in this niche.
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Affiliation(s)
- Hee-Jeong Yang
- Department of Microbial and Molecular Pathogenesis, College of Medicine, Texas A&M University System Health Science Center, Bryan, TX, United States of America
| | - Lydia Bogomolnaya
- Department of Microbial and Molecular Pathogenesis, College of Medicine, Texas A&M University System Health Science Center, Bryan, TX, United States of America
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, and Pathology and Laboratory Medicine, University of California, Irvine, CA, United States of America
| | - Helene Andrews-Polymenis
- Department of Microbial and Molecular Pathogenesis, College of Medicine, Texas A&M University System Health Science Center, Bryan, TX, United States of America
- * E-mail:
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43
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Rossi E, Motta S, Aliverti A, Cossu F, Gourlay L, Mauri P, Landini P. Cellulose production is coupled to sensing of the pyrimidine biosynthetic pathway via c-di-GMP production by the DgcQ protein of Escherichia coli. Environ Microbiol 2017; 19:4551-4563. [PMID: 28892259 DOI: 10.1111/1462-2920.13918] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 08/18/2017] [Accepted: 08/26/2017] [Indexed: 01/28/2023]
Abstract
Production of cellulose, a stress response-mediated process in enterobacteria, is modulated in Escherichia coli by the activity of the two pyrimidine nucleotide biosynthetic pathways, namely, the de novo biosynthetic pathway and the salvage pathway, which relies on the environmental availability of pyrimidine nitrogenous bases. We had previously reported that prevalence of the salvage over the de novo pathway triggers cellulose production via synthesis of the second messenger c-di-GMP by the DgcQ (YedQ) diguanylate cyclase. In this work, we show that DgcQ enzymatic activity is enhanced by UTP, whilst being inhibited by N-carbamoyl-aspartate, an intermediate of the de novo pathway. Thus, direct allosteric control by these ligands allows full DgcQ activity exclusively in cells actively synthesizing pyrimidine nucleotides via the salvage pathway. Inhibition of DgcQ activity by N-carbamoyl-aspartate appears to be favoured by protein-protein interaction between DgcQ and PyrB, a subunit of aspartate transcarbamylase, which synthesizes N-carbamoyl-aspartate. Our results suggest that availability of pyrimidine bases might be sensed, somehow paradoxically, as an environmental stress by E. coli. We hypothesize that this link might have evolved since stress events, leading to extensive DNA/RNA degradation or lysis of neighbouring cells, can result in increased pyrimidine concentrations and activation of the salvage pathway.
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Affiliation(s)
- Elio Rossi
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Sara Motta
- Institute of Biomedical Technologies, National Research Council, Milan, Segrate, Italy
| | | | - Federica Cossu
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Louise Gourlay
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Pierluigi Mauri
- Institute of Biomedical Technologies, National Research Council, Milan, Segrate, Italy
| | - Paolo Landini
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
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44
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Yssel AEJ, Vanderleyden J, Steenackers HP. Repurposing of nucleoside- and nucleobase-derivative drugs as antibiotics and biofilm inhibitors. J Antimicrob Chemother 2017; 72:2156-2170. [DOI: 10.1093/jac/dkx151] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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45
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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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46
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Hur J, Özgür A, He Y. Ontology-based literature mining of E. coli vaccine-associated gene interaction networks. J Biomed Semantics 2017; 8:12. [PMID: 28288685 PMCID: PMC5348867 DOI: 10.1186/s13326-017-0122-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 03/03/2017] [Indexed: 12/21/2022] Open
Abstract
Background Pathogenic Escherichia coli infections cause various diseases in humans and many animal species. However, with extensive E. coli vaccine research, we are still unable to fully protect ourselves against E. coli infections. To more rational development of effective and safe E. coli vaccine, it is important to better understand E. coli vaccine-associated gene interaction networks. Methods In this study, we first extended the Vaccine Ontology (VO) to semantically represent various E. coli vaccines and genes used in the vaccine development. We also normalized E. coli gene names compiled from the annotations of various E. coli strains using a pan-genome-based annotation strategy. The Interaction Network Ontology (INO) includes a hierarchy of various interaction-related keywords useful for literature mining. Using VO, INO, and normalized E. coli gene names, we applied an ontology-based SciMiner literature mining strategy to mine all PubMed abstracts and retrieve E. coli vaccine-associated E. coli gene interactions. Four centrality metrics (i.e., degree, eigenvector, closeness, and betweenness) were calculated for identifying highly ranked genes and interaction types. Results Using vaccine-related PubMed abstracts, our study identified 11,350 sentences that contain 88 unique INO interactions types and 1,781 unique E. coli genes. Each sentence contained at least one interaction type and two unique E. coli genes. An E. coli gene interaction network of genes and INO interaction types was created. From this big network, a sub-network consisting of 5 E. coli vaccine genes, including carA, carB, fimH, fepA, and vat, and 62 other E. coli genes, and 25 INO interaction types was identified. While many interaction types represent direct interactions between two indicated genes, our study has also shown that many of these retrieved interaction types are indirect in that the two genes participated in the specified interaction process in a required but indirect process. Our centrality analysis of these gene interaction networks identified top ranked E. coli genes and 6 INO interaction types (e.g., regulation and gene expression). Conclusions Vaccine-related E. coli gene-gene interaction network was constructed using ontology-based literature mining strategy, which identified important E. coli vaccine genes and their interactions with other genes through specific interaction types. Electronic supplementary material The online version of this article (doi:10.1186/s13326-017-0122-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Junguk Hur
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58202, USA.
| | - Arzucan Özgür
- Department of Computer Engineering, Bogazici University, Istanbul, 34342, Turkey
| | - Yongqun He
- Department of Microbiology and Immunology, Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA. .,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA. .,Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA. .,Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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Longo F, Motta S, Mauri P, Landini P, Rossi E. Interplay of the modified nucleotide phosphoadenosine 5'-phosphosulfate (PAPS) with global regulatory proteins in Escherichia coli: modulation of cyclic AMP (cAMP)-dependent gene expression and interaction with the HupA regulatory protein. Chem Biol Interact 2016; 259:39-47. [PMID: 27091548 DOI: 10.1016/j.cbi.2016.04.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 03/31/2016] [Accepted: 04/11/2016] [Indexed: 11/17/2022]
Abstract
In the bacterium Escherichia coli, some intermediates of the sulfate assimilation and cysteine biosynthesis pathway can act as signal molecules and modulate gene expression. In addition to sensing and utilization of sulphur sources, these signaling mechanisms also impact more global cell processes, such as resistance to antimicrobial agents and biofilm formation. In a recent work, we have shown that inactivation of the cysH gene, encoding phosphoadenosine-phosphosulfate (PAPS) reductase, and the consequent increase in intracellular PAPS concentration, strongly affect production of several cell surface-associated structures, enhancing surface adhesion and cell aggregation. In order to identify the molecular mechanism relaying intracellular PAPS concentration to regulation of cell surface-associated structures, we looked for mutations able to suppress the effects of cysH inactivation. We found that mutations in the adenylate cyclase-encoding cyaA gene abolished the effects of PAPS accumulation; consistent with this result, cyclic AMP (cAMP)-dependent gene expression appears to be increased in the cysH mutant. Experiments aimed at the direct identification of proteins interacting with either CysC or CysH, i.e. the PAPS-related proteins APS kinase and PAPS reductase, allowed us to identify several regulators, namely, CspC, CspE, HNS and HupA. Protein-protein interaction between HupA and CysH was confirmed by a bacterial two hybrid system, and inactivation of the hupA gene enhanced the effects of the cysH mutation in terms of production of cell surface-associated factors. Our results indicate that PAPS can modulate different regulatory systems, providing evidence that this molecule acts as a global signal molecule in E. coli.
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Affiliation(s)
- Francesca Longo
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy.
| | - Sara Motta
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20090, Segrate, Milan, Italy.
| | - Pierluigi Mauri
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20090, Segrate, Milan, Italy.
| | - Paolo Landini
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy.
| | - Elio Rossi
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy.
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Surekha K, Prabhu D, Richard M, Nachiappan M, Biswal J, Jeyakanthan J. Investigation of vital pathogenic target orotate phosphoribosyltransferases (OPRTase) from Thermus thermophilus HB8: Phylogenetic and molecular modeling approach. Gene 2016; 583:102-111. [PMID: 26861612 DOI: 10.1016/j.gene.2016.02.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 01/16/2016] [Accepted: 02/05/2016] [Indexed: 01/28/2023]
Abstract
Biosynthesis pathways of pyrimidine and purine are shown to play an important role in regular cellular activities. The biosynthesis can occur either through de novo or salvage pathways based on the requirement of the cell. The pyrimidine biosynthesis pathway has been linked to several disorders and various autoimmune diseases. Orotate phosphoribosyl transferase (OPRTase) is an important enzyme which catalyzes the conversion of orotate to orotate monophosphate in the fifth step of pyrimidine biosynthesis. Phylogenetic analysis of 228 OPRTase sequences shows the distribution of proteins across different living forms of life. High structural similarities between Thermusthermophilus and other organisms kindled us to concentrate on OPRTase as an anti-pathogenic target. In this study, a homology model of OPRTase was constructed using 2P1Z as a template. About 100 ns molecular dynamics simulation was performed to investigate the conformational stability and dynamic patterns of the protein. The amino acid residues (Met1, Asp2, Glu43, Ala44, Glu47, Lys51, Ala157 and Leu158) lining in the binding site were predicted using SiteMap. Further, structure based virtual screening was performed on the predicted binding site using ChemBridge, Asinex, Binding, NCI, TosLab and Zinc databases. Compounds retrieved from the screening collections were manually clustered. The resultant protein-ligand complexes were subjected to molecular dynamics simulations, which further validates the binding modes of the hits. The study may provide better insight for designing potent anti-pathogenic agent.
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Affiliation(s)
- Kanagarajan Surekha
- Room No. 402, Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Science Campus, Karaikudi 630004, India
| | - Damodharan Prabhu
- Room No. 402, Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Science Campus, Karaikudi 630004, India
| | - Mariadasse Richard
- Room No. 402, Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Science Campus, Karaikudi 630004, India
| | - Mutharasappan Nachiappan
- Room No. 402, Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Science Campus, Karaikudi 630004, India
| | - Jayashree Biswal
- Room No. 402, Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Science Campus, Karaikudi 630004, India
| | - Jeyaraman Jeyakanthan
- Room No. 402, Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Science Campus, Karaikudi 630004, India.
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Guo Q, Wei Y, Xia B, Jin Y, Liu C, Pan X, Shi J, Zhu F, Li J, Qian L, Liu X, Cheng Z, Jin S, Lin J, Wu W. Identification of a small molecule that simultaneously suppresses virulence and antibiotic resistance of Pseudomonas aeruginosa. Sci Rep 2016; 6:19141. [PMID: 26751736 PMCID: PMC4707474 DOI: 10.1038/srep19141] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 12/07/2015] [Indexed: 12/20/2022] Open
Abstract
The rising antibiotic resistance of bacteria imposes a severe threat on human health. Inhibition of bacterial virulence is an alternative approach to develop new antimicrobials. Molecules targeting antibiotic resistant enzymes have been used in combination with cognate antibiotics. It might be ideal that a molecule can simultaneously suppress virulence factors and antibiotic resistance. Here we combined genetic and computer-aided inhibitor screening to search for such molecules against the bacterial pathogen Pseudomonas aeruginosa. To identify target proteins that control both virulence and antibiotic resistance, we screened for mutants with defective cytotoxicity and biofilm formation from 93 transposon insertion mutants previously reported with increased antibiotic susceptibility. A pyrD mutant displayed defects in cytotoxicity, biofilm formation, quorum sensing and virulence in an acute mouse pneumonia model. Next, we employed a computer-aided screening to identify potential inhibitors of the PyrD protein, a dihydroorotate dehydrogenase (DHODase) involved in pyrimidine biosynthesis. One of the predicted inhibitors was able to suppress the enzymatic activity of PyrD as well as bacterial cytotoxicity, biofilm formation and antibiotic resistance. A single administration of the compound reduced the bacterial colonization in the acute mouse pneumonia model. Therefore, we have developed a strategy to identify novel treatment targets and antimicrobial molecules.
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Affiliation(s)
- Qiaoyun Guo
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yu Wei
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Bin Xia
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Chang Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xiaolei Pan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jing Shi
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Feng Zhu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jinlong Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Lei Qian
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xinqi Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shouguang Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
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Zhuo T, Rou W, Song X, Guo J, Fan X, Kamau GG, Zou H. Molecular study on the carAB operon reveals that carB gene is required for swimming and biofilm formation in Xanthomonas citri subsp. citri. BMC Microbiol 2015; 15:225. [PMID: 26494007 PMCID: PMC4619228 DOI: 10.1186/s12866-015-0555-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 10/08/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The carA and carB genes code the small and large subunits of carbamoyl-phosphate synthase (CPS) that responsible for arginine and pyrimidine production. The purpose of this work was to study the gene organization and expression pattern of carAB operon, and the biological functions of carA and carB genes in Xanthomonas citri subsp. citri. METHODS RT-PCR method was employed to identify the full length of carAB operon transcript in X. citri subsp. citri. The promoter of carAB operon was predicted and analyzed its activity by fusing a GUS reporter gene. The swimming motility was tested on 0.25% agar NY plates with 1% glucose. Biofilm was measured by cell adhesion to polyvinyl chloride 96-well plate. RESULTS The results indicated that carAB operon was composed of five gene members carA-orf-carB-greA-rpfE. A single promoter was predicted from the nucleotide sequence upstream of carAB operon, and its sensitivity to glutamic acid, uracil and arginine was confirmed by fusing a GUS reporter gene. Deletion mutagenesis of carB gene resulted in reduced abilities in swimming on soft solid media and in forming biofilm on polystyrene microtiter plates. CONCLUSIONS From these results, we concluded that carAB operon was involved in multiple biological processes in X. citri subsp. citri.
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Affiliation(s)
- Tao Zhuo
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Wei Rou
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Xue Song
- Hebei Institute of Engineering Technology, Shijiazhuang, 050091, China.
| | - Jing Guo
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Xiaojing Fan
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Gicharu Gibson Kamau
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Huasong Zou
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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