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Meidaninikjeh S, Mohammadi P, Elikaei A. Bacteriophages and bacterial extracellular vesicles, threat or opportunity? Life Sci 2024; 350:122749. [PMID: 38821215 DOI: 10.1016/j.lfs.2024.122749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/25/2024] [Accepted: 05/23/2024] [Indexed: 06/02/2024]
Abstract
Emergence of antimicrobial-resistant bacteria (AMR) is one of the health major problems worldwide. The scientists are looking for a novel method to treat infectious diseases. Phage therapy is considered a suitable approach for treating infectious diseases. However, there are different challenges in this way. Some biological aspects can probably influence on therapeutic results and further investigations are necessary to reach a successful phage therapy. Bacteriophage activity can influence by bacterial defense system. Bacterial extracellular vesicles (BEVs) are one of the bacterial defense mechanisms which can modify the results of bacteriophage activity. BEVs have the significant roles in the gene transferring, invasion, escape, and spreading of bacteriophages. In this review, the defense mechanisms of bacteria against bacteriophages, especially BEVs secretion, the hidden linkage of BEVs and bacteriophages, and its possible consequences on the bacteriophage activity as well phage therapy will be discussed.
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Affiliation(s)
- Sepideh Meidaninikjeh
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Parisa Mohammadi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology, Alzahra University, Tehran, Iran.
| | - Ameneh Elikaei
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology, Alzahra University, Tehran, Iran.
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2
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Shan L, Zheng W, Xu S, Zhu Z, Pei Y, Bao X, Yuan Y. Effect of household pipe materials on formation and chlorine resistance of the early-stage biofilm: various interspecific interactions exhibited by the same microbial biofilm in different pipe materials. Arch Microbiol 2024; 206:295. [PMID: 38856934 DOI: 10.1007/s00203-024-04013-4] [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: 04/02/2024] [Revised: 05/14/2024] [Accepted: 05/19/2024] [Indexed: 06/11/2024]
Abstract
Microbial community biofilm exists in the household drinking water system and would pose threat to water quality. This paper explored biofilm formation and chlorination resistance of ten dual-species biofilms in three typical household pipes (stainless steel (SS), polypropylene random (PPR), and copper), and investigated the role of interspecific interaction. Biofilm biomass was lowest in copper pipes and highest in PPR pipes. A synergistic or neutralistic relationship between bacteria was evident in most biofilms formed in SS pipes, whereas four groups displayed a competitive relationship in biofilms formed in copper pipe. Chlorine resistance of biofilms was better in SS pipes and worse in copper pipes. It may be helped by interspecific relationships, but was more dependent on bacteria and resistance mechanisms such as more stable extracellular polymeric substance. The corrosion sites may also protect bacteria from chlorination. The findings provide useful insights for microbial control strategies in household drinking water systems.
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Affiliation(s)
- Lili Shan
- School of Civil Engineering and Architecture, East China Jiao Tong University, Nanchang, 330013, PR China
| | - Wanjun Zheng
- School of Civil Engineering and Architecture, East China Jiao Tong University, Nanchang, 330013, PR China
| | - Siyang Xu
- School of Civil Engineering and Architecture, East China Jiao Tong University, Nanchang, 330013, PR China
- Department of Transportation of Jiangxi Province, Comprehensive Transportation Development Research Center of Jiangxi Provincial, Nanchang, PR China
| | - Zebing Zhu
- School of Civil Engineering and Architecture, East China Jiao Tong University, Nanchang, 330013, PR China.
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, PR China.
| | - Yunyan Pei
- School of Civil Engineering and Architecture, East China Jiao Tong University, Nanchang, 330013, PR China
| | - Xiajun Bao
- School of Civil Engineering and Architecture, East China Jiao Tong University, Nanchang, 330013, PR China
| | - Yixing Yuan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, PR China
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3
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Sharma DK, Rajpurohit YS. Multitasking functions of bacterial extracellular DNA in biofilms. J Bacteriol 2024; 206:e0000624. [PMID: 38445859 PMCID: PMC11025335 DOI: 10.1128/jb.00006-24] [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] [Indexed: 03/07/2024] Open
Abstract
Bacterial biofilms are intricate ecosystems of microbial communities that adhere to various surfaces and are enveloped by an extracellular matrix composed of polymeric substances. Within the context of bacterial biofilms, extracellular DNA (eDNA) originates from cell lysis or is actively secreted, where it exerts a significant influence on the formation, stability, and resistance of biofilms to environmental stressors. The exploration of eDNA within bacterial biofilms holds paramount importance in research, with far-reaching implications for both human health and the environment. An enhanced understanding of the functions of eDNA in biofilm formation and antibiotic resistance could inspire the development of strategies to combat biofilm-related infections and improve the management of antibiotic resistance. This comprehensive review encapsulates the latest discoveries concerning eDNA, encompassing its origins, functions within bacterial biofilms, and significance in bacterial pathogenesis.
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Affiliation(s)
- Dhirendra Kumar Sharma
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Schools of Life Sciences, Homi Bhabha National Institute (DAE—Deemed University), Mumbai, India
| | - Yogendra Singh Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Schools of Life Sciences, Homi Bhabha National Institute (DAE—Deemed University), Mumbai, India
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4
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Qin C, Zhang RH, Li Z, Zhao HM, Li YW, Feng NX, Li H, Cai QY, Hu X, Gao Y, Xiang L, Mo CH, Xing B. Insights into the enzymatic degradation of DNA expedited by typical perfluoroalkyl acids. ECO-ENVIRONMENT & HEALTH (ONLINE) 2023; 2:278-286. [PMID: 38435362 PMCID: PMC10902504 DOI: 10.1016/j.eehl.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/27/2023] [Accepted: 09/05/2023] [Indexed: 03/05/2024]
Abstract
Perfluoroalkyl acids (PFAAs) are considered forever chemicals, gaining increasing attention for their hazardous impacts. However, the ecological effects of PFAAs remain unclear. Environmental DNA (eDNA), as the environmental gene pool, is often collected for evaluating the ecotoxicological effects of pollutants. In this study, we found that all PFAAs investigated, including perfluorohexanoic acid, perfluorooctanoic acid, perfluorononanoic acid, and perfluorooctane sulfonate, even at low concentrations (0.02 and 0.05 mg/L), expedited the enzymatic degradation of DNA in a nonlinear dose-effect relationship, with DNA degradation fragment sizes being lower than 1,000 bp and 200 bp after 15 and 30 min of degradation, respectively. This phenomenon was attributed to the binding interaction between PFAAs and AT bases in DNA via groove binding. van der Waals force (especially dispersion force) and hydrogen bonding are the main binding forces. DNA binding with PFAAs led to decreased base stacking and right-handed helicity, resulting in loose DNA structure exposing more digestion sites for degrading enzymes, and accelerating the enzymatic degradation of DNA. The global ecological risk evaluation results indicated that PFAA contamination could cause medium and high molecular ecological risk in 497 samples from 11 contamination-hot countries (such as the USA, Canada, and China). The findings of this study show new insights into the influence of PFAAs on the environmental fates of biomacromolecules and reveal the hidden molecular ecological effects of PFAAs in the environment.
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Affiliation(s)
- Chao Qin
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Run-Hao Zhang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zekai Li
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Nai-Xian Feng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, United States
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Enriquez KT, Plummer WD, Neufer PD, Chazin WJ, Dupont WD, Skaar EP. Temporal modelling of the biofilm lifecycle (TMBL) establishes kinetic analysis of plate-based bacterial biofilm dynamics. J Microbiol Methods 2023; 212:106808. [PMID: 37595876 PMCID: PMC10528067 DOI: 10.1016/j.mimet.2023.106808] [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: 06/30/2023] [Revised: 08/12/2023] [Accepted: 08/12/2023] [Indexed: 08/20/2023]
Abstract
Bacterial biofilms are critical to pathogenesis and infection. They are associated with rising rates of antimicrobial resistance. Biofilms are correlated with worse clinical outcomes, making them important to infectious diseases research. There is a gap in knowledge surrounding biofilm kinetics and dynamics which makes biofilm research difficult to translate from bench to bedside. To address this gap, this work employs a well-characterized crystal violet biomass accrual and planktonic cell density assay across a clinically relevant time course and expands statistical analysis to include kinetic information in a protocol termed the TMBL (Temporal Mapping of the Biofilm Lifecycle) assay. TMBL's statistical framework quantitatively compares biofilm communities across time, species, and media conditions in a 96-well format. Measurements from TMBL can reliably be condensed into response features that inform the time-dependent behavior of adherent biomass and planktonic cell populations. Staphylococcus aureus and Pseudomonas aeruginosa biofilms were grown in conditions of metal starvation in nutrient-variable media to demonstrate the rigor and translational potential of this strategy. Significant differences in single-species biofilm formation are seen in metal-deplete conditions as compared to their controls which is consistent with the consensus literature on nutritional immunity that metal availability drives transcriptomic and metabolomic changes in numerous pathogens. Taken together, these results suggest that kinetic analysis of biofilm by TMBL represents a statistically and biologically rigorous approach to studying the biofilm lifecycle as a time-dependent process. In addition to current methods to study the impact of microbe and environmental factors on the biofilm lifecycle, this kinetic assay can inform biological discovery in biofilm formation and maintenance.
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Affiliation(s)
- Kyle T Enriquez
- Vanderbilt University Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN, United States of America; Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, United States of America; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - W Dale Plummer
- Department of Biostatistics, Vanderbilt University, Nashville, TN, United States of America
| | - Preston D Neufer
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America; Department of Biochemistry, Vanderbilt University, Nashville, TN, United States of America
| | - Walter J Chazin
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, United States of America; Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America; Department of Biochemistry, Vanderbilt University, Nashville, TN, United States of America
| | - William D Dupont
- Department of Biostatistics, Vanderbilt University, Nashville, TN, United States of America
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, United States of America; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, United States of America.
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Giallonardi G, Letizia M, Mellini M, Frangipani E, Halliday N, Heeb S, Cámara M, Visca P, Imperi F, Leoni L, Williams P, Rampioni G. Alkyl-quinolone-dependent quorum sensing controls prophage-mediated autolysis in Pseudomonas aeruginosa colony biofilms. Front Cell Infect Microbiol 2023; 13:1183681. [PMID: 37305419 PMCID: PMC10250642 DOI: 10.3389/fcimb.2023.1183681] [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: 03/10/2023] [Accepted: 05/02/2023] [Indexed: 06/13/2023] Open
Abstract
Pseudomonas aeruginosa is a model quorum sensing (QS) pathogen with three interconnected QS circuits that control the production of virulence factors and antibiotic tolerant biofilms. The pqs QS system of P. aeruginosa is responsible for the biosynthesis of diverse 2-alkyl-4-quinolones (AQs), of which 2-heptyl-4-hydroxyquinoline (HHQ) and 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS) function as QS signal molecules. Transcriptomic analyses revealed that HHQ and PQS influenced the expression of multiple genes via PqsR-dependent and -independent pathways whereas 2-heptyl-4-hydroxyquinoline N-oxide (HQNO) had no effect on P. aeruginosa transcriptome. HQNO is a cytochrome bc 1 inhibitor that causes P. aeruginosa programmed cell death and autolysis. However, P. aeruginosa pqsL mutants unable to synthesize HQNO undergo autolysis when grown as colony biofilms. The mechanism by which such autolysis occurs is not understood. Through the generation and phenotypic characterization of multiple P. aeruginosa PAO1 mutants producing altered levels of AQs in different combinations, we demonstrate that mutation of pqsL results in the accumulation of HHQ which in turn leads to Pf4 prophage activation and consequently autolysis. Notably, the effect of HHQ on Pf4 activation is not mediated via its cognate receptor PqsR. These data indicate that the synthesis of HQNO in PAO1 limits HHQ-induced autolysis mediated by Pf4 in colony biofilms. A similar phenomenon is shown to occur in P. aeruginosa cystic fibrosis (CF) isolates, in which the autolytic phenotype can be abrogated by ectopic expression of pqsL.
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Affiliation(s)
| | | | - Marta Mellini
- Department of Science, University Roma Tre, Rome, Italy
| | | | - Nigel Halliday
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Stephan Heeb
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Miguel Cámara
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Paolo Visca
- Department of Science, University Roma Tre, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Francesco Imperi
- Department of Science, University Roma Tre, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy
| | - Paul Williams
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Giordano Rampioni
- Department of Science, University Roma Tre, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
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7
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Ibáñez-Cervantes G, Cruz-Cruz C, Durán-Manuel EM, Loyola-Cruz MÁ, Cureño-Díaz MA, Castro-Escarpulli G, Lugo-Zamudio GE, Rojo-Gutiérrez MI, Razo-Blanco Hernández DM, López-Ornelas A, Bello-López JM. Disinfection efficacy of ozone on ESKAPE bacteria biofilms: Potential use in difficult-to-access medical devices. Am J Infect Control 2023; 51:11-17. [PMID: 35483519 DOI: 10.1016/j.ajic.2022.03.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND Medical devices can be reservoirs of multidrug-resistant bacteria that may be involved in the acquisition of infections since bacteria with the ability to form biofilms that are difficult to eradicate, mainly in mechanical ventilators. The aim of this work was to evaluate the efficacy of O3 against biofilms of bacteria ESKAPE group through disinfection studies. METHODS The formation of biofilms of ESKAPE group bacteria was induced in vitro. O3 was injected at different exposure times at a constant dose of 600 mg/h. The recovery of surviving bacteria after O3 treatment was assessed by bacterial counts and biofilm disruption was analyzed. Finally, the viability and integrity of biofilms after O3 treatment was determined by confocal laser scanning microscopy (CLSM). RESULTS O3 showed bactericidal activity on biofilms from 12 min/7.68 ppm for A. baumannii and C. freundii. P. aeruginosa, K. pneumoniae and S. aureus were killed after 15 min/9.60 ppm. Correlation analyses showed inversely proportional relationships between the variables "disruption versus O3". CLSM revealed that death was time-dependent of biofilms upon O3 exposure. Orthogonal plane analysis showed that bacteria located in the outer region of the biofilms were the ones that initially suffered damage from O3 exposure. CONCLUSIONS Our findings suggest that this method could be an alternative for the disinfection in mechanical ventilators colonized by bacteria biofilm forming.
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Affiliation(s)
- Gabriela Ibáñez-Cervantes
- División de Investigación, Hospital Juárez de México, Mexico City, Mexico; Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Clemente Cruz-Cruz
- División de Investigación, Hospital Juárez de México, Mexico City, Mexico
| | | | - Miguel Ángel Loyola-Cruz
- División de Investigación, Hospital Juárez de México, Mexico City, Mexico; Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | | | | | | | | | | | - Adolfo López-Ornelas
- División de Investigación, Hospital Juárez de México, Mexico City, Mexico; Laboratorio de Reprogramación Celular, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Mexico City, Mexico.
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8
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Moshynets OV, Pokholenko I, Iungin O, Potters G, Spiers AJ. eDNA, Amyloid Fibers and Membrane Vesicles Identified in Pseudomonas fluorescens SBW25 Biofilms. Int J Mol Sci 2022; 23:ijms232315096. [PMID: 36499433 PMCID: PMC9738004 DOI: 10.3390/ijms232315096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022] Open
Abstract
Pseudomonas fluorescens SBW25 is a model soil- and plant-associated bacterium capable of forming a variety of air-liquid interface biofilms in experimental microcosms and on plant surfaces. Previous investigations have shown that cellulose is the primary structural matrix component in the robust and well-attached Wrinkly Spreader biofilm, as well as in the fragile Viscous Mass biofilm. Here, we demonstrate that both biofilms include extracellular DNA (eDNA) which can be visualized using confocal laser scanning microscopy (CLSM), quantified by absorbance measurements, and degraded by DNase I treatment. This eDNA plays an important role in cell attachment and biofilm development. However, exogenous high-molecular-weight DNA appears to decrease the strength and attachment levels of mature Wrinkly Spreader biofilms, whereas low-molecular-weight DNA appears to have little effect. Further investigation with CLSM using an amyloid-specific fluorophore suggests that the Wrinkly Spreader biofilm might also include Fap fibers, which might be involved in attachment and contribute to biofilm strength. The robust nature of the Wrinkly Spreader biofilm also allowed us, using MALDI-TOF mass spectrometry, to identify matrix-associated proteins unable to diffuse out of the structure, as well as membrane vesicles which had a different protein profile compared to the matrix-associated proteins. CLSM and DNase I treatment suggest that some vesicles were also associated with eDNA. These findings add to our understanding of the matrix components in this model pseudomonad, and, as found in other biofilms, biofilm-specific products and material from lysed cells contribute to these structures through a range of complex interactions.
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Affiliation(s)
- Olena V. Moshynets
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Ianina Pokholenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Olga Iungin
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
- Department of Biotechnology, Leather and Fur, Kyiv National University of Technologies and Design, 01011 Kyiv, Ukraine
| | - Geert Potters
- Antwerp Maritime Academy, 2030 Antwerp, Belgium
- Department of Bioscience Engineering, University of Antwerp, 2000 Antwerp, Belgium
- Correspondence:
| | - Andrew J. Spiers
- School of Applied Sciences, Abertay University, Dundee DD1 1HG, UK
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9
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Qin C, Lu YX, Borch T, Yang LL, Li YW, Zhao HM, Hu X, Gao Y, Xiang L, Mo CH, Li QX. Interactions between Extracellular DNA and Perfluoroalkyl Acids (PFAAs) Decrease the Bioavailability of PFAAs in Pakchoi ( Brassica chinensis L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14622-14632. [PMID: 36375011 DOI: 10.1021/acs.jafc.2c04597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Perfluoroalkyl acids (PFAAs) are emerging ionic organic pollutants worldwide. Great amounts of extracellular DNA (∼mg/kg) coexist with PFAAs in the environment. However, PFAA-DNA interactions and effects of such interactions have not been well studied. Herein, we used isothermal titration calorimetry (ITC), spectroscopy, and computational simulations to investigate the PFAA-DNA interactions. ITC assays showed that specific binding affinities of PFHxA-DNA, PFOA-DNA, PFNA-DNA, and PFOS-DNA were 5.14 × 105, 3.29 × 105, 1.99 × 105, and 2.18 × 104 L/mol, respectively, which were about 1-2 orders of magnitude stronger than those of PFAAs with human serum albumin. Spectral analysis suggested interactions of PFAAs with adenine (A), cytosine (C), guanine (G), and thymine (T), among which grooves associated with thymine were the major binding sites. Molecular dynamics simulations and quantum chemical calculations suggested that hydrogen bonds and van der Waals forces were the main interaction forces. Such a PFAA-DNA binding decreased the bioavailability of PFAAs in plant seedlings. The findings will help to improve the current understanding of the interaction between PFAAs and biomacromolecules, as well as how such interactions affect the bioavailability of PFAAs.
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Affiliation(s)
- Chao Qin
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing210095, China
| | - Ying-Xin Lu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Thomas Borch
- Department of Chemistry, Colorado State University, 1872 Campus Delivery, Fort Collins, Colorado80523, United States
- Department of Soil and Crop Sciences, Colorado State University, 1170 Campus Delivery, Fort Collins, Colorado80523, United States
| | - Ling-Ling Yang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing210095, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii96822, United States
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10
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The Origin, Function, Distribution, Quantification, and Research Advances of Extracellular DNA. Int J Mol Sci 2022; 23:ijms232213690. [PMID: 36430193 PMCID: PMC9698649 DOI: 10.3390/ijms232213690] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
In nature, DNA is ubiquitous, existing not only inside but also outside of the cells of organisms. Intracellular DNA (iDNA) plays an essential role in different stages of biological growth, and it is defined as the carrier of genetic information. In addition, extracellular DNA (eDNA) is not enclosed in living cells, accounting for a large proportion of total DNA in the environment. Both the lysis-dependent and lysis-independent pathways are involved in eDNA release, and the released DNA has diverse environmental functions. This review provides an insight into the origin as well as the multiple ecological functions of eDNA. Furthermore, the main research advancements of eDNA in the various ecological environments and the various model microorganisms are summarized. Furthermore, the major methods for eDNA extraction and quantification are evaluated.
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11
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The resurgence of phage-based therapy in the era of increasing antibiotic resistance: from research progress to challenges and prospects. Microbiol Res 2022; 264:127155. [DOI: 10.1016/j.micres.2022.127155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 12/23/2022]
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12
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Filloux A. Bacterial protein secretion systems: Game of types. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35536734 DOI: 10.1099/mic.0.001193] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein trafficking across the bacterial envelope is a process that contributes to the organisation and integrity of the cell. It is the foundation for establishing contact and exchange between the environment and the cytosol. It helps cells to communicate with one another, whether they establish symbiotic or competitive behaviours. It is instrumental for pathogenesis and for bacteria to subvert the host immune response. Understanding the formation of envelope conduits and the manifold strategies employed for moving macromolecules across these channels is a fascinating playground. The diversity of the nanomachines involved in this process logically resulted in an attempt to classify them, which is where the protein secretion system types emerged. As our knowledge grew, so did the number of types, and their rightful nomenclature started to be questioned. While this may seem a semantic or philosophical issue, it also reflects scientific rigour when it comes to assimilating findings into textbooks and science history. Here I give an overview on bacterial protein secretion systems, their history, their nomenclature and why it can be misleading for newcomers in the field. Note that I do not try to suggest a new nomenclature. Instead, I explore the reasons why naming could have escaped our control and I try to reiterate basic concepts that underlie protein trafficking cross membranes.
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Affiliation(s)
- Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
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Ran M, Gounani Z, Yan J, Rosenholm JM, Zhang H. Ca
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enhanced photosensitizer/DNase I nanocomposite mediated bacterial eradication through biofilm disruption and photothermal therapy. NANO SELECT 2022. [DOI: 10.1002/nano.202200026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Meixin Ran
- Pharmaceutical Sciences Laboratory Åbo Akademi University Turku 20520 Finland
- Turku Bioscience Centre University of Turku and Åbo Akademi University Turku 20520 Finland
| | - Zahra Gounani
- Physics Faculty of Science and Engineering Åbo Akademi Turku 20500 Finland
| | - Jiaqi Yan
- Pharmaceutical Sciences Laboratory Åbo Akademi University Turku 20520 Finland
- Turku Bioscience Centre University of Turku and Åbo Akademi University Turku 20520 Finland
| | | | - Hongbo Zhang
- Pharmaceutical Sciences Laboratory Åbo Akademi University Turku 20520 Finland
- Turku Bioscience Centre University of Turku and Åbo Akademi University Turku 20520 Finland
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14
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Yasuda M, Yamamoto T, Nagakubo T, Morinaga K, Obana N, Nomura N, Toyofuku M. Phage Genes Induce Quorum Sensing Signal Release through Membrane Vesicle Formation. Microbes Environ 2022; 37. [PMID: 35082176 PMCID: PMC8958291 DOI: 10.1264/jsme2.me21067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Membrane vesicles (MVs) released from the bacterium Paracoccus denitrificans Pd1222 are enriched with the quorum sensing (QS) signaling molecule N-hexadecanoyl-l-homoserine lactone (C16-HSL). However, the biogenesis of MVs in Pd1222 remains unclear. Investigations on MV formation are crucial for obtaining a more detailed understanding of the dynamics of MV-assisted signaling. In the present study, live-cell imaging showed that P. denitrificans Pd1222 produced MVs through cell lysis under DNA-damaging conditions. DNA sequencing of MVs and a transcriptome ana-lysis of cells indicated that the expression of a prophage region was up-regulated at the onset of MV formation under DNA-damaging conditions. A further sequence ana-lysis identified a putative endolysin (Pden_0381) and holin (Pden_0382) in the prophage region. The expression of these genes was regulated by RecA. Using gene knockout mutants, we showed that prophage-encoded endolysin was critical for MV formation by P. denitrificans Pd1222 under DNA-damaging conditions. MV triggering by endolysin was dependent on the putative holin, which presumably transported endolysin to the periplasmic space. C16-HSL quantification revealed that more signals were released into the milieu as a consequence of the effects of endolysin. Using a QS reporter strain, we found that the QS response in P. denitrificans was stimulated by inducing the expression of endolysin. Collectively, these results provide novel insights into the mechanisms by which a bacterial cell-to-cell communication system is manipulated by phage genes.
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Affiliation(s)
- Marina Yasuda
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Tatsuya Yamamoto
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | - Toshiki Nagakubo
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | - Kana Morinaga
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Nozomu Obana
- Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba.,Microbiology Research Center for Sustainability, University of Tsukuba
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba.,Microbiology Research Center for Sustainability, University of Tsukuba
| | - Masanori Toyofuku
- Faculty of Life and Environmental Sciences, University of Tsukuba.,Microbiology Research Center for Sustainability, University of Tsukuba.,Suntory Rising Stars Encouragement Program in Life Sciences (SunRiSE)
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15
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Interbacterial Transfer of Carbapenem Resistance and Large Antibiotic Resistance Islands by Natural Transformation in Pathogenic Acinetobacter. mBio 2022; 13:e0263121. [PMID: 35073754 PMCID: PMC8787482 DOI: 10.1128/mbio.02631-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Acinetobacter baumannii infection poses a major health threat, with recurrent treatment failure due to antibiotic resistance, notably to carbapenems. While genomic analyses of clinical strains indicate that homologous recombination plays a major role in the acquisition of antibiotic resistance genes, the underlying mechanisms of horizontal gene transfer often remain speculative. Our understanding of the acquisition of antibiotic resistance is hampered by the lack of experimental systems able to reproduce genomic observations. We here report the detection of recombination events occurring spontaneously in mixed bacterial populations and which can result in the acquisition of resistance to carbapenems. We show that natural transformation is the main driver of intrastrain but also interstrain recombination events between A. baumannii clinical isolates and pathogenic species of Acinetobacter. We observed that interbacterial natural transformation in mixed populations is more efficient at promoting the acquisition of large resistance islands (AbaR4 and AbaR1) than when the same bacteria are supplied with large amounts of purified genomic DNA. Importantly, analysis of the genomes of the recombinant progeny revealed large recombination tracts (from 13 to 123 kb) similar to those observed in the genomes of clinical isolates. Moreover, we highlight that transforming DNA availability is a key determinant of the rate of recombinants and results from both spontaneous release and interbacterial predatory behavior. In the light of our results, natural transformation should be considered a leading mechanism of genome recombination and horizontal gene transfer of antibiotic resistance genes in Acinetobacter baumannii.
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Integrating transcriptomics and metabolomics analysis on kojic acid combating Acinetobacter baumannii biofilm and its potential roles. Microbiol Res 2021; 254:126911. [PMID: 34763140 DOI: 10.1016/j.micres.2021.126911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/20/2022]
Abstract
As a major secondary metabolite derived from a dominant marine filamentous fungus A7, kojic acid might confer the strain a competitive advantage in natural colonization. The bioactivities of kojic acid against bacterial growth and biofilm formation were investigated against Acinetobacter baumannii (A. baumannii) ATCC 19606. Then, transcriptomics and metabolomics were integrated to characterize the underlying mechanisms. It turned out that kojic acid exhibited a significantly suppressive impact against biofilm but a weak bacteriostatic activity. Meanwhile, a variety of transcriptional and metabolomic profiles were altered within biofilm formation as a result of kojic acid exposure. The alterations highlighted the mechanisms underlying biofilm formation, comprising of quorum sensing, fimbria assembly, bacterial virulence and metabolic plasticity, which could somewhat be hampered by kojic acid. The present study comprehensively elucidated multifactorial schemes for kojic acid combating biofilm formation of A. baumannii, which might provide mechanistic insights into the development of therapeutic strategies against this notorious pathogen. Meanwhile, our observations might shed new light on the ecological roles of kojic acid, e.g., serving as chemical deterrents for host adaptation to marine niches, which, however, awaits further validation.
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Thomas GH. Microbial Musings – April 2021. Microbiology (Reading) 2021; 167. [PMID: 33945459 PMCID: PMC8289222 DOI: 10.1099/mic.0.001061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Mandal PK, Ballerin G, Nolan LM, Petty NK, Whitchurch CB. Bacteriophage infection of Escherichia coli leads to the formation of membrane vesicles via both explosive cell lysis and membrane blebbing. MICROBIOLOGY (READING, ENGLAND) 2021; 167:001021. [PMID: 33871329 PMCID: PMC8289217 DOI: 10.1099/mic.0.001021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/01/2021] [Indexed: 12/27/2022]
Abstract
Membrane vesicles (MVs) are membrane-bound spherical nanostructures that prevail in all three domains of life. In Gram-negative bacteria, MVs are thought to be produced through blebbing of the outer membrane and are often referred to as outer membrane vesicles (OMVs). We have recently described another mechanism of MV formation in Pseudomonas aeruginosa that involves explosive cell-lysis events, which shatters cellular membranes into fragments that rapidly anneal into MVs. Interestingly, MVs are often observed within preparations of lytic bacteriophage, however the source of these MVs and their association with bacteriophage infection has not been explored. In this study we aimed to determine if MV formation is associated with lytic bacteriophage infection. Live super-resolution microscopy demonstrated that explosive cell lysis of Escherichia coli cells infected with either bacteriophage T4 or T7, resulted in the formation of MVs derived from shattered membrane fragments. Infection by either bacteriophage was also associated with the formation of membrane blebs on intact bacteria. TEM revealed multiple classes of MVs within phage lysates, consistent with multiple mechanisms of MV formation. These findings suggest that bacteriophage infection may be a major contributor to the abundance of bacterial MVs in nature.
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Affiliation(s)
- Pappu K. Mandal
- The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Giulia Ballerin
- The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Laura M. Nolan
- National Heart and Lung Institute, Imperial College London, London, SW3 6LR, UK
| | - Nicola K. Petty
- The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Cynthia B. Whitchurch
- The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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Thomas GH. Microbial Musings - February 2021. MICROBIOLOGY-SGM 2021; 167. [PMID: 33635187 PMCID: PMC8131028 DOI: 10.1099/mic.0.001046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Gavin H Thomas
- Department of Biology, University of York, York YO10 5YW, UK
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