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Tian Z, Shao D, Tang L, Li Z, Chen Q, Song Y, Li T, Simmel FC, Song J. Circular single-stranded DNA as a programmable vector for gene regulation in cell-free protein expression systems. Nat Commun 2024; 15:4635. [PMID: 38821953 PMCID: PMC11143192 DOI: 10.1038/s41467-024-49021-6] [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: 10/12/2023] [Accepted: 05/22/2024] [Indexed: 06/02/2024] Open
Abstract
Cell-free protein expression (CFE) systems have emerged as a critical platform for synthetic biology research. The vectors for protein expression in CFE systems mainly rely on double-stranded DNA and single-stranded RNA for transcription and translation processing. Here, we introduce a programmable vector - circular single-stranded DNA (CssDNA), which is shown to be processed by DNA and RNA polymerases for gene expression in a yeast-based CFE system. CssDNA is already widely employed in DNA nanotechnology due to its addressability and programmability. To apply above methods in the context of synthetic biology, CssDNA can not only be engineered for gene regulation via the different pathways of sense CssDNA and antisense CssDNA, but also be constructed into several gene regulatory logic gates in CFE systems. Our findings advance the understanding of how CssDNA can be utilized in gene expression and gene regulation, and thus enrich the synthetic biology toolbox.
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Affiliation(s)
- Zhijin Tian
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui, 230026, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Dandan Shao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Linlin Tang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhen Li
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Chen
- College of Forestry, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Yongxiu Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Ningbo institute of Dalian University of Technology, Ningbo, 315016, China
| | - Tao Li
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui, 230026, China
| | - Friedrich C Simmel
- Department of Bioscience, School of Natural Sciences, Technische Universität München, Garching, Germany
| | - Jie Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
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2
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Tong Z, Wang YC, Jiang GY, Hu XR, Xue YM, Wang C. A method establishment and application for biofilm quorum quenching activity assay. CHEMOSPHERE 2023; 328:138549. [PMID: 37001755 DOI: 10.1016/j.chemosphere.2023.138549] [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: 10/14/2022] [Revised: 01/31/2023] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
The existence of quorum sensing (QS) and quorum quenching (QQ) plays important roles in biofilm formation. However, direct detection of QS ability is difficult due to the low concentrations of signal molecules inside the biofilm. Therefore, QQ activity is typically used to indicate the attribution of QS/QQ to the biofilm. Nevertheless, current detection methods of QQ activity based on biosensors present undesirable operability and accuracy. In this study, the 96-well plate assay based on a specific biosensor, Agrobacterium tumefaciens A136, and a colorimetric substance, X-gal was established. The reliable fitting results were obtained by standardizing the composition of the A136 X-gal assay solution and optimizing the operating conditions. This method improved the accuracy of QQ activity detection and reduced time and cost consumption. Finally, the 96-well plate assay was successfully applied to detect the QQ activities of biofilm samples and explore possible environmental influencing factors. In general, this study provided a new strategy for understanding the QQ effect in biofilm systems.
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Affiliation(s)
- Zhen Tong
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China; Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, 300072, China
| | - Yong-Chao Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China; Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, 300072, China.
| | - Guan-Yu Jiang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China; Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, 300072, China
| | - Xu-Rui Hu
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China; Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, 300072, China
| | - Yi-Mei Xue
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China; Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, 300072, China
| | - Can Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China; Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, 300072, China.
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3
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Cell-free protein synthesis system for bioanalysis: Advances in methods and applications. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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4
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Identification of AHL Synthase in Desulfovibrio vulgaris Hildenborough Using an In-Silico Methodology. Catalysts 2023. [DOI: 10.3390/catal13020364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) are anaerobic bacteria that form biofilm and induce corrosion on various material surfaces. The quorum sensing (QS) system that employs acyl homoserine lactone (AHL)-type QS molecules primarily govern biofilm formation. Studies on SRB have reported the presence of AHL, but no AHL synthase have been annotated in SRB so far. In this computational study, we used a combination of data mining, multiple sequence alignment (MSA), homology modeling and docking to decode a putative AHL synthase in the model SRB, Desulfovibrio vulgaris Hildenborough (DvH). Through data mining, we shortlisted 111 AHL synthase genes. Conserved domain analysis of 111 AHL synthase genes generated a consensus sequence. Subsequent MSA of the consensus sequence with DvH genome indicated that DVU_2486 (previously uncharacterized protein from acetyltransferase family) is the gene encoding for AHL synthase. Homology modeling revealed the existence of seven α-helices and six β sheets in the DvH AHL synthase. The amalgamated study of hydrophobicity, binding energy, and tunnels and cavities revealed that Leu99, Trp104, Arg139, Trp97, and Tyr36 are the crucial amino acids that govern the catalytic center of this putative synthase. Identifying AHL synthase in DvH would provide more comprehensive knowledge on QS mechanism and help design strategies to control biofilm formation.
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5
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Ramos P, Honda R, Hoek EMV, Mahendra S. Carbon/nitrogen ratios determine biofilm formation and characteristics in model microbial cultures. CHEMOSPHERE 2023; 313:137628. [PMID: 36565767 DOI: 10.1016/j.chemosphere.2022.137628] [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: 11/02/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
The influence of growth medium water chemistry, specifically carbon/nitrogen (C/N) molar ratios, on the characteristics and development of biofilms of the model microorganism Pseudomonas aeruginosa was investigated. C/N = 9 had a unique effect on biofilm composition as well as quorum sensing (QS) pathways, with higher concentrations of carbohydrates and proteins in the biofilm and a significant upregulation of the QS gene lasI in planktonic cells. The effect of C/N ratio on total attached biomass was negligible. Principal component analysis revealed a different behavior of most outputs such as carbohydrates and QS chemicals at C/N = 9, and pointed to correlations between parameters of biofilm formation and steady state distribution of cells and extracellular components. C/N ratio was also shown to influence organic compound utilization by both planktonic and sessile organisms, with a maximum chemical oxygen demand (COD) removal of 83% achieved by biofilms at C/N = 21. Planktonic cells achieved higher COD removal rates, but greater overall rates after six days occurred in biofilms. The development of a dual-species biofilm of P. aeruginosa and Nitrobacter winogradskyi was also influenced by C/N, with increase in the relative abundance of the slower-growing N. winogradskyi above C/N = 9. These results indicate that altering operational parameters related to C/N would be relevant for mitigating or promoting biofilm formation and function depending on the desired industrial application or treatment configuration.
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Affiliation(s)
- Pia Ramos
- Department of Civil and Environmental Engineering, University of California Los Angeles, 5732 Boelter Hall, Los Angeles, CA, 90095, USA
| | - Ryo Honda
- Faculty of Geoscience and Civil Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Eric M V Hoek
- Department of Civil and Environmental Engineering, University of California Los Angeles, 5732 Boelter Hall, Los Angeles, CA, 90095, USA; UCLA California NanoSystems Institute, Los Angeles, CA, 90095, USA; UCLA Institute of the Environment & Sustainability, Los Angeles, CA, 90095, USA
| | - Shaily Mahendra
- Department of Civil and Environmental Engineering, University of California Los Angeles, 5732 Boelter Hall, Los Angeles, CA, 90095, USA; UCLA California NanoSystems Institute, Los Angeles, CA, 90095, USA; UCLA Institute of the Environment & Sustainability, Los Angeles, CA, 90095, USA.
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6
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Vasudevan S, Srinivasan P, Neelakantan P, Rayappan JBB, Solomon AP. Photoluminescence-Based Bioassay With Cysteamine-Capped TiO 2 Nanoparticles for the Selective Recognition of N-Acyl Homoserine Lactones. Front Bioeng Biotechnol 2021; 9:750933. [PMID: 34926417 PMCID: PMC8678280 DOI: 10.3389/fbioe.2021.750933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Currently available diagnostic procedures for infections are laborious and time-consuming, resulting in a substantial financial burden by increasing morbidity, increased costs of hospitalization, and mortality. Therefore, innovative approaches to design diagnostic biomarkers are imperative to assist in the rapid and sensitive diagnosis of microbial infections. Acyl homoserine lactones (AHLs) are ubiquitous bacterial signaling molecules that are found to be significantly upregulated in infected sites. In this pioneering work, we have developed a simple photoluminescence-based assay using cysteamine-capped titanium oxide (TiO2) nanoparticles for AHL detection. The PL intensity variation of the oxygen defect state of TiO2 was used for the biosensing measurements. The bioassays were validated using two well-studied AHL molecules (C4-HSL and 3-oxo-C12 HSL) of an important human pathogen, Pseudomonas aeruginosa. The developed system has a maximum relative response of 98%. Furthermore, the efficacy of the system in simulated host urine using an artificial urine medium showed a linear detection range of 10-160 nM. Also, we confirmed the relative response and specificity of the system in detecting AHLs produced by P. aeruginosa in a temporal manner.
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Affiliation(s)
- Sahana Vasudevan
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Parthasarathy Srinivasan
- Nanosensors Laboratory, School of Electrical & Electronics Engineering, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), SASTRA Deemed University, Thanjavur, India
- Department of Electronics and Communication Engineering, Amrita School of Engineering, AMRITA Vishwa Vidyapeetham Chennai Campus, Chennai, India
| | - Prasanna Neelakantan
- Faculty of Dentistry, The University of Hong Kong, Pokfulam, Hong KongSAR, China
| | - John Bosco Balaguru Rayappan
- Nanosensors Laboratory, School of Electrical & Electronics Engineering, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), SASTRA Deemed University, Thanjavur, India
| | - Adline Princy Solomon
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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7
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Vivero-Gomez RJ, Mesa GB, Higuita-Castro J, Robledo SM, Moreno-Herrera CX, Cadavid-Restrepo G. Detection of Quorum Sensing Signal Molecules, Particularly N-Acyl Homoserine Lactones, 2-Alky-4-Quinolones, and Diketopiperazines, in Gram-Negative Bacteria Isolated From Insect Vector of Leishmaniasis. FRONTIERS IN TROPICAL DISEASES 2021. [DOI: 10.3389/fitd.2021.760228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Gram-negative bacteria are known to use a quorum sensing system to facilitate and stimulate cell to cell communication, mediated via regulation of specific genes. This system is further involved in the modulation of cell density and metabolic and physiological processes that putatively either affect the survival of insect vectors or the establishment of pathogens transmitted by them. The process of quorum sensing generally involves N-acyl homoserine lactones and 2-alkyl-4-quinolones signaling molecules. The present study aimed to detect and identify quorum sensing signaling molecules of AHLs and AHQs type that are secreted by intestinal bacteria, and link their production to their extracellular milieu and intracellular content. Isolates for assessment were obtained from the intestinal tract of Pintomyia evansi (Leishmania insect vector). AHLs and AHQs molecules were detected using chromatography (TLC) assays, with the aid of specific and sensitive biosensors. For identity confirmation, ultra-high-performance liquid chromatography coupled with mass spectrometry was used. TLC assays detected quorum sensing molecules (QSM) in the supernatant of the bacterial isolates and intracellular content. Interestingly, Pseudomonas otitidis, Enterobacter aerogenes, Enterobacter cloacae, and Pantoea ananatis isolates showed a migration pattern similar to the synthetic molecule 3-oxo-C6-HSL (OHHL), which was used as a control. Enterobacter cancerogenus secreted C6-HSL, a related molecules to N-hexanoyl homoserine lactone (HHL), while Acinetobacter gyllenbergii exhibited a migration pattern similar to 2-heptyl-4-quinolone (HHQ) molecules. In comparison to this, 3-oxo-C12-HSL (OdDHL) type molecules were produced by Lysobacter soli, Pseudomonas putida, A. gyllenbergii, Acinetobacter calcoaceticus, and Pseudomonas aeruginosa, while Enterobacter cloacae produced molecules similar to 2-heptyl-3-hydroxy-4-quinolone (PQS). For Pseudomonas putida, Enterobacter aerogenes, P. ananatis, and Pseudomonas otitidis extracts, peak chromatograms with distinct retention times and areas, consistent with the molecules described in case of TLC, were obtained using HPLC. Importantly, P. ananatis produced a greater variety of high QSM concentration, and thus served as a reference for confirmation and identification by UHPLC-MRM-MS/MS. The molecules that were identified included N-hexanoyl-L-homoserine lactone [HHL, C10H18NO3, (M + H)], N-(3-oxohexanoyl)-L-homoserine lactone [OHHL, C10H16NO4, (M + H)], N-(3-oxododecanoyl)-L-homoserine lactone [OdDHL, C16H28NO4, (M + H)], and 2-heptyl-3-hydroxy-4(1H)-quinolone [PQS, C16H22NO2, (M + H)]. Besides this, the detection of diketopiperazines, namely L-Pro-L-Tyr and ΔAla-L-Val cyclopeptides was reported for P. ananatis. These molecules might be potentially associated with the regulation of QSM system, and might represent another small molecule-mediated bacterial sensing system. This study presents the first report regarding the detection and identification of QSM and diketopiperazines in the gut sand fly bacteria. The possible effect of QSM on the establishment of Leishmania must be explored to determine its role in the modulation of intestinal microbiome and the life cycle of Pi. evansi.
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8
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Taşkan B, Taşkan E. Inhibition of AHL-mediated quorum sensing to control biofilm thickness in microbial fuel cell by using Rhodococcus sp. BH4. CHEMOSPHERE 2021; 285:131538. [PMID: 34273699 DOI: 10.1016/j.chemosphere.2021.131538] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/16/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Anode biofilm thickness is a key point for high and sustainable power generation in microbial fuel cells (MFCs). Over time, the formation of a thicker biofilm on anode electrode hinders the power generation performance of MFC by causing a longer electron transfer path and the accumulation of undesirable components in anode biofilm. To overcome these limitations, we used a novel strategy named quorum quenching (QQ) for the first time in order to control the biofilm thickness on the anode surface by inactivation of signal molecules among microorganisms. For this purpose, the isolated QQ bacteria (Rhodococcus sp. BH4) were immobilized into alginate beads (20, 40, and 80 mg/10 ml sodium alginate) and added to the anode chamber of MFCs. The MFC exhibited the best electrochemical activity (1924 mW m-2) with a biofilm thickness of 26 μm at 40 mg Rhodococcus sp. BH4/10 ml sodium alginate. The inhibition of signal molecules in anode chamber reduced the production of extracellular polymeric substance (EPS) by preventing microbial communication amonganode microorganisms. Microscopic observations revealed that anode biofilm thickness and the abundance of dead bacteria significantly decreased with an increase in Rhodococcus sp. BH4 concentration in MFCs. Microbiome diversity showed an apparent difference among the microbial community structures of anode biofilms in MFCs containing vacant and Rhodococcus sp. BH4 beads. The data revealed that the QQ strategy is an efficient application for improving MFC performance and may shed light on future studies.
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Affiliation(s)
- Banu Taşkan
- Firat University, Department of Environmental Engineering, Elazig, 23119, Turkey.
| | - Ergin Taşkan
- Firat University, Department of Environmental Engineering, Elazig, 23119, Turkey.
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9
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Tripathi AK, Thakur P, Saxena P, Rauniyar S, Gopalakrishnan V, Singh RN, Gadhamshetty V, Gnimpieba EZ, Jasthi BK, Sani RK. Gene Sets and Mechanisms of Sulfate-Reducing Bacteria Biofilm Formation and Quorum Sensing With Impact on Corrosion. Front Microbiol 2021; 12:754140. [PMID: 34777309 PMCID: PMC8586430 DOI: 10.3389/fmicb.2021.754140] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/24/2021] [Indexed: 01/02/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) have a unique ability to respire under anaerobic conditions using sulfate as a terminal electron acceptor, reducing it to hydrogen sulfide. SRB thrives in many natural environments (freshwater sediments and salty marshes), deep subsurface environments (oil wells and hydrothermal vents), and processing facilities in an industrial setting. Owing to their ability to alter the physicochemical properties of underlying metals, SRB can induce fouling, corrosion, and pipeline clogging challenges. Indigenous SRB causes oil souring and associated product loss and, subsequently, the abandonment of impacted oil wells. The sessile cells in biofilms are 1,000 times more resistant to biocides and induce 100-fold greater corrosion than their planktonic counterparts. To effectively combat the challenges posed by SRB, it is essential to understand their molecular mechanisms of biofilm formation and corrosion. Here, we examine the critical genes involved in biofilm formation and microbiologically influenced corrosion and categorize them into various functional categories. The current effort also discusses chemical and biological methods for controlling the SRB biofilms. Finally, we highlight the importance of surface engineering approaches for controlling biofilm formation on underlying metal surfaces.
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Affiliation(s)
- Abhilash Kumar Tripathi
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Payal Thakur
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Priya Saxena
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Shailabh Rauniyar
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Vinoj Gopalakrishnan
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Ram Nageena Singh
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Venkataramana Gadhamshetty
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States.,BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Department of Civil and Environmental Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Etienne Z Gnimpieba
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Biomedical Engineering Program, University of South Dakota, Sioux Falls, SD, United States
| | - Bharat K Jasthi
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Department of Materials and Metallurgical Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States.,BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Composite and Nanocomposite Advanced Manufacturing Centre-Biomaterials, Rapid City, SD, United States
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10
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Yamabe K, Arakawa Y, Shoji M, Onda M, Miyamoto K, Tsuchiya T, Akeda Y, Terada K, Tomono K. Direct anti-biofilm effects of macrolides on Acinetobacter baumannii: comprehensive and comparative demonstration by a simple assay using microtiter plate combined with peg-lid. Biomed Res 2021; 41:259-268. [PMID: 33268670 DOI: 10.2220/biomedres.41.259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Recently, opportunistic nosocomial infections caused by Acinetobacter baumannii have become increasingly prevalent worldwide. The pathogen often establishes biofilms that adhere to medical devices, causing chronic infections refractory to antimicrobial therapy. Clinical reports have indicated that some macrolide antibiotics are effective against chronic biofilm-related infections. In this study, we examined the direct anti-biofilm effects of seven macrolides (azithromycin, clarithromycin, erythromycin, josamycin, spiramycin, fidaxomicin, and ivermectin) on A. baumannii using a simple and newly established in vitro assay system for the swift and serial spectrophotometric determinations of two biofilm-amount indexes of viability and biomass. These macrolides were found to possess direct anti-biofilm effects exerting specific anti-biofilm effects not exclusively depending on their bacteriostatic/bactericidal effects. The anti-biofilm effect of azithromycin was found to be the strongest, while those of fidaxomicin and ivermectin were weak and limited. These results provide insights into possible adjunctive chemotherapy with macrolides for A. baumannii infection. Common five macrolides also interfered with the Agrobacterium tumefaciens NTL(pCF218) (pCF372) bioassay system of N-acyl homoserine lactones, providing insights into sample preparation for the bioassay, and putatively suggesting the actions of macrolides as remote signals in bacterial quorum sensing systems.
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Affiliation(s)
- Kaoru Yamabe
- Graduate School of Public Policy, The University of Tokyo
| | - Yukio Arakawa
- Department of Social and Administrative Pharmacy, Osaka University of Pharmaceutical Sciences
| | - Masaki Shoji
- Department of Social and Administrative Pharmacy, Osaka University of Pharmaceutical Sciences
| | - Mitsuko Onda
- Department of Social and Administrative Pharmacy, Osaka University of Pharmaceutical Sciences
| | - Katsushiro Miyamoto
- Department of Microbiology and Infection Control, Osaka University of Pharmaceutical Sciences
| | - Takahiro Tsuchiya
- Department of Microbiology and Infection Control, Osaka University of Pharmaceutical Sciences
| | - Yukihiro Akeda
- Division of Infection Control and Prevention, Graduate School of Medicine, Osaka University
| | | | - Kazunori Tomono
- Division of Infection Control and Prevention, Graduate School of Medicine, Osaka University
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11
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Li E, Wu J, Zhang D. Exogenous autoinducer-2 inhibits biofilm development of Desulfovibrio sp. Huiquan2017. World J Microbiol Biotechnol 2021; 37:124. [PMID: 34170406 DOI: 10.1007/s11274-021-03071-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 05/16/2021] [Indexed: 11/28/2022]
Abstract
Sulfate-reducing bacteria (SRB) are culprits for microbiologically influenced corrosion, and biofilms are believed to play essential roles in the corrosion induced by SRB. However, little is known about the regulation of SRB biofilms. Quorum sensing signal molecules acyl-homoserine lactones (AHLs) and autoinducer-2 (AI-2) regulate biofilm formation of many bacteria. In this study, the production of AHLs and AI-2 by one SRB strain, Desulfovibrio sp. Huiquan2017, was detected, and the effect of exogenous AI-2 on bacterial biofilm formation was discussed. It was found that the cell-free supernatants of Desulfovibrio sp. Huiquan2017 induced luminescence in a ∆luxS mutant strain Vibrio harveyi BB170, indicating the production of functional AI-2 by the bacterium. In the presence of exogenous AI-2, the growth of Desulfovibrio sp. Huiquan2017 and early biofilm formation were not affected, but the later stage of biofilm development was inhibited significantly. The biofilms became looser, smaller, and thinner, and contained less bacteria and extracellular polymeric substances (EPS). The inhibition effect of AI-2 on the biofilm development of Desulfovibrio sp. Huiquan2017 was mainly achieved through reducing the amount of EPS in biofilms. These findings shed light on the biofilm regulation of SRB.
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Affiliation(s)
- Ee Li
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
- Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China
| | - Jiajia Wu
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
- Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.
| | - Dun Zhang
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
- Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.
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12
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N-acyl homoserine lactone molecules assisted quorum sensing: effects consequences and monitoring of bacteria talking in real life. Arch Microbiol 2021; 203:3739-3749. [PMID: 34002253 DOI: 10.1007/s00203-021-02381-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 12/19/2022]
Abstract
Bacteria utilize small signal molecules to monitor population densities. Bacteria arrange gene regulation in a method called Quorum Sensing (QS). The most widespread signalling molecules are N-Acyl Homoserine Lactones (AHLs/HSLs) for Gram-negative bacteria communities. QS plays significant role in the organizing of the bacterial gene that adapts to harsh environmental conditions for bacteria. It is involved in the arrangement of duties, such as biofilm formation occurrence, virulence activity of bacteria, production of antibiotics, plasmid conjugal transfer incident, pigmentation phenomenon and production of exopolysaccharide (EPS). QS obviously impacts on human health, agriculture and environment. AHL-related QS researches have been extensively studied and understood in depth for cell to cell intercommunication channel in Gram-negative bacteria. It is understood that AHL-based QS research has been extensively studied for cell-to-cell communication in Gram-negative bacteria; hence, a comprehensive study of AHLs, which are bacterial signal molecules, is required. The purpose of this review is to examine the effects of QS-mediated AHLs in many areas by looking at them from a different perspectives, such as clinic samples, food industry, aquatic life and wastewater treatment system.
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13
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Ranava D, Backes C, Karthikeyan G, Ouari O, Soric A, Guiral M, Cárdenas ML, Giudici-Orticoni MT. Metabolic Exchange and Energetic Coupling between Nutritionally Stressed Bacterial Species: Role of Quorum-Sensing Molecules. mBio 2021; 12:e02758-20. [PMID: 33468690 PMCID: PMC7845633 DOI: 10.1128/mbio.02758-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/18/2020] [Indexed: 12/29/2022] Open
Abstract
Formation of multispecies communities allows nearly every niche on earth to be colonized, and the exchange of molecular information among neighboring bacteria in such communities is key for bacterial success. To clarify the principles controlling interspecies interactions, we previously developed a coculture model with two anaerobic bacteria, Clostridium acetobutylicum (Gram positive) and Desulfovibrio vulgaris Hildenborough (Gram negative, sulfate reducing). Under conditions of nutritional stress for D. vulgaris, the existence of tight cell-cell interactions between the two bacteria induced emergent properties. Here, we show that the direct exchange of carbon metabolites produced by C. acetobutylicum allows D vulgaris to duplicate its DNA and to be energetically viable even without its substrates. We identify the molecular basis of the physical interactions and how autoinducer-2 (AI-2) molecules control the interactions and metabolite exchanges between C. acetobutylicum and D. vulgaris (or Escherichia coli and D. vulgaris). With nutrients, D. vulgaris produces a small molecule that inhibits in vitro the AI-2 activity and could act as an antagonist in vivo Sensing of AI-2 by D. vulgaris could induce formation of an intercellular structure that allows directly or indirectly metabolic exchange and energetic coupling between the two bacteria.IMPORTANCE Bacteria have usually been studied in single culture in rich media or under specific starvation conditions. However, in nature they coexist with other microorganisms and build an advanced society. The molecular bases of the interactions controlling this society are poorly understood. Use of a synthetic consortium and reducing complexity allow us to shed light on the bacterial communication at the molecular level. This study presents evidence that quorum-sensing molecule AI-2 allows physical and metabolic interactions in the synthetic consortium and provides new insights into the link between metabolism and bacterial communication.
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Affiliation(s)
- David Ranava
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, Mediterranean Institute of Microbiology, Marseille, France
| | - Cassandra Backes
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, Mediterranean Institute of Microbiology, Marseille, France
| | | | - Olivier Ouari
- Aix-Marseille University, CNRS, UMR 7273, ICR, Marseille, France
| | - Audrey Soric
- Aix-Marseille University, CNRS, Centrale Marseille, M2P2, Marseille, France
| | - Marianne Guiral
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, Mediterranean Institute of Microbiology, Marseille, France
| | - María Luz Cárdenas
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, Mediterranean Institute of Microbiology, Marseille, France
| | - Marie Thérèse Giudici-Orticoni
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, Mediterranean Institute of Microbiology, Marseille, France
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14
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Lin X, Li Y, Li Z, Hua R, Xing Y, Lu Y. Portable environment-signal detection biosensors with cell-free synthetic biosystems. RSC Adv 2020; 10:39261-39265. [PMID: 35518409 PMCID: PMC9057330 DOI: 10.1039/d0ra05293k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/09/2020] [Indexed: 01/27/2023] Open
Abstract
By embedding regulated genetic circuits and cell-free systems onto a paper, the portable in vitro biosensing platform showed the possibility of detecting environmental pollutants, namely arsenic ions and bacterial quorum-sensing signal AHLs (N-acyl homoserine lactones). This platform has a great potential for practical environmental management and diagnosis. By embedding the regulated genetic circuits and cell-free systems onto a paper, a portable in vitro biosensing platform has been established.![]()
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Affiliation(s)
- Xiaomei Lin
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University Beijing 100084 China
| | - Yuting Li
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University Beijing 100084 China
| | - Zhixia Li
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University Beijing 100084 China
| | - Rui Hua
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University Beijing 100084 China
| | - Yuyang Xing
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University Beijing 100084 China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University Beijing 100084 China
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15
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Chicca I, Becarelli S, Dartiahl C, La China S, De Kievit T, Petroni G, Di Gregorio S, Levin DB. Degradation of BTEX mixture by a new Pseudomonas putida strain: role of the quorum sensing in the modulation of the upper BTEX oxidative pathway. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:36203-36214. [PMID: 32557076 DOI: 10.1007/s11356-020-09650-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
A new Pseudomonas putida strain (AQ8) was isolated from a decommissioned oil refinery's soil in Italy and characterized for its ability to degrade BTEX. The draft genome of the new strain was sequenced and annotated for genes that encode enzymes putatively involved in BTEX degradation and quorum sensing. The strain was transformed with a plasmid expressing lactonase, which cleaves the autoinducer quorum sensing signal molecule, the acyl-homoserine lactone, to obtain a quorum sensing minus strain. P. putida AQ8 depleted the 40% on average of all the components of the initial BTEX concentration in 36 h. The quorum sensing minus strain, in the same time interval, depleted only the 10% of the initial BTEX concentration. The role of quorum sensing in regulating the expression of the annotated benzene/toluene dioxygenase gene (benzA) and biphenyl/toluene/benzene dioxygenase (bphA) genes, which are involved in BTEX degradation, was studied by quantitative RT-real-time quantitative (q)PCR analysis. The qPCR data showed decreased levels of expression of the benzA and bphA genes in the quorum sensing minus strain. Our results showed, for the first time, quorum sensing modulation of the level of transcription of dioxygenase genes in the upper BTEX oxidation pathway.
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Affiliation(s)
- Ilaria Chicca
- Department of Biology, University of Pisa, Pisa, Italy
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Christopher Dartiahl
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Salvatore La China
- Department of Life Sciences, University of Modena and Reggio-Emilia, Modena, Italy
| | - Teresa De Kievit
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | | | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
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16
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Shivaprasad DP, Taneja NK, Lakra A, Sachdev D. In vitro and in situ abrogation of biofilm formation in E. coli by vitamin C through ROS generation, disruption of quorum sensing and exopolysaccharide production. Food Chem 2020; 341:128171. [PMID: 33035856 DOI: 10.1016/j.foodchem.2020.128171] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/13/2020] [Accepted: 09/20/2020] [Indexed: 01/12/2023]
Abstract
Emergence of antimicrobial drug-resistance amongst food-borne pathogens has led to severe deficit of available therapeutics and requires novel interventions. This study determined the activity of vitamin C (VitC), a natural antioxidant as powerful antibacterial agent against multidrug-resistant (MDR), biofilm-forming E. coli. Our findings revealed that VitC wield antibacterial action in dose-time dependent manner with minimum inhibitory concentration (MIC) of 125 mM. At these concentrations VitC impaired quorum sensing (QS) and exopolysaccharide (EPS) production and induced sugar and protein leakage from the bacterial cells by virtue of reactive oxygen species (ROS) generation. Furthermore, VitC-treated bacteria showed downregulation of genes underpinning biofilm signaling (luxS) and regulation (bssR) by up to 27-folds. Finally, this study demonstrated the promising antimicrobial application of VitC, in situ, in Indian soft cheese (paneer) when applied as a coating. Therefore, VitC can be applied as natural and safe 'antimicrobial' against biofilm-forming bacteria in food systems vis-à-vis other conventional antimicrobials.
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Affiliation(s)
- D P Shivaprasad
- Department of Food Technology, Vignan's Foundation for Science Technology and Research (Deemed to be University), Vadlamudi, Guntur 522213, Andhra Pradesh, India; Department of Basic and Applied Sciences, NIFTEM, Sonipat 131028, Haryana, India
| | - Neetu Kumra Taneja
- Department of Basic and Applied Sciences, NIFTEM, Sonipat 131028, Haryana, India.
| | - Anupama Lakra
- Department of Basic and Applied Sciences, NIFTEM, Sonipat 131028, Haryana, India
| | - Divya Sachdev
- Department of Basic and Applied Sciences, NIFTEM, Sonipat 131028, Haryana, India
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17
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Zhang L, Guo W, Lu Y. Advances in Cell‐Free Biosensors: Principle, Mechanism, and Applications. Biotechnol J 2020; 15:e2000187. [DOI: 10.1002/biot.202000187] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/22/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Liyuan Zhang
- Key Laboratory of Industrial Biocatalysis Ministry of Education Department of Chemical Engineering Tsinghua University Beijing 100084 China
- Department of Ecology Shenyang Agricultural University Shenyang Liaoning Province 110866 China
| | - Wei Guo
- Department of Ecology Shenyang Agricultural University Shenyang Liaoning Province 110866 China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis Ministry of Education Department of Chemical Engineering Tsinghua University Beijing 100084 China
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18
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Billot R, Plener L, Jacquet P, Elias M, Chabrière E, Daudé D. Engineering acyl-homoserine lactone-interfering enzymes toward bacterial control. J Biol Chem 2020; 295:12993-13007. [PMID: 32690609 DOI: 10.1074/jbc.rev120.013531] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/17/2020] [Indexed: 12/20/2022] Open
Abstract
Enzymes able to degrade or modify acyl-homoserine lactones (AHLs) have drawn considerable interest for their ability to interfere with the bacterial communication process referred to as quorum sensing. Many proteobacteria use AHL to coordinate virulence and biofilm formation in a cell density-dependent manner; thus, AHL-interfering enzymes constitute new promising antimicrobial candidates. Among these, lactonases and acylases have been particularly studied. These enzymes have been isolated from various bacterial, archaeal, or eukaryotic organisms and have been evaluated for their ability to control several pathogens. Engineering studies on these enzymes were carried out and successfully modulated their capacity to interact with specific AHL, increase their catalytic activity and stability, or enhance their biotechnological potential. In this review, special attention is paid to the screening, engineering, and applications of AHL-modifying enzymes. Prospects and future opportunities are also discussed with a view to developing potent candidates for bacterial control.
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Affiliation(s)
- Raphaël Billot
- Gene&GreenTK, Marseille, France; IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | | | | | - Mikael Elias
- Molecular Biology and Biophysics and Biotechnology Institute, Department of Biochemistry, University of Minnesota, St. Paul, Minnesota, USA
| | - Eric Chabrière
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille Université, Marseille, France.
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19
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Miller C, Gilmore J. Detection of Quorum-Sensing Molecules for Pathogenic Molecules Using Cell-Based and Cell-Free Biosensors. Antibiotics (Basel) 2020; 9:antibiotics9050259. [PMID: 32429345 PMCID: PMC7277912 DOI: 10.3390/antibiotics9050259] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 11/18/2022] Open
Abstract
Since the discovery and subsequent use of penicillin, antibiotics have been used to treat most bacterial infections in the U.S. Over time, the repeated prescription of many antibiotics has given rise to many antibiotic-resistant microbes. A bacterial strain becomes resistant by horizontal gene transfer, where surviving microbes acquire genetic material or DNA fragments from adjacent bacteria that encode for resistance. In order to avoid significant bacterial resistance, novel and target therapeutics are needed. Further advancement of diagnostic technologies could be used to develop novel treatment strategies. The use of biosensors to detect quorum-sensing signaling molecules has the potential to provide timely diagnostic information toward mitigating the multidrug-resistant bacteria epidemic. Resistance and pathogenesis are controlled by quorum-sensing (QS) circuits. QS systems secrete or passively release signaling molecules when the bacterial concentration reaches a certain threshold. Signaling molecules give an early indication of virulence. Detection of these compounds in vitro or in vivo can be used to identify the onset of infection. Whole-cell and cell-free biosensors have been developed to detect quorum-sensing signaling molecules. This review will give an overview of quorum networks in the most common pathogens found in chronic and acute infections. Additionally, the current state of research surrounding the detection of quorum-sensing molecules will be reviewed. Followed by a discussion of future works toward the advancement of technologies to quantify quorum signaling molecules in chronic and acute infections.
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20
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Thavarajah W, Verosloff MS, Jung JK, Alam KK, Miller JD, Jewett MC, Young SL, Lucks JB. A Primer on Emerging Field-Deployable Synthetic Biology Tools for Global Water Quality Monitoring. NPJ CLEAN WATER 2020; 3:18. [PMID: 34267944 PMCID: PMC8279131 DOI: 10.1038/s41545-020-0064-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/09/2020] [Indexed: 05/22/2023]
Abstract
Tracking progress towards Target 6.1 of the United Nations Sustainable Development Goals, "achieving universal and equitable access to safe and affordable drinking water for all", necessitates the development of simple, inexpensive tools to monitor water quality. The rapidly growing field of synthetic biology has the potential to address this need by taking DNA-encoded sensing elements from nature and reassembling them to create field-deployable 'biosensors' that can detect pathogenic or chemical water contaminants. Here we describe water quality monitoring strategies enabled by synthetic biology and compare them to previous approaches used to detect three priority water contaminants: fecal pathogens, arsenic, and fluoride in order to explain the potential for engineered biosensors to simplify and decentralize water quality monitoring. We also briefly discuss expanding biosensors to detect emerging contaminants including metals and pharmaceuticals. We conclude with an outlook on the future of biosensor development, in which we discuss adaptability to emerging contaminants, outline current limitations, and propose steps to overcome the field's outstanding challenges to facilitate global water quality monitoring.
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Affiliation(s)
- Walter Thavarajah
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Matthew S. Verosloff
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, 2204 Tech Drive, Evanston, IL, 60208, USA
| | - Jaeyoung K. Jung
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Khalid K. Alam
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Joshua D. Miller
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Department of Anthropology, Northwestern University, 1810 Hinman Ave., Evanston, IL, 60208, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Sera L. Young
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Department of Anthropology, Northwestern University, 1810 Hinman Ave., Evanston, IL, 60208, USA
- Institute for Policy Research, Northwestern University, 2040 Sheridan Rd, Evanston, IL, 60208 USA
- To whom correspondence should be addressed, ,
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- To whom correspondence should be addressed, ,
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21
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Meyer A, Saaem I, Silverman A, Varaljay VA, Mickol R, Blum S, Tobias AV, Schwalm ND, Mojadedi W, Onderko E, Bristol C, Liu S, Pratt K, Casini A, Eluere R, Moser F, Drake C, Gupta M, Kelley-Loughnane N, Lucks JP, Akingbade KL, Lux MP, Glaven S, Crookes-Goodson W, Jewett MC, Gordon DB, Voigt CA. Organism Engineering for the Bioproduction of the Triaminotrinitrobenzene (TATB) Precursor Phloroglucinol (PG). ACS Synth Biol 2019; 8:2746-2755. [PMID: 31750651 DOI: 10.1021/acssynbio.9b00393] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Organism engineering requires the selection of an appropriate chassis, editing its genome, combining traits from different source species, and controlling genes with synthetic circuits. When a strain is needed for a new target objective, for example, to produce a chemical-of-need, the best strains, genes, techniques, software, and expertise may be distributed across laboratories. Here, we report a project where we were assigned phloroglucinol (PG) as a target, and then combined unique capabilities across the United States Army, Navy, and Air Force service laboratories with the shared goal of designing an organism to produce this molecule. In addition to the laboratory strain Escherichia coli, organisms were screened from soil and seawater. Putative PG-producing enzymes were mined from a strain bank of bacteria isolated from aircraft and fuel depots. The best enzyme was introduced into the ocean strain Marinobacter atlanticus CP1 with its genome edited to redirect carbon flux from natural fatty acid ester (FAE) production. PG production was also attempted in Bacillus subtilis and Clostridium acetobutylicum. A genetic circuit was constructed in E. coli that responds to PG accumulation, which was then ported to an in vitro paper-based system that could serve as a platform for future low-cost strain screening or for in-field sensing. Collectively, these efforts show how distributed biotechnology laboratories with domain-specific expertise can be marshalled to quickly provide a solution for a targeted organism engineering project, and highlights data and material sharing protocols needed to accelerate future efforts.
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Affiliation(s)
- Adam Meyer
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ishtiaq Saaem
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Adam Silverman
- Center for Synthetic Biology, Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Vanessa A. Varaljay
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Rebecca Mickol
- American Society for Engineering Education, 1818 N Street NW Suite 600, Washington, D.C. 20036, United States
| | - Steven Blum
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Alexander V. Tobias
- U.S. Army Research Laboratory, FCDD-RLS-EB, 2800 Powder Mill Road, Adelphi, Maryland 20783, United States
| | - Nathan D. Schwalm
- U.S. Army Research Laboratory, FCDD-RLS-EB, 2800 Powder Mill Road, Adelphi, Maryland 20783, United States
| | - Wais Mojadedi
- Oak Ridge Associate Universities, P.O.
Box 117, MS-29, Oak Ridge, Tennessee 37831, United States
| | - Elizabeth Onderko
- National Research Council, 500 5th Street NW, Washington, D.C. 20001, United States
| | - Cassandra Bristol
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Shangtao Liu
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
| | - Katelin Pratt
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Arturo Casini
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Raissa Eluere
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Felix Moser
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Carrie Drake
- UES, Inc., 4401 Dayton-Xenia Road, Dayton, Ohio 45432, United States
| | - Maneesh Gupta
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Nancy Kelley-Loughnane
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Julius P. Lucks
- Center for Synthetic Biology, Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Katherine L. Akingbade
- U.S. Army Research Laboratory, FCDD-RLS-EB, 2800 Powder Mill Road, Adelphi, Maryland 20783, United States
| | - Matthew P. Lux
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Sarah Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Wendy Crookes-Goodson
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Michael C. Jewett
- Center for Synthetic Biology, Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - D. Benjamin Gordon
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Christopher A. Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
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22
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Effect of Quorum Sensing on the Ability of Desulfovibrio vulgaris To Form Biofilms and To Biocorrode Carbon Steel in Saline Conditions. Appl Environ Microbiol 2019; 86:AEM.01664-19. [PMID: 31628147 DOI: 10.1128/aem.01664-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 10/13/2019] [Indexed: 11/20/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) are key contributors to microbe-induced corrosion (MIC), which can lead to serious economic and environmental impact. The presence of a biofilm significantly increases the MIC rate. Inhibition of the quorum-sensing (QS) system is a promising alternative approach to prevent biofilm formation in various industrial settings, especially considering the significant ecological impact of conventional chemical-based mitigation strategies. In this study, the effect of the QS stimulation and inhibition on Desulfovibrio vulgaris is described in terms of anaerobic respiration, cell activity, biofilm formation, and biocorrosion of carbon steel. All these traits were repressed when bacteria were in contact with QS inhibitors but enhanced upon exposure to QS signal molecules compared to the control. The difference in the treatments was confirmed by transcriptomic analysis performed at different time points after treatment application. Genes related to lactate and pyruvate metabolism, sulfate reduction, electron transfer, and biofilm formation were downregulated upon QS inhibition. In contrast, QS stimulation led to an upregulation of the above-mentioned genes compared to the control. In summary, these results reveal the impact of QS on the activity of D. vulgaris, paving the way toward the prevention of corrosive SRB biofilm formation via QS inhibition.IMPORTANCE Sulfate-reducing bacteria (SRB) are considered key contributors to biocorrosion, particularly in saline environments. Biocorrosion imposes tremendous economic costs, and common approaches to mitigate this problem involve the use of toxic and hazardous chemicals (e.g., chlorine), which raise health and environmental safety concerns. Quorum-sensing inhibitors (QSIs) can be used as an alternative approach to inhibit biofilm formation and biocorrosion. However, this approach would only be effective if SRB rely on QS for the pathways associated with biocorrosion. These pathways would include biofilm formation, electron transfer, and metabolism. This study demonstrates the role of QS in Desulfovibrio vulgaris on the above-mentioned pathways through both phenotypic measurements and transcriptomic approach. The results of this study suggest that QSIs can be used to mitigate SRB-induced corrosion problems in ecologically sensitive areas.
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Silverman AD, Karim AS, Jewett MC. Cell-free gene expression: an expanded repertoire of applications. Nat Rev Genet 2019; 21:151-170. [DOI: 10.1038/s41576-019-0186-3] [Citation(s) in RCA: 246] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/24/2022]
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Lee KH, Kim DM. In Vitro Use of Cellular Synthetic Machinery for Biosensing Applications. Front Pharmacol 2019; 10:1166. [PMID: 31680954 PMCID: PMC6803485 DOI: 10.3389/fphar.2019.01166] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 09/10/2019] [Indexed: 12/25/2022] Open
Abstract
The application of biosensors is expanding in diverse fields due to their high selectivity and sensitivity. Biosensors employ biological components for the recognition of target analytes. In addition, the amplifying nature of biosynthetic processes can potentially be harnessed to for biological transduction of detection signals. Recent advances in the development of highly productive and cost-effective cell-free synthesis systems make it possible to use these systems as the biological transducers to generate biosensing signals. This review surveys recent developments in cell-free biosensors, focusing on the newly devised mechanisms for the biological recognition of analytes to initiate the amplification processes of transcription and translation.
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Affiliation(s)
- Kyung-Ho Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, South Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, South Korea
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Yu H, Li J, Han Y, Shi G, Liu Z, Zeng M. AHLs-produced bacteria in refrigerated shrimp enhanced the growth and spoilage ability of Shewanella baltica. Journal of Food Science and Technology 2019; 56:114-121. [PMID: 30728552 DOI: 10.1007/s13197-018-3464-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 10/03/2018] [Accepted: 10/16/2018] [Indexed: 11/25/2022]
Abstract
Shewanella baltica is the predominant bacteria in spoiled shrimp (Litopenaeus vannamei), however, the spoilage ability and the mechanism of S. baltica is still unknown. S. baltica can't produce the signal molecule of acyl-homoserine-lactones (AHLs), so the aim of this study was to investigate how wild type S. baltica SA03 (WT SA03) eavesdrop exogenous AHLs to enhance its spoilage ability through LuxR receptor. The results indicated that Aeromonas spp. (Aer), Acinetobacter spp. (Aci) and Serratia spp. (Ser) isolated from refrigerated shrimp can produce different AHLs. WT SA03 can eavesdrop the AHLs of Aer (C4-HSL), Aci (O-C6-HSL) and Ser (C6-HSL, O-C6-HSL) to enhance its growth, especially Ser. Exogenous C4-HSL and C6-HSL enhanced biofilm formation of WT SA03, and C6-HSL and O-C6-HSL enhanced thioredoxin reductase trxB mRNA expression. However, the luxR mutant of WT SA03 (ΔluxR SA03) lost or weakened the role of using environmental AHLs. In vivo experiments, the lag time of WT SA03 was shortened by 6.4 h, 6.2 h and 14.4 h by co-inoculated with Aer, Aci and Ser, respectively. The total volatile basic nitrogen (TVB-N) were significantly enhanced in the samples co-inoculated with WT SA03 and Aer (or Aci, Ser) than those of ΔluxR SA03 and Aer (or Aci, Ser) (p < 0.05). The results showed that S. baltica SA03 can utilize AHLs produced by other bacteria to enhance its growth and spoilage ability through LuxR receptor system. Quorum sensing based on AHLs of bacteria might as the potential targets for food spoilage control.
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Affiliation(s)
- Honglei Yu
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao, 266003 China
| | - Jianpeng Li
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao, 266003 China
| | - Yunyan Han
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao, 266003 China
| | - Guocui Shi
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao, 266003 China
| | - Zunying Liu
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao, 266003 China
| | - Mingyong Zeng
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao, 266003 China
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Sivakumar K, Scarascia G, Zaouri N, Wang T, Kaksonen AH, Hong PY. Salinity-Mediated Increment in Sulfate Reduction, Biofilm Formation, and Quorum Sensing: A Potential Connection Between Quorum Sensing and Sulfate Reduction? Front Microbiol 2019; 10:188. [PMID: 30787924 PMCID: PMC6373464 DOI: 10.3389/fmicb.2019.00188] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/23/2019] [Indexed: 11/30/2022] Open
Abstract
Biocorrosion in marine environment is often associated with biofilms of sulfate reducing bacteria (SRB). However, not much information is available on the mechanism underlying exacerbated rates of SRB-mediated biocorrosion under saline conditions. Using Desulfovibrio (D.) vulgaris and Desulfobacterium (Db.) corrodens as model SRBs, the enhancement effects of salinity on sulfate reduction, N-acyl homoserine lactone (AHL) production and biofilm formation by SRBs were demonstrated. Under saline conditions, D. vulgaris and Db. corrodens exhibited significantly higher specific sulfate reduction and specific AHL production rates as well as elevated rates of biofilm formation compared to freshwater medium. Salinity-induced enhancement traits were also confirmed at transcript level through reverse transcription quantitative polymerase chain reaction (RT-qPCR) approach, which showed salinity-influenced increase in the expression of genes associated with carbon metabolism, sulfate reduction, biofilm formation and histidine kinase signal transduction. In addition, by deploying quorum sensing (QS) inhibitors, a potential connection between sulfate reduction and AHL production under saline conditions was demonstrated, which is most significant during early stages of sulfate metabolism. The findings collectively revealed the interconnection between QS, sulfate reduction and biofilm formation among SRBs, and implied the potential of deploying quorum quenching approaches to control SRB-based biocorrosion in saline conditions.
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Affiliation(s)
- Krishnakumar Sivakumar
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Giantommaso Scarascia
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Noor Zaouri
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Tiannyu Wang
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Anna H Kaksonen
- Land and Water, Commonwealth Scientific and Industrial Research Organization, Floreat, WA, Australia
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Soltani M, Davis BR, Ford H, Nelson JAD, Bundy BC. Reengineering cell-free protein synthesis as a biosensor: Biosensing with transcription, translation, and protein-folding. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.06.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Acyl-homoserine-lactones receptor LuxR of Shewanella baltica involved in the development of microbiota and spoilage of refrigerated shrimp. Journal of Food Science and Technology 2018; 55:2795-2800. [PMID: 30042596 DOI: 10.1007/s13197-018-3172-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 03/30/2018] [Accepted: 04/09/2018] [Indexed: 10/17/2022]
Abstract
Numerous bacterial species utilize quorum sensing molecules acyl-homoserine-lactones (AHLs) to communicate, however, crosstalk often complicates the dynamics and behaviors of mixed populations. In this study, we developed a luxR mutant of wild type Shewanella baltica SA03 (WT SA03), and aimed to investigate the role of S. baltica LuxR (AHLs receptor) involved in the spoilage of refrigerated shrimp (Litopenaeus vannamei) by inoculating WT SA03 and luxR mutant of S. baltica SA03 (ΔluxR SA03), respectively. The results indicated the maximum growth rate of total viable bacteria in shrimp inoculated with ΔluxR SA03 was 73.34% lower than that of WT SA03. The lag time of total bacteria in shrimp treated with ΔluxR SA03 were 87.6 h, significantly longer than that of WT SA03. Meanwhile, the total volatile basic nitrogen concentrations of shrimp treated with WT SA03 were significantly higher than that of ΔluxR SA03 after 2 days of storage, which were in agreement with the decrease of the content of AHLs of the shrimp. The results indicated S. baltica might utilize AHLs produced by other bacteria and accelerate the shrimp spoilage process through LuxR receptor system.
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Zhu S, Wu H, Zhang C, Jie J, Liu Z, Zeng M, Wang C. Spoilage of refrigerated Litopenaeus vannamei: eavesdropping on Acinetobacter acyl-homoserine lactones promotes the spoilage potential of Shewanella baltica. Journal of Food Science and Technology 2018; 55:1903-1912. [PMID: 29666543 DOI: 10.1007/s13197-018-3108-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 10/18/2017] [Accepted: 03/05/2018] [Indexed: 10/17/2022]
Abstract
Shewanella baltica and Acinetobacter are among the predominant spoilage bacteria in refrigerated shrimp (Litopenaeus vannamei). S. baltica are incapable of producing acyl-homoserine lactone (AHL) quorum sensing signals, but can respond to environmental AHLs. In this paper, Acinetobacter was found to produce three AHLs, i.e. N-butanoyl-l-homoserine lactone (C4-HSL), N-(3-oxohexanoyl)-l-homoserine lactone (O-C6-HSL) and N-(3-oxooctanoyl)-l-homoserine lactone (O-C8-HSL), according to thin-layer chromatography using the bioreporter Agrobacterium tumefaciens A136. The agar diffusion and β-galactosidase assays revealed that S. baltica could eavesdrop on these three AHLs from Acinetobacter. Eavesdropping on Acinetobacter AHLs especially C4-HSL was found to boost the growth of S. baltica particularly under nutrient limiting conditions (up to 40-fold increase) in the co-culture experiments. The azocasein assay revealed that S. baltica produced fourfold more extracellular proteases in response to Acinetobacter AHLs. As demonstrated by the biofilm crystal violet staining assay and confocal laser scanning microscopy, eavesdropping also decreased the biofilm-forming capacity of Acinetobacter. By inoculation of S. baltica and Acinetobacter onto surface-sterilized shrimp, eavesdropping was found to endow a growth advantage to S. baltica in vivo, resulting in a 0.5 day shortened shelf life of shrimp according to total volatile basic nitrogen levels and sensory analysis. Overall, the AHL-dependent eavesdropping increased the spoilage potential of S. baltica, providing a fresh perspective on the spoilage process of refrigerated L. vannamei, and this may inspire the development of novel preservation techniques in the future to further reduce post-harvest loss of shrimp.
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Affiliation(s)
- Suqin Zhu
- 1College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao, 266003 Shandong Province China
| | - Haohao Wu
- 1College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao, 266003 Shandong Province China
| | - Caili Zhang
- 1College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao, 266003 Shandong Province China
| | - Jinxin Jie
- 1College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao, 266003 Shandong Province China
| | - Zunying Liu
- 1College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao, 266003 Shandong Province China
| | - Mingyong Zeng
- 1College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao, 266003 Shandong Province China
| | - Changyun Wang
- 2School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003 Shandong Province China
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Jiang L, Zhao J, Lian J, Xu Z. Cell-free protein synthesis enabled rapid prototyping for metabolic engineering and synthetic biology. Synth Syst Biotechnol 2018; 3:90-96. [PMID: 29900421 PMCID: PMC5995451 DOI: 10.1016/j.synbio.2018.02.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 02/11/2018] [Accepted: 02/14/2018] [Indexed: 11/15/2022] Open
Abstract
Advances in metabolic engineering and synthetic biology have facilitated the manufacturing of many valuable-added compounds and commodity chemicals using microbial cell factories in the past decade. However, due to complexity of cellular metabolism, the optimization of metabolic pathways for maximal production represents a grand challenge and an unavoidable barrier for metabolic engineering. Recently, cell-free protein synthesis system (CFPS) has been emerging as an enabling alternative to address challenges in biomanufacturing. This review summarizes the recent progresses of CFPS in rapid prototyping of biosynthetic pathways and genetic circuits (biosensors) to speed up design-build-test (DBT) cycles of metabolic engineering and synthetic biology.
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Affiliation(s)
- Lihong Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiarun Zhao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
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Homogentisic acid γ-lactone suppresses the virulence factors of Pseudomonas aeruginosa by quenching its quorum sensing signal molecules. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.09.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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A Culture-Dependent Method for the Identification of Quorum Quenching Enzymes of Microbial Origin. Methods Mol Biol 2018; 1673:297-309. [PMID: 29130182 DOI: 10.1007/978-1-4939-7309-5_23] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
Abstract
Although it has been more than a decade since the first discovery of AHL lactonase AiiA in Bacillus sp. 240B1, we are only beginning to understand the diversity of quorum quenching (QQ) enzymes. Most of the previously identified QQ enzymes are derived from nonmarine microorganisms. A novel marine-derived secretory AHL lactonase, MomL, was found in Muricauda olearia in our previous work and represents a novel type of AHL lactonase widespread in the ocean. Herein, we describe a culture-dependent method for the identification of microbial QQ enzymes, especially the high-throughput method for screening QQ bacteria from cultivable bacterial strains. This method should be capable of efficiently identifying QQ enzymes from various microbial origins. The discovery of more QQ enzymes will help us to understand their ecological roles and may provide potential as therapeutic agents.
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Wen KY, Cameron L, Chappell J, Jensen K, Bell DJ, Kelwick R, Kopniczky M, Davies JC, Filloux A, Freemont PS. A Cell-Free Biosensor for Detecting Quorum Sensing Molecules in P. aeruginosa-Infected Respiratory Samples. ACS Synth Biol 2017; 6:2293-2301. [PMID: 28981256 DOI: 10.1021/acssynbio.7b00219] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Synthetic biology designed cell-free biosensors are a promising new tool for the detection of clinically relevant biomarkers in infectious diseases. Here, we report that a modular DNA-encoded biosensor in cell-free protein expression systems can be used to measure a bacterial biomarker of Pseudomonas aeruginosa infection from human sputum samples. By optimizing the cell-free system and sample extraction, we demonstrate that the quorum sensing molecule 3-oxo-C12-HSL in sputum samples from cystic fibrosis lungs can be quantitatively measured at nanomolar levels using our cell-free biosensor system, and is comparable to LC-MS measurements of the same samples. This study further illustrates the potential of modular cell-free biosensors as rapid, low-cost detection assays that can inform clinical practice.
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Affiliation(s)
- Ke Yan Wen
- Section of Structural Biology, Department of Medicine, Imperial College London , London SW7 2AZ, U.K.,Centre for Synthetic Biology and Innovation, Imperial College London , London SW7 2AZ, U.K
| | - Loren Cameron
- Section of Structural Biology, Department of Medicine, Imperial College London , London SW7 2AZ, U.K.,Centre for Synthetic Biology and Innovation, Imperial College London , London SW7 2AZ, U.K.,MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London , London SW7 2AZ, U.K
| | - James Chappell
- Centre for Synthetic Biology and Innovation, Imperial College London , London SW7 2AZ, U.K
| | - Kirsten Jensen
- Section of Structural Biology, Department of Medicine, Imperial College London , London SW7 2AZ, U.K.,Centre for Synthetic Biology and Innovation, Imperial College London , London SW7 2AZ, U.K.,SynbiCITE, Imperial College London , London SW7 2AZ, U.K
| | - David J Bell
- Section of Structural Biology, Department of Medicine, Imperial College London , London SW7 2AZ, U.K.,SynbiCITE, Imperial College London , London SW7 2AZ, U.K
| | - Richard Kelwick
- Section of Structural Biology, Department of Medicine, Imperial College London , London SW7 2AZ, U.K.,Centre for Synthetic Biology and Innovation, Imperial College London , London SW7 2AZ, U.K
| | - Margarita Kopniczky
- Section of Structural Biology, Department of Medicine, Imperial College London , London SW7 2AZ, U.K.,Centre for Synthetic Biology and Innovation, Imperial College London , London SW7 2AZ, U.K
| | - Jane C Davies
- Chronic Suppurative Lung Disease, National Heart and Lung Institute, Imperial College London , London SW7 2AZ, U.K.,Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Foundation Trust , London SW3 6NP, U.K
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London , London SW7 2AZ, U.K
| | - Paul S Freemont
- Section of Structural Biology, Department of Medicine, Imperial College London , London SW7 2AZ, U.K.,Centre for Synthetic Biology and Innovation, Imperial College London , London SW7 2AZ, U.K.,SynbiCITE, Imperial College London , London SW7 2AZ, U.K
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Effects of quorum quenching by AHL lactonase on AHLs, protease, motility and proteome patterns in Aeromonas veronii LP-11. Int J Food Microbiol 2017; 252:61-68. [DOI: 10.1016/j.ijfoodmicro.2017.04.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 04/05/2017] [Accepted: 04/13/2017] [Indexed: 01/07/2023]
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Karig DK. Cell-free synthetic biology for environmental sensing and remediation. Curr Opin Biotechnol 2017; 45:69-75. [DOI: 10.1016/j.copbio.2017.01.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/24/2017] [Indexed: 01/15/2023]
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Ergön-Can T, Köse-Mutlu B, Koyuncu İ, Lee CH. Biofouling control based on bacterial quorum quenching with a new application: Rotary microbial carrier frame. J Memb Sci 2017. [DOI: 10.1016/j.memsci.2016.10.036] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Quorum Sensing and the Use of Quorum Quenchers as Natural Biocides to Inhibit Sulfate-Reducing Bacteria. Antibiotics (Basel) 2016; 5:antibiotics5040039. [PMID: 27983678 PMCID: PMC5187520 DOI: 10.3390/antibiotics5040039] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/23/2016] [Accepted: 12/06/2016] [Indexed: 11/17/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) are one of the main protagonist groups of biocorrosion in the seawater environment. Given their principal role in biocorrosion, it remains a crucial task to develop strategies to reduce the abundance of SRBs. Conventional approaches include the use of biocides and antibiotics, which can impose health, safety, and environmental concerns. This review examines an alternative approach to this problem. This is achieved by reviewing the role of quorum sensing (QS) in SRB populations and its impact on the biofilm formation process. Genome databases of SRBs are mined to look for putative QS systems and homologous protein sequences representative of autoinducer receptors or synthases. Subsequently, this review puts forward the potential use of quorum quenchers as natural biocides against SRBs and outlines the potential strategies for the implementation of this approach.
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John J, Saranathan R, Adigopula LN, Thamodharan V, Singh SP, Lakshmi TP, CharanTej MA, Rao RS, Krishna R, Rao HSP, Prashanth K. The quorum sensing molecule N-acyl homoserine lactone produced by Acinetobacter baumannii displays antibacterial and anticancer properties. BIOFOULING 2016; 32:1029-1047. [PMID: 27643959 DOI: 10.1080/08927014.2016.1221946] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 08/04/2016] [Indexed: 06/06/2023]
Abstract
Secretory N-acyl homoserine lactones (AHLs) mediate quorum sensing (QS) in bacteria. AHLs are shown to be inhibitory for an unrelated group of bacteria and might mimic host signalling elements, thereby subverting the regulatory events in host cells. This study investigated the AHL produced by Acinetobacter baumannii and analysed its effect on other bacterial species and mammalian cells. Chemically characterized AHL had an m/z value of 325 with a molecular formula C18H31NO4 and showed its inhibitory potential against Staphylococcus aureus. Molecular docking studies identified D-alanine-D-alanine synthetase A, a cell wall synthesizing enzyme of S. aureus having a strong binding affinity towards AHL. Electron microscopy showed the disruption and sloughing off of the S. aureus cell wall when treated with AHL. In vitro experiments revealed that this bacteriostatic AHL showed time-dependent activity and induced apoptosis in cancer cell lines. This compound could be a potential structural backbone for constructing new AHL analogues against S. aureus. The findings emphasize the need to re-evaluate all previously characterized AHLs for any additional new biological functions other than QS.
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Affiliation(s)
- James John
- a Department of Biotechnology , School of Life Sciences, Pondicherry University , Puducherry , India
- d Department of Biotechnology , SRF, Interdisciplinary Program in Life Sciences, Pondicherry University , Puducherry , India
| | - Rajagopalan Saranathan
- a Department of Biotechnology , School of Life Sciences, Pondicherry University , Puducherry , India
| | | | - Vasanth Thamodharan
- a Department of Biotechnology , School of Life Sciences, Pondicherry University , Puducherry , India
| | - Satya Prakash Singh
- a Department of Biotechnology , School of Life Sciences, Pondicherry University , Puducherry , India
| | - T Pragna Lakshmi
- c Centre for Bioinformatics , School of Life Sciences, Pondicherry University , Puducherry , India
| | - Mallu Abhiram CharanTej
- a Department of Biotechnology , School of Life Sciences, Pondicherry University , Puducherry , India
| | - R Srinivasa Rao
- a Department of Biotechnology , School of Life Sciences, Pondicherry University , Puducherry , India
| | - R Krishna
- c Centre for Bioinformatics , School of Life Sciences, Pondicherry University , Puducherry , India
| | | | - K Prashanth
- a Department of Biotechnology , School of Life Sciences, Pondicherry University , Puducherry , India
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Kumari S, Mangwani N, Das S. Synergistic effect of quorum sensing genes in biofilm development and PAHs degradation by a marine bacterium. Bioengineered 2016; 7:205-11. [PMID: 27111260 DOI: 10.1080/21655979.2016.1174797] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Quorum sensing (QS) is a prevalently found intercellular signaling system in bacteria. QS system bestows behavioral coordination ability in bacteria at high population density. QS via acylated homoserine lactone (AHL) is extensively conserved in Gram-negative bacteria and plays crucial role in regulating many biological processes. The role of QS genes coding for AHL synthase enzyme (lasI and rhlI) was established in bioremediation of polycyclic aromatic hydrocarbons (PAHs) viz. phenanthrene and pyrene. AHL producing biofilm forming marine bacterium Pseudomonas aeruginosa N6P6 was isolated by selective enrichment on PAHs. AHL production was confirmed using AHL bioreporters and GC-MS analysis. Biofilm development and its architecture was significantly (P < 0.05) affected by alterations in lasI/rhlI expression. The lasI/rhlI gene expression pattern significantly influences biofilm formation and subsequent degradation of PAHs. The integrated density of Pseudomonas aeruginosa N6P6 biofilm was highest for 48 h old biofilm and the PAHs (phenanthrene and pyrene) degradation was also found maximum (85.6 % and 47.56 %) with this biofilm. A significant positive correlation (P < 0.05) was observed between lasI expression and PAHs degradation. The role of QS genes in biofilm formation and degradation of PAHs was validated by blocking the transcription of lasI/rhlI by a QS inhibitor (QSI) tannic acid. Further, application of such QS positive isolates in PAHs contaminated sites could be a promising strategy to improve the PAHs bioremediation.
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Affiliation(s)
- Supriya Kumari
- a Laboratory of Environmental Microbiology and Ecology (LEnME) , Department of Life Science , National Institute of Technology , Rourkela , Odisha , India
| | - Neelam Mangwani
- a Laboratory of Environmental Microbiology and Ecology (LEnME) , Department of Life Science , National Institute of Technology , Rourkela , Odisha , India
| | - Surajit Das
- a Laboratory of Environmental Microbiology and Ecology (LEnME) , Department of Life Science , National Institute of Technology , Rourkela , Odisha , India
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41
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Khan R, Shen F, Khan K, Liu LX, Wu HH, Luo JQ, Wan YH. Biofouling control in a membrane filtration system by a newly isolated novel quorum quenching bacterium, Bacillus methylotrophicus sp. WY. RSC Adv 2016. [DOI: 10.1039/c6ra01663d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A newly isolated QQ bacterium, Bacillus methylotrophicus strain WY substantially enhanced the membrane performance by reducing the rate of biofouling.
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Affiliation(s)
- R. Khan
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - F. Shen
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - K. Khan
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - L. X. Liu
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - H. H. Wu
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - J. Q. Luo
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Y. H. Wan
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
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42
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Gopu V, Meena CK, Murali A, Shetty PH. Quorum quenching activity in the cell-free lysate of Enterobacter ludwigii isolated from beef and its effect on quorum sensing regulation in Yersinia enterocolitica. RSC Adv 2016. [DOI: 10.1039/c5ra25440j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A wide range of Gram negative bacteria regulate their phenotypic characteristics through an auto-inducing signaling mechanism called Quorum Sensing (QS).
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43
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Grandclément C, Tannières M, Moréra S, Dessaux Y, Faure D. Quorum quenching: role in nature and applied developments. FEMS Microbiol Rev 2015; 40:86-116. [PMID: 26432822 DOI: 10.1093/femsre/fuv038] [Citation(s) in RCA: 338] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2015] [Indexed: 12/11/2022] Open
Abstract
Quorum sensing (QS) refers to the capacity of bacteria to monitor their population density and regulate gene expression accordingly: the QS-regulated processes deal with multicellular behaviors (e.g. growth and development of biofilm), horizontal gene transfer and host-microbe (symbiosis and pathogenesis) and microbe-microbe interactions. QS signaling requires the synthesis, exchange and perception of bacterial compounds, called autoinducers or QS signals (e.g. N-acylhomoserine lactones). The disruption of QS signaling, also termed quorum quenching (QQ), encompasses very diverse phenomena and mechanisms which are presented and discussed in this review. First, we surveyed the QS-signal diversity and QS-associated responses for a better understanding of the targets of the QQ phenomena that organisms have naturally evolved and are currently actively investigated in applied perspectives. Next the mechanisms, targets and molecular actors associated with QS interference are presented, with a special emphasis on the description of natural QQ enzymes and chemicals acting as QS inhibitors. Selected QQ paradigms are detailed to exemplify the mechanisms and biological roles of QS inhibition in microbe-microbe and host-microbe interactions. Finally, some QQ strategies are presented as promising tools in different fields such as medicine, aquaculture, crop production and anti-biofouling area.
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Affiliation(s)
- Catherine Grandclément
- Institut for Integrative Biology of the Cell, Department of Microbiology, CNRS CEA Paris-Sud University, Saclay Plant Sciences, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
| | - Mélanie Tannières
- Institut for Integrative Biology of the Cell, Department of Microbiology, CNRS CEA Paris-Sud University, Saclay Plant Sciences, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
| | - Solange Moréra
- Institut for Integrative Biology of the Cell, Department of Structural Biology, CNRS CEA Paris-Sud University, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
| | - Yves Dessaux
- Institut for Integrative Biology of the Cell, Department of Microbiology, CNRS CEA Paris-Sud University, Saclay Plant Sciences, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
| | - Denis Faure
- Institut for Integrative Biology of the Cell, Department of Microbiology, CNRS CEA Paris-Sud University, Saclay Plant Sciences, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
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44
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Rojo D, Hevia A, Bargiela R, López P, Cuervo A, González S, Suárez A, Sánchez B, Martínez-Martínez M, Milani C, Ventura M, Barbas C, Moya A, Suárez A, Margolles A, Ferrer M. Ranking the impact of human health disorders on gut metabolism: systemic lupus erythematosus and obesity as study cases. Sci Rep 2015; 5:8310. [PMID: 25655524 PMCID: PMC4319156 DOI: 10.1038/srep08310] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/08/2015] [Indexed: 12/27/2022] Open
Abstract
Multiple factors have been shown to alter intestinal microbial diversity. It remains to be seen, however, how multiple collective pressures impact the activity in the gut environment and which, if any, is positioned as a dominant driving factor determining the final metabolic outcomes. Here, we describe the results of a metabolome-wide scan of gut microbiota in 18 subjects with systemic lupus erythematosus (SLE) and 17 healthy control subjects and demonstrate a statistically significant difference (p < 0.05) between the two groups. Healthy controls could be categorized (p < 0.05) based on their body mass index (BMI), whereas individuals with SLE could not. We discuss the prevalence of SLE compared with BMI as the dominant factor that regulates gastrointestinal microbial metabolism and provide plausible explanatory causes. Our results uncover novel perspectives with clinical relevance for human biology. In particular, we rank the importance of various pathophysiologies for gut homeostasis.
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Affiliation(s)
- David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid
| | - Arancha Hevia
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Asturias, Spain
| | | | - Patricia López
- Immunology Area, Department of Functional Biology, University of Oviedo, Asturias, Spain
| | - Adriana Cuervo
- Physiology Area, Department of Functional Biology, University of Oviedo, Asturias, Spain
| | - Sonia González
- Physiology Area, Department of Functional Biology, University of Oviedo, Asturias, Spain
| | - Ana Suárez
- Immunology Area, Department of Functional Biology, University of Oviedo, Asturias, Spain
| | | | | | - Christian Milani
- Department of Life Sciences, Laboratory of Probiogenomics, University of Parma, Parma, Italy
| | - Marco Ventura
- Department of Life Sciences, Laboratory of Probiogenomics, University of Parma, Parma, Italy
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid
| | - Andrés Moya
- 1] Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO) and Instituto Cavanilles de Biodiversidad y Biología Evolutiva de la Universitat de València, València, Spain [2] CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Antonio Suárez
- Department of Biochemistry and Molecular Biology, Biomedical Research Centre, University of Granada, Granada, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Asturias, Spain
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45
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Kim SR, Lee KB, Kim JE, Won YJ, Yeon KM, Lee CH, Lim DJ. Macroencapsulation of quorum quenching bacteria by polymeric membrane layer and its application to MBR for biofouling control. J Memb Sci 2015. [DOI: 10.1016/j.memsci.2014.09.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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46
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Use of aiiA gene amplification for AHL-lactonase production from endophytic bacterium Enterobacter species. Int J Biol Macromol 2015; 72:1013-9. [DOI: 10.1016/j.ijbiomac.2014.09.049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/25/2014] [Accepted: 09/26/2014] [Indexed: 11/18/2022]
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47
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Kubacka A, Diez MS, Rojo D, Bargiela R, Ciordia S, Zapico I, Albar JP, Barbas C, Martins dos Santos VAP, Fernández-García M, Ferrer M. Understanding the antimicrobial mechanism of TiO₂-based nanocomposite films in a pathogenic bacterium. Sci Rep 2014; 4:4134. [PMID: 24549289 PMCID: PMC3928576 DOI: 10.1038/srep04134] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 02/05/2014] [Indexed: 02/07/2023] Open
Abstract
Titania (TiO2)-based nanocomposites subjected to light excitation are remarkably effective in eliciting microbial death. However, the mechanism by which these materials induce microbial death and the effects that they have on microbes are poorly understood. Here, we assess the low dose radical-mediated TiO2 photocatalytic action of such nanocomposites and evaluate the genome/proteome-wide expression profiles of Pseudomonas aeruginosa PAO1 cells after two minutes of intervention. The results indicate that the impact on the gene-wide flux distribution and metabolism is moderate in the analysed time span. Rather, the photocatalytic action triggers the decreased expression of a large array of genes/proteins specific for regulatory, signalling and growth functions in parallel with subsequent selective effects on ion homeostasis, coenzyme-independent respiration and cell wall structure. The present work provides the first solid foundation for the biocidal action of titania and may have an impact on the design of highly active photobiocidal nanomaterials.
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Affiliation(s)
- Anna Kubacka
- Institute of Catalysis, CSIC, 28049 Madrid, Spain
| | - María Suárez Diez
- Chair of Systems and Synthetic Biology, Wageningen University, 6703 HB Wageningen, The Netherlands
| | - David Rojo
- Center for Metabolomics and Bioanalysis, University CEU San Pablo, Boadilla del Monte, 28668 Madrid, Spain
| | | | - Sergio Ciordia
- Proteomic Facility, CNB-National Centre for Biotechnology, CSIC, 28049 Madrid, Spain
| | - Inés Zapico
- Proteomic Facility, CNB-National Centre for Biotechnology, CSIC, 28049 Madrid, Spain
| | - Juan P Albar
- Proteomic Facility, CNB-National Centre for Biotechnology, CSIC, 28049 Madrid, Spain
| | - Coral Barbas
- Center for Metabolomics and Bioanalysis, University CEU San Pablo, Boadilla del Monte, 28668 Madrid, Spain
| | - Vitor A P Martins dos Santos
- 1] Chair of Systems and Synthetic Biology, Wageningen University, 6703 HB Wageningen, The Netherlands [2] LifeGlimmer GmbH, 12163 Berlin, Germany
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48
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Petrisor AI, Szyjka S, Kawaguchi T, Visscher PT, Norman RS, Decho AW. Changing microspatial patterns of sulfate-reducing microorganisms (SRM) during cycling of marine stromatolite mats. Int J Mol Sci 2014; 15:850-77. [PMID: 24413754 PMCID: PMC3907843 DOI: 10.3390/ijms15010850] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 12/20/2013] [Accepted: 12/30/2013] [Indexed: 11/17/2022] Open
Abstract
Microspatial arrangements of sulfate-reducing microorganisms (SRM) in surface microbial mats (~1.5 mm) forming open marine stromatolites were investigated. Previous research revealed three different mat types associated with these stromatolites, each with a unique petrographic signature. Here we focused on comparing "non-lithifying" (Type-1) and "lithifying" (Type-2) mats. Our results revealed three major trends: (1) Molecular typing using the dsrA probe revealed a shift in the SRM community composition between Type-1 and Type-2 mats. Fluorescence in-situ hybridization (FISH) coupled to confocal scanning-laser microscopy (CSLM)-based image analyses, and 35SO4(2-)-silver foil patterns showed that SRM were present in surfaces of both mat types, but in significantly (p < 0.05) higher abundances in Type-2 mats. Over 85% of SRM cells in the top 0.5 mm of Type-2 mats were contained in a dense 130 µm thick horizontal layer comprised of clusters of varying sizes; (2) Microspatial mapping revealed that locations of SRM and CaCO3 precipitation were significantly correlated (p < 0.05); (3) Extracts from Type-2 mats contained acylhomoserine-lactones (C4- ,C6- ,oxo-C6,C7- ,C8- ,C10- ,C12- , C14-AHLs) involved in cell-cell communication. Similar AHLs were produced by SRM mat-isolates. These trends suggest that development of a microspatially-organized SRM community is closely-associated with the hallmark transition of stromatolite surface mats from a non-lithifying to a lithifying state.
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Affiliation(s)
- Alexandru I Petrisor
- Department of Urban and Landscape Planning, School of Urban Planning, "Ion Mincu" University of Architecture and Urban Planning, str. Academiei nr. 18-20, sector 1, Bucharest 010014, Romania.
| | - Sandra Szyjka
- Department of Urban and Landscape Planning, School of Urban Planning, "Ion Mincu" University of Architecture and Urban Planning, str. Academiei nr. 18-20, sector 1, Bucharest 010014, Romania.
| | - Tomohiro Kawaguchi
- Department of Urban and Landscape Planning, School of Urban Planning, "Ion Mincu" University of Architecture and Urban Planning, str. Academiei nr. 18-20, sector 1, Bucharest 010014, Romania.
| | - Pieter T Visscher
- Department of Urban and Landscape Planning, School of Urban Planning, "Ion Mincu" University of Architecture and Urban Planning, str. Academiei nr. 18-20, sector 1, Bucharest 010014, Romania.
| | - Robert Sean Norman
- Department of Urban and Landscape Planning, School of Urban Planning, "Ion Mincu" University of Architecture and Urban Planning, str. Academiei nr. 18-20, sector 1, Bucharest 010014, Romania.
| | - Alan W Decho
- Department of Urban and Landscape Planning, School of Urban Planning, "Ion Mincu" University of Architecture and Urban Planning, str. Academiei nr. 18-20, sector 1, Bucharest 010014, Romania.
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49
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Rajesh P, Rai VR. Molecular identification of aiiA homologous gene from endophytic Enterobacter species and in silico analysis of putative tertiary structure of AHL-lactonase. Biochem Biophys Res Commun 2014; 443:290-5. [DOI: 10.1016/j.bbrc.2013.11.101] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 11/24/2013] [Indexed: 11/28/2022]
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50
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Zhang QQ, Wang HH, Zhuang S, Xiao HM, Xu XL, Zhou GH. Application of Mathematical Model for the Quantification of Acylated Homoserine Lactones Produces by P
seudomonas aeruginosa
in Chicken Breast Meat and Broth. J Food Saf 2013. [DOI: 10.1111/jfs.12079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Qiu-Qin Zhang
- Key Laboratory of Meat Processing and Quality Control; Ministry of Education; College of Food Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - Hu-Hu Wang
- Key Laboratory of Meat Processing and Quality Control; Ministry of Education; College of Food Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - Su Zhuang
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - Hong-Mei Xiao
- Key Laboratory of Meat Processing and Quality Control; Ministry of Education; College of Food Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - Xing-Lian Xu
- Key Laboratory of Meat Processing and Quality Control; Ministry of Education; College of Food Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - Guang-Hong Zhou
- Key Laboratory of Meat Processing and Quality Control; Ministry of Education; College of Food Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
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