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McCuskey SR, Quek G, Vázquez RJ, Kundukad B, Bin Ismail MH, Astorga SE, Jiang Y, Bazan GC. Evolving Synergy Between Synthetic and Biotic Elements in Conjugated Polyelectrolyte/Bacteria Composite Improves Charge Transport and Mechanical Properties. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2405242. [PMID: 39262122 DOI: 10.1002/advs.202405242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/29/2024] [Indexed: 09/13/2024]
Abstract
gLiving materials can achieve unprecedented function by combining synthetic materials with the wide range of cellular functions. Of interest are situations where the critical properties of individual abiotic and biotic elements improve via their combination. For example, integrating electroactive bacteria into conjugated polyelectrolyte (CPE) hydrogels increases biocurrent production. One observes more efficient electrical charge transport within the CPE matrix in the presence of Shewanella oneidensis MR-1 and more current per cell is extracted, compared to traditional biofilms. Here, the origin of these synergistic effects are examined. Transcriptomics reveals that genes in S. oneidensis MR-1 related to bacteriophages and energy metabolism are upregulated in the composite material. Fluorescent staining and rheological measurements before and after enzymatic treatment identified the importance of extracellular biomaterials in increasing matrix cohesion. The synergy between CPE and S. oneidensis MR-1 thus arises from initially unanticipated changes in matrix composition and bacteria adaption within the synthetic environment.
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Affiliation(s)
- Samantha R McCuskey
- Department of Chemistry and Chemical & Biomolecular Engineering, National University of Singapore, Singapore, 119077, Singapore
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, 637551, Singapore
| | - Glenn Quek
- Department of Chemistry and Chemical & Biomolecular Engineering, National University of Singapore, Singapore, 119077, Singapore
| | - Ricardo Javier Vázquez
- Institute for Functional Intelligent Materials (I-FIM), National University of Singapore, Singapore, 117544, Singapore
| | - Binu Kundukad
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, 637551, Singapore
| | - Muhammad Hafiz Bin Ismail
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, 637551, Singapore
| | - Solange E Astorga
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, 637551, Singapore
| | - Yan Jiang
- Department of Chemistry and Chemical & Biomolecular Engineering, National University of Singapore, Singapore, 119077, Singapore
| | - Guillermo C Bazan
- Department of Chemistry and Chemical & Biomolecular Engineering, National University of Singapore, Singapore, 119077, Singapore
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, 637551, Singapore
- Institute for Functional Intelligent Materials (I-FIM), National University of Singapore, Singapore, 117544, Singapore
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Peng J, Feng F, Zhang G, Zou L. Transcriptome Analysis Reveals the Inhibitory Effect of Cu 2+ on Polyferric Sulfate Floc Reduction by Shewanella putrefaciens CN32. Appl Biochem Biotechnol 2024; 196:4862-4873. [PMID: 37979084 DOI: 10.1007/s12010-023-04787-1] [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] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
Polyferric sulfate (PFS), an economical coagulant widely used for removing heavy metal contaminants from water, is susceptible to reduction and transformation by iron-reducing bacteria prevalent in sediments. However, the effect of heavy metal ions adsorbed in PFS flocs on this biological process remains unclear. According to our results, compared with other heavy metal cations (e.g., Cu2+, Cd2+, Zn2+, Ni2+, Pb2+, and Co2+), Cu2+ had a stronger inhibitory effect on PFS floc reduction by Shewanella putrefaciens CN32, a typical dissimilatory iron-reducing bacterium. The presence of Cu2+ remarkably influenced the global transcription of CN32, resulting in 782 upregulated genes and 713 downregulated genes that are mainly annotated in energy production, amino acid metabolism, protein biosynthesis, and oxidation‒reduction processes. The anaerobic TCA cycle for energy (electron) production was significantly activated in the presence of Cu2+, while the transcription of many genes related to the extracellular electron transfer pathway was downregulated, which is responsible for the decreased Fe3+ reduction. Moreover, the pathways of assimilatory sulfate reduction and subsequent cysteine biosynthesis were significantly enriched, which is hypothesized to result in the consumption of abundant energy produced from the enhanced anaerobic TCA cycle, revealing a strategy to address the oxidative stress caused by Cu2+. This work elucidates the unusual suppressive effects of Cu2+ on the microbial reduction of PFS flocs, which reveals the high resistance of PFS flocs to microbial destruction when used to treat Cu2+ pollution in water, thus demonstrating their tremendous practical prospects.
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Affiliation(s)
- Jiaxin Peng
- Nanchang Key Laboratory of Microbial Resources Exploitation & Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Fei Feng
- Nanchang Key Laboratory of Microbial Resources Exploitation & Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Gang Zhang
- Nanchang Key Laboratory of Microbial Resources Exploitation & Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Long Zou
- Nanchang Key Laboratory of Microbial Resources Exploitation & Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China.
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
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Tucci M, Viggi CC, Crognale S, Matturro B, Rossetti S, Capriotti AL, Cavaliere C, Cerrato A, Montone CM, Harnisch F, Aulenta F. Insights into the syntrophic microbial electrochemical oxidation of toluene: a combined chemical, electrochemical, taxonomical, functional gene-based, and metaproteomic approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:157919. [PMID: 35964739 DOI: 10.1016/j.scitotenv.2022.157919] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Biodegradation of aromatic hydrocarbons in anoxic contaminated environments is typically limited by the lack of bioavailable electron acceptors. Microbial electrochemical technologies (METs) are able to provide a virtually inexhaustible electron acceptor in the form of a solid electrode. Recently, we provided first experimental evidence for the syntrophic degradation of toluene in a continuous-flow bioelectrochemical reactor known as the "bioelectric well". Herein, we further analyzed the structure and function of the electroactive toluene-degrading microbiome using a suite of chemical, electrochemical, phylogenetic, proteomic, and functional gene-based analyses. The bioelectric well removed 83 ± 7 % of the toluene from the influent with a coulombic efficiency of 84 %. Cyclic voltammetry allowed to identify the formal potentials of four putative electron transfer sites, which ranged from -0.2 V to +0.1 V vs. SHE, consistent with outer membrane c-type cytochromes and pili of electroactive Geobacter species. The biofilm colonizing the surface of the anode was indeed highly enriched in Geobacter species. On the other hand, the planktonic communities thriving in the bulk of the reactor harbored aromatic hydrocarbons degraders and fermentative propionate-producing microorganisms, as revealed by phylogenetic and proteomic analyses. Most likely, propionate, acetate or other VFAs produced in the bulk liquid from the degradation of toluene were utilized as substrates by the electroactive biofilm. Interestingly, key-functional genes related to the degradation of toluene were found both in the biofilm and in the planktonic communities. Taken as a whole, the herein reported results highlight the importance of applying a comprehensive suite of techniques to unravel the complex cooperative metabolisms occurring in METs.
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Affiliation(s)
- Matteo Tucci
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy
| | - Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy
| | - Simona Crognale
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy
| | - Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy
| | | | - Chiara Cavaliere
- Department of Chemistry, Sapienza - University of Rome, Rome, Italy
| | - Andrea Cerrato
- Department of Chemistry, Sapienza - University of Rome, Rome, Italy
| | | | - Falk Harnisch
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy.
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Chislett M, Guo J, Bond PL, Wang Y, Donose BC, Yuan Z. Reactive nitrogen species from free nitrous acid (FNA) cause cell lysis. WATER RESEARCH 2022; 217:118401. [PMID: 35427827 DOI: 10.1016/j.watres.2022.118401] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Free nitrous acid (FNA, i.e. HNO2) has been demonstrated to have broad biocidal effects on a range of microorganisms, which has direct implications for wastewater management. However, the biocidal mechanisms still remain largely unknown. This study aims to test the hypothesis that FNA will induce cell lysis via cell membrane perforations, and consequently cause cell death via proteolysis, through the use of two model organisms namely Escherichia coli K12 and Pseudomonas putida KT2440. A combination of analytical techniques that included viability assays, atomic force microscopy (AFM), protein abundance assays and proteomic analysis using Quadruple-Orbitrap™ Mass spectrometry was used to evaluate the extent of cell death and possible cell lysis mechanisms. FNA treatment at 6.09 mg/L for 24 h (conditions typically applied in applications) induced 36 ± 4.2% and 91 ± 3.5% cell death/lysis of E. coli and P. putida, respectively. AFM showed that the lysis of cells was observed via perforations in the cell membrane; cells also appeared to shrink and become flat following FNA treatment. By introducing a reactive nitrogen species (RNS) scavenger to act as a treatment control, we further revealed that it was the nitrosative decomposition species of FNA, such as .NO that caused the cell lysis through the destruction of protein macromolecules found in the cell membrane (proteolysis). Subsequently, the RNS went on to cause the destruction of protein macromolecules within the cells. The death of these model organisms E. coli and P. putida following exposure to FNA treatment provides insights into the use of FNA as an antimicrobial agent in wastewater treatment.
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Affiliation(s)
- Mariella Chislett
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Philip L Bond
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Yue Wang
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Bogdan C Donose
- School of Information Technology and Electrical Engineering, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
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Xie W, Zhang D, Wen X, Zhang Y, Zhang Z, Jin Y, Du Y. A practical technique for rapid characterisation of ent-kaurane diterpenoids in Isodon serra (Maxim.) Hara by UHPLC-Q-TOF-MS/MS. PHYTOCHEMICAL ANALYSIS : PCA 2022; 33:517-532. [PMID: 35144310 DOI: 10.1002/pca.3106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
INTRODUCTION The diterpenoids are the most important active constituents that contribute to the pharmacological efficacy of Isodon serra (Maxim.) Hara. Clinical studies have revealed that diterpenoids possess multiple features, e.g. antitumour, antitubercular and anti-ischemic activities. Therefore, the identification and detection of diterpenoids may be equally important for understanding the pharmacological basis of diterpenoids and enhancing the product quality control of I. serra. OBJECTIVES The purpose of this study was to develop a practical analysis approach of rapid characterisation using ultrahigh-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS) for the structure characterisation of the ent-kaurane diterpenoids from I. serra. METHODOLOGY The analytical strategy was as follows: first, ent-kaurane diterpenoids were detected by a novel on-line data acquisition approach, i.e. sequential window acquisition of all theoretical fragment-ion spectra (SWATH). Second, the MS of eight ent-kaurane diterpenoids was explored, and their mass spectrum cleavage pathways were summarised and determined. Finally, the methanol extract of I. serra was studied using SWATH and identified by extracted ion chromatography (XIC). RESULTS Compared to the traditional information-dependent acquisition (IDA) method, SWATH significantly improved the hit rate of ent-kaurane diterpenoids. With support from UHPLC separation and specific detection by tandem mass spectrometry (MS/MS), 48 ent-kaurane diterpenoids were successfully characterised and classified as ent-kaurane diterpenoids from a complex matrix. CONCLUSIONS These combined qualitative methods were used to provide a potential approach for the characterisation of traditional Chinese medicine (TCM) and its preparations. Meanwhile, the SWATH provided a novel and reliable method for the structural characterisation of ent-kaurane diterpenoids from other complicated TCMs.
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Affiliation(s)
- Weiwei Xie
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, P. R. China
| | - Dedong Zhang
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, P. R. China
| | - Xuqing Wen
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, P. R. China
| | - Yuqian Zhang
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, P. R. China
| | - Zhiqing Zhang
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, P. R. China
| | - Yiran Jin
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, P. R. China
| | - Yingfeng Du
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, Hebei, P. R. China
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Wang Z, Mülleder M, Batruch I, Chelur A, Textoris-Taube K, Schwecke T, Hartl J, Causon J, Castro-Perez J, Demichev V, Tate S, Ralser M. High-throughput proteomics of nanogram-scale samples with Zeno SWATH MS. eLife 2022; 11:83947. [PMID: 36449390 PMCID: PMC9711518 DOI: 10.7554/elife.83947] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/08/2022] [Indexed: 12/03/2022] Open
Abstract
The possibility to record proteomes in high throughput and at high quality has opened new avenues for biomedical research, drug discovery, systems biology, and clinical translation. However, high-throughput proteomic experiments often require high sample amounts and can be less sensitive compared to conventional proteomic experiments. Here, we introduce and benchmark Zeno SWATH MS, a data-independent acquisition technique that employs a linear ion trap pulsing (Zeno trap pulsing) to increase the sensitivity in high-throughput proteomic experiments. We demonstrate that when combined with fast micro- or analytical flow-rate chromatography, Zeno SWATH MS increases protein identification with low sample amounts. For instance, using 20 min micro-flow-rate chromatography, Zeno SWATH MS identified more than 5000 proteins consistently, and with a coefficient of variation of 6%, from a 62.5 ng load of human cell line tryptic digest. Using 5 min analytical flow-rate chromatography (800 µl/min), Zeno SWATH MS identified 4907 proteins from a triplicate injection of 2 µg of a human cell lysate, or more than 3000 proteins from a 250 ng tryptic digest. Zeno SWATH MS hence facilitates sensitive high-throughput proteomic experiments with low sample amounts, mitigating the current bottlenecks of high-throughput proteomics.
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Affiliation(s)
- Ziyue Wang
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu BerlinBerlinGermany
| | - Michael Mülleder
- Core Facility – High-Throughput Mass Spectrometry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Core Facility – High-Throughput Mass SpectrometryBerlinGermany
| | | | | | - Kathrin Textoris-Taube
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu BerlinBerlinGermany,Core Facility – High-Throughput Mass Spectrometry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Core Facility – High-Throughput Mass SpectrometryBerlinGermany
| | - Torsten Schwecke
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu BerlinBerlinGermany
| | - Johannes Hartl
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu BerlinBerlinGermany
| | | | | | - Vadim Demichev
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu BerlinBerlinGermany
| | | | - Markus Ralser
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu BerlinBerlinGermany,The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
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Wang Y, Lu J, Zhang S, Li J, Mao L, Yuan Z, Bond PL, Guo J. Non-antibiotic pharmaceuticals promote the transmission of multidrug resistance plasmids through intra- and intergenera conjugation. THE ISME JOURNAL 2021; 15:2493-2508. [PMID: 33692486 PMCID: PMC8397710 DOI: 10.1038/s41396-021-00945-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/14/2021] [Accepted: 02/18/2021] [Indexed: 12/30/2022]
Abstract
Antibiotic resistance is a global threat to public health. The use of antibiotics at sub-inhibitory concentrations has been recognized as an important factor in disseminating antibiotic resistance via horizontal gene transfer. Although non-antibiotic, human-targeted pharmaceuticals are widely used by society (95% of the pharmaceuticals market), the potential contribution to the spread of antibiotic resistance is not clear. Here, we report that commonly consumed, non-antibiotic pharmaceuticals, including nonsteroidal anti-inflammatories (ibuprofen, naproxen, diclofenac), a lipid-lowering drug (gemfibrozil), and a β-blocker (propranolol), at clinically and environmentally relevant concentrations, significantly accelerated the dissemination of antibiotic resistance via plasmid-borne bacterial conjugation. Various indicators were used to study the bacterial response to these drugs, including monitoring reactive oxygen species (ROS) and cell membrane permeability by flow cytometry, cell arrangement, and whole-genome RNA and protein sequencing. Enhanced conjugation correlated well with increased production of ROS and cell membrane permeability. Additionally, these non-antibiotic pharmaceuticals induced responses similar to those detected when bacteria are exposed to antibiotics, such as inducing the SOS response and enhancing efflux pumps. The findings advance understanding of the transfer of antibiotic resistance genes, emphasizing the concern that non-antibiotic, human-targeted pharmaceuticals enhance the spread of antibiotic resistance among bacterial populations.
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Affiliation(s)
- Yue Wang
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, Australia
| | - Ji Lu
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, Australia
| | - Shuai Zhang
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, Australia
| | - Jie Li
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, Australia
| | - Likai Mao
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, Australia
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, Australia.
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Chen H, Dong F, Minteer SD. The progress and outlook of bioelectrocatalysis for the production of chemicals, fuels and materials. Nat Catal 2020. [DOI: 10.1038/s41929-019-0408-2] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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9
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Gao SH, Ho JY, Fan L, Nouwens A, Hoelzle RD, Schulz B, Guo J, Zhou J, Yuan Z, Bond PL. A comparative proteomic analysis of Desulfovibrio vulgaris Hildenborough in response to the antimicrobial agent free nitrous acid. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 672:625-633. [PMID: 30974354 DOI: 10.1016/j.scitotenv.2019.03.442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/12/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Sulfate reducing bacteria (SRB) can contribute to facilitating serious concrete corrosion through the production of hydrogen sulfide in sewers. Recently, free nitrous acid (FNA) was discovered as a promising antimicrobial agent to inhibit SRB activities thereby limiting hydrogen sulfide production in sewers. However, knowledge of the bacterial response to increasing levels of the antimicrobial agent is unknown. Here we report the proteomic response of Desulfovibrio vulgaris Hildenborough and reveal that the antimicrobial effect of FNA is multi-targeted and dependent on the FNA levels. This was achieved using a sequential window acquisition of all theoretical mass spectrometry analysis to determine protein abundance variations in D. vulgaris during exposure to different FNA concentrations. When exposed to 1.0 μg N/L FNA, nitrite reduction (nitrite reductase) related proteins and nitrosative stress related proteins, including the hybrid cluster protein, showed distinct increased abundances. When exposed to 4.0 and 8.0 μg N/L FNA, increased abundance was detected for proteins putatively involved in nitrite reduction. Abundance of proteins involved in the sulfate reduction pathway (from adenylylphophosulfate to sulfite) and lactate oxidation pathway (from pyruvate to acetate) were initially inhibited in response to FNA at 8 h incubation, and then recovered at 12 h incubation. Lowered ribosomal protein abundance in D. vulgaris was detected, however, total cellular protein levels were mostly constant in the presence or absence of FNA. In addition, this study indicates that proteins coded by genes DVU2543, DVU0772, and DVU3212 potentially participate in resisting oxidative stress with FNA exposure. These findings share new insights for understanding the dynamic responses of D. vulgaris to FNA and could be useful to guide and improve the practical applications of FNA-based technologies for control of sewer corrosion.
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Affiliation(s)
- Shu-Hong Gao
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Jun Yuan Ho
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Amanda Nouwens
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Robert D Hoelzle
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Benjamin Schulz
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
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10
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Hirose A, Kasai T, Koga R, Suzuki Y, Kouzuma A, Watanabe K. Understanding and engineering electrochemically active bacteria for sustainable biotechnology. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0245-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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11
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Wang Y, Lu J, Mao L, Li J, Yuan Z, Bond PL, Guo J. Antiepileptic drug carbamazepine promotes horizontal transfer of plasmid-borne multi-antibiotic resistance genes within and across bacterial genera. THE ISME JOURNAL 2019; 13:509-522. [PMID: 30291330 PMCID: PMC6331567 DOI: 10.1038/s41396-018-0275-x] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/18/2018] [Accepted: 08/26/2018] [Indexed: 02/02/2023]
Abstract
Antibiotic resistance is a severe global threat for public health, causing around 700,000 deaths per year. Horizontal gene transfer (HGT) is one of the most significant pathways to disseminate antibiotic resistance. It is commonly acknowledged that sub-minimum inhibition concentrations of antibiotics are major contributors in promoting antibiotic resistance through HGT. Pharmaceuticals are occurring in our environments at increased levels, yet little is known whether non-antibiotic pharmaceuticals cause or accelerate the dissemination of antibiotic resistance. Here, we report for the first time that the antiepileptic drug, carbamazepine, promotes conjugative transfer of antibiotic resistance genes. It was seen that environmentally relevant concentrations of carbamazepine (e.g., 0.05 mg/L) significantly enhanced the conjugative transfer of multiresistance genes carried by plasmid within and across bacterial genera. The underlying mechanisms of the enhanced HGT were revealed by detecting oxidative stress and cell membrane permeability, in combination with MinION DNA sequencing, genome-wide RNA sequencing, and proteomic analysis. Carbamazepine induced a series of acute responses, including increased levels of reactive oxygen species, the SOS response; increased cell membrane permeability, and pilus generation. Expressional levels of genes related to these processes were significantly upregulated during carbamazepine exposure. Given that HGT occurs widely among different species in various environments, these findings are an early warning for a wide assessment of the roles of non-antibiotic pharmaceuticals in the spread of antibiotic resistance.
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Affiliation(s)
- Yue Wang
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Ji Lu
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Likai Mao
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Jie Li
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia.
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Krasny L, Bland P, Kogata N, Wai P, Howard BA, Natrajan RC, Huang PH. SWATH mass spectrometry as a tool for quantitative profiling of the matrisome. J Proteomics 2018; 189:11-22. [PMID: 29501709 PMCID: PMC6215756 DOI: 10.1016/j.jprot.2018.02.026] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 12/16/2022]
Abstract
Proteomic analysis of extracellular matrix (ECM) and ECM-associated proteins, collectively known as the matrisome, is a challenging task due to the inherent complexity and insolubility of these proteins. Here we present sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH MS) as a tool for the quantitative analysis of matrisomal proteins in both non-enriched and ECM enriched tissue without the need for prior fractionation. Utilising a spectral library containing 201 matrisomal proteins, we compared the performance and reproducibility of SWATH MS over conventional data-dependent analysis mass spectrometry (DDA MS) in unfractionated murine lung and liver. SWATH MS conferred a 15-20% increase in reproducible peptide identification across replicate experiments in both tissue types and identified 54% more matrisomal proteins in the liver versus DDA MS. We further use SWATH MS to evaluate the quantitative changes in matrisome content that accompanies ECM enrichment. Our data shows that ECM enrichment led to a systematic increase in core matrisomal proteins but resulted in significant losses in matrisome-associated proteins including the cathepsins and proteins of the S100 family. Our proof-of-principle study demonstrates the utility of SWATH MS as a versatile tool for in-depth characterisation of the matrisome in unfractionated and non-enriched tissues. SIGNIFICANCE: The matrisome is a complex network of extracellular matrix (ECM) and ECM-associated proteins that provides scaffolding function to tissues and plays important roles in the regulation of fundamental cellular processes. However, due to its inherent complexity and insolubility, proteomic studies of the matrisome typically require the application of enrichment workflows prior to MS analysis. Such enrichment strategies often lead to losses in soluble matrisome-associated components. In this study, we present sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH MS) as a tool for the quantitative analysis of matrisomal proteins. We show that SWATH MS provides a more reproducible coverage of the matrisome compared to data-dependent analysis (DDA) MS. We also demonstrate that SWATH MS is capable of accurate quantification of matrisomal proteins without prior ECM enrichment and fractionation, which may simplify sample handling workflows and avoid losses in matrisome-associated proteins commonly linked to ECM enrichment.
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Affiliation(s)
- Lukas Krasny
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Philip Bland
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Naoko Kogata
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Patty Wai
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK; The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Beatrice A Howard
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rachael C Natrajan
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK; The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK.
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13
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Pal S, Qureshi A, Purohit HJ. Intercepting signalling mechanism to control environmental biofouling. 3 Biotech 2018; 8:364. [PMID: 30105189 DOI: 10.1007/s13205-018-1383-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 07/29/2018] [Indexed: 12/29/2022] Open
Abstract
Biofouling in environmental systems employs bacterial quorum sensing signals (autoinducers) and extracellular polymeric substances to onset the event. The present review has highlighted on the fundamental mechanisms behind biofilm formation over broad spectrum environmental niches especially membrane biofouling in water systems and consequent chances of pathogenic contamination leading to global economic loss. It has broadly discussed on bioelectrical signal (via, potassium gradient) and molecular signal (via, AHLs) mediated quorum sensing which help to propagate biofilm formation. The review has illustrated the potential of genomic intervention towards biofouled membrane microbial community and has uncovered possible features of biofilm microenvironment like quorum quenching bacteria, bioelectrical waves capture, siderophores arrest and surface modifications. Based on information, the concept of interception of quorum signals (AHLs) and bioelectrical signals (K+) by employing electro-modified (negative charges) membrane surface have been hypothesized in the present review to favour anti-biofouling.
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Affiliation(s)
- Smita Pal
- 1Academy of Scientific and Innovative Research (AcSIR), CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, Maharashtra 440020 India
- 2CSIR-Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, Maharashtra 440020 India
| | - Asifa Qureshi
- 1Academy of Scientific and Innovative Research (AcSIR), CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, Maharashtra 440020 India
- 2CSIR-Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, Maharashtra 440020 India
| | - Hemant J Purohit
- 2CSIR-Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, Maharashtra 440020 India
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14
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Laloo AE, Wei J, Wang D, Narayanasamy S, Vanwonterghem I, Waite D, Steen J, Kaysen A, Heintz-Buschart A, Wang Q, Schulz B, Nouwens A, Wilmes P, Hugenholtz P, Yuan Z, Bond PL. Mechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5386-5397. [PMID: 29620869 DOI: 10.1021/acs.est.7b04273] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Free nitrous acid (FNA) exerts a broad range of antimicrobial effects on bacteria, although susceptibility varies considerably among microorganisms. Among nitrifiers found in activated sludge of wastewater treatment processes (WWTPs), nitrite-oxidizing bacteria (NOB) are more susceptible to FNA compared to ammonia-oxidizing bacteria (AOB). This selective inhibition of NOB over AOB in WWTPs bypasses nitrate production and improves the efficiency and costs of the nitrogen removal process in both the activated sludge and anaerobic ammonium oxidation (Anammox) system. However, the molecular mechanisms governing this atypical tolerance of AOB to FNA have yet to be understood. Herein we investigate the varying effects of the antimicrobial FNA on activated sludge containing AOB and NOB using an integrated metagenomics and label-free quantitative sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) metaproteomic approach. The Nitrosomonas genus of AOB, on exposure to FNA, maintains internal homeostasis by upregulating a number of known oxidative stress enzymes, such as pteridine reductase and dihydrolipoyl dehydrogenase. Denitrifying enzymes were upregulated on exposure to FNA, suggesting the detoxification of nitrite to nitric oxide. Interestingly, proteins involved in stress response mechanisms, such as DNA and protein repair enzymes, phage prevention proteins, and iron transport proteins, were upregulated on exposure to FNA. In addition enzymes involved in energy generation were also upregulated on exposure to FNA. The total proteins specifically derived from the NOB genus Nitrobacter was low and, as such, did not allow for the elucidation of the response mechanism to FNA exposure. These findings give us an understanding of the adaptive mechanisms of tolerance within the AOB Nitrosomonas to the biocidal agent FNA.
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Affiliation(s)
- Andrew E Laloo
- Advanced Water Management Centre , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Justin Wei
- Advanced Water Management Centre , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Dongbo Wang
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control, Ministry of Education , Hunan University , Changsa 410082 , China
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine , Université du Luxembourg , L-4362 Esch-sur-Alzette , Luxembourg
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Bioscience , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - David Waite
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Bioscience , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Jason Steen
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Bioscience , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Anne Kaysen
- Luxembourg Centre for Systems Biomedicine , Université du Luxembourg , L-4362 Esch-sur-Alzette , Luxembourg
| | - Anna Heintz-Buschart
- Luxembourg Centre for Systems Biomedicine , Université du Luxembourg , L-4362 Esch-sur-Alzette , Luxembourg
| | - Qilin Wang
- Griffith School of Engineering & Centre for Clean Environment and Energy , Griffith University , Nathan , QLD 4111 , Australia
| | - Benjamin Schulz
- School of Chemistry and Molecular Biosciences , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Amanda Nouwens
- School of Chemistry and Molecular Biosciences , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine , Université du Luxembourg , L-4362 Esch-sur-Alzette , Luxembourg
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Bioscience , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
| | - Philip L Bond
- Advanced Water Management Centre , The University of Queensland , St. Lucia , Brisbane , QLD 4072 , Australia
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15
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Effect of anode polarization on biofilm formation and electron transfer in Shewanella oneidensis /graphite felt microbial fuel cells. Bioelectrochemistry 2018; 120:1-9. [DOI: 10.1016/j.bioelechem.2017.10.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 10/30/2017] [Accepted: 10/30/2017] [Indexed: 11/20/2022]
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16
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Hirose A, Kasai T, Aoki M, Umemura T, Watanabe K, Kouzuma A. Electrochemically active bacteria sense electrode potentials for regulating catabolic pathways. Nat Commun 2018; 9:1083. [PMID: 29540717 PMCID: PMC5852097 DOI: 10.1038/s41467-018-03416-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 02/09/2018] [Indexed: 01/08/2023] Open
Abstract
Electrochemically active bacteria (EAB) receive considerable attention for their utility in bioelectrochemical processes. Although electrode potentials are known to affect the metabolic activity of EAB, it is unclear whether EAB are able to sense and respond to electrode potentials. Here, we show that, in the presence of a high-potential electrode, a model EAB Shewanella oneidensis MR-1 can utilize NADH-dependent catabolic pathways and a background formate-dependent pathway to achieve high growth yield. We also show that an Arc regulatory system is involved in sensing electrode potentials and regulating the expression of catabolic genes, including those for NADH dehydrogenase. We suggest that these findings may facilitate the use of EAB in biotechnological processes and offer the molecular bases for their ecological strategies in natural habitats.
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Affiliation(s)
- Atsumi Hirose
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Takuya Kasai
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Motohide Aoki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Tomonari Umemura
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Kazuya Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan.
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17
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Effect of the anode potential on the physiology and proteome of Shewanella oneidensis MR-1. Bioelectrochemistry 2018; 119:172-179. [DOI: 10.1016/j.bioelechem.2017.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 10/02/2017] [Accepted: 10/02/2017] [Indexed: 11/19/2022]
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18
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Balancing cellular redox metabolism in microbial electrosynthesis and electro fermentation - A chance for metabolic engineering. Metab Eng 2017; 45:109-120. [PMID: 29229581 DOI: 10.1016/j.ymben.2017.12.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 09/15/2017] [Accepted: 12/06/2017] [Indexed: 01/05/2023]
Abstract
More and more microbes are discovered that are capable of extracellular electron transfer, a process in which they use external electrodes as electron donors or acceptors for metabolic reactions. This feature can be used to overcome cellular redox limitations and thus optimizing microbial production. The technologies, termed microbial electrosynthesis and electro-fermentation, have the potential to open novel bio-electro production platforms from sustainable energy and carbon sources. However, the performance of reported systems is currently limited by low electron transport rates between microbes and electrodes and our limited ability for targeted engineering of these systems due to remaining knowledge gaps about the underlying fundamental processes. Metabolic engineering offers many opportunities to optimize these processes, for instance by genetic engineering of pathways for electron transfer on the one hand and target product synthesis on the other hand. With this review, we summarize the status quo of knowledge and engineering attempts around chemical production in bio-electrochemical systems from a microbe perspective. Challenges associated with the introduction or enhancement of extracellular electron transfer capabilities into production hosts versus the engineering of target compound synthesis pathways in natural exoelectrogens are discussed. Recent advances of the research community in both directions are examined critically. Further, systems biology approaches, for instance using metabolic modelling, are examined for their potential to provide insight into fundamental processes and to identify targets for metabolic engineering.
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19
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Nöbauer K, Hummel K, Mayrhofer C, Ahrens M, Setyabudi FMC, Schmidt-Heydt M, Eisenacher M, Razzazi-Fazeli E. Comprehensive proteomic analysis of Penicillium verrucosum. Proteomics 2017; 17. [PMID: 28267294 DOI: 10.1002/pmic.201600467] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/23/2017] [Accepted: 03/01/2017] [Indexed: 11/11/2022]
Abstract
Mass spectrometric identification of proteins in species lacking validated sequence information is a major problem in veterinary science. In the present study, we used ochratoxin A producing Penicillium verrucosum to identify and quantitatively analyze proteins of an organism with yet no protein information available. The work presented here aimed to provide a comprehensive protein identification of P. verrucosum using shotgun proteomics. We were able to identify 3631 proteins in an "ab initio" translated database from DNA sequences of P. verrucosum. Additionally, a sequential window acquisition of all theoretical fragment-ion spectra analysis was done to find differentially regulated proteins at two different time points of the growth curve. We compared the proteins at the beginning (day 3) and at the end of the log phase (day 12).
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Affiliation(s)
- Katharina Nöbauer
- VetCore Facility for Research, University of Veterinary Medicine, Vienna, Austria
| | - Karin Hummel
- VetCore Facility for Research, University of Veterinary Medicine, Vienna, Austria
| | - Corina Mayrhofer
- Department for Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria.,Interuniversity Department for Agrobiotechnology (IFA Tulln), Institute of Biotechnology in Animal Production, University of Natural Resources and Applied Life Sciences, Vienna, Tulln, Austria
| | - Maike Ahrens
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
| | | | - Markus Schmidt-Heydt
- Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Department of Safety and Quality of Fruits and Vegetables, Karlsruhe, Germany
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
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20
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Thermophilic Moorella thermoautotrophica -immobilized cathode enhanced microbial electrosynthesis of acetate and formate from CO 2. Bioelectrochemistry 2017; 117:23-28. [DOI: 10.1016/j.bioelechem.2017.05.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/12/2017] [Accepted: 05/12/2017] [Indexed: 11/20/2022]
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21
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Xie W, Jin Y, Hou L, Ma Y, Xu H, Zhang K, Zhang L, Du Y. A practical strategy for the characterization of ponicidin metabolites in vivo and in vitro by UHPLC-Q-TOF-MS based on nontargeted SWATH data acquisition. J Pharm Biomed Anal 2017; 145:865-878. [PMID: 28830062 DOI: 10.1016/j.jpba.2017.08.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 12/23/2022]
Abstract
Ponicidin is an active natural ent-kaurane diterpenoid ingredient originating from many Isondon herbs and is expected to become a new anticancer agent. In this study, a practical strategy was developed for the identification of ponicidin metabolites in vivo and in vitro utilizing ultra-high-performance liquid chromatography coupled with hybrid triple quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS). The analytical strategy was as follows: potential ponicidin metabolites were detected by a novel on-line data acquisition approach, i.e., sequential window acquisition of all theoretical fragment-ion spectra (SWATH™). Compared to the traditional information-dependent acquisition (IDA) method, SWATH™ significantly improved the hit rate of low-level or trace metabolites because it could obtain all MS/MS spectra. Moreover, many data post-processing methods were used to deduce the metabolites structures. As a result, a total of 20 metabolites were characterized in vivo and in vitro. The results showed that ponicidin could undergo general metabolic reactions, such as oxidation, reduction, hydrolysis, methylation and glucuronidation. Furthermore, there was an obvious difference in the ponicidin metabolites among four species in vitro. This is the first time that the SWATH™ data acquisition mode has been used to characterize ponicidin metabolites in trace amounts or in a biological matrix. These results not only provided a better understanding of the safety and efficacy of ponicidin but also showed a valuable methodology for the identification of other ent-kaurane diterpenoid metabolites.
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Affiliation(s)
- Weiwei Xie
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, Hebei, 050017, PR China
| | - Yiran Jin
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, Hebei, 050017, PR China; The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050000, PR China
| | - Ludan Hou
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, Hebei, 050017, PR China
| | - Yinghua Ma
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, Hebei, 050017, PR China
| | - Huijun Xu
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, Hebei, 050017, PR China
| | - Kerong Zhang
- Applied Biosystems Trading Co., Ltd., Beijing Branch Office, Beijing 100027, PR China
| | - Lantong Zhang
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, Hebei, 050017, PR China
| | - Yingfeng Du
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, Hebei, 050017, PR China.
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22
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Anjo SI, Santa C, Manadas B. SWATH-MS as a tool for biomarker discovery: From basic research to clinical applications. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600278] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 01/05/2017] [Accepted: 01/23/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Sandra Isabel Anjo
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
- Faculty of Sciences and Technology; University of Coimbra; Coimbra Portugal
| | - Cátia Santa
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
- Institute for Interdisciplinary Research (III); University of Coimbra; Coimbra Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
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23
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Fowler GJS, Pereira-Medrano AG, Jaffe S, Pasternak G, Pham TK, Ledezma P, Hall STE, Ieropoulos IA, Wright PC. An iTRAQ characterisation of the role of TolC during electron transfer from Shewanella oneidensis MR-1. Proteomics 2016; 16:2764-2775. [PMID: 27599463 DOI: 10.1002/pmic.201500538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 07/20/2016] [Accepted: 09/02/2016] [Indexed: 02/04/2023]
Abstract
Anodophilic bacteria have the ability to generate electricity in microbial fuel cells (MFCs) by extracellular electron transfer to the anode. We investigated the anode-specific responses of Shewanella oneidensis MR-1, an exoelectroactive Gammaproteobacterium, using for the first time iTRAQ and 2D-LC MS/MS driven membrane proteomics to compare protein abundances in S. oneidensis when generating power in MFCs, and growing in a continuous culture. The regulated dataset produced was enriched in membrane proteins. Proteins shown to be more abundant in anaerobic electroactive anodic cells included efflux pump TolC and an uncharacterised tetratricopeptide repeat (TPR) protein, whilst the TonB2 system and associated uncharacterised proteins such as TtpC2 and DUF3450 were more abundant in microaerobic planktonic cells. In order to validate the iTRAQ data, the functional role for TolC was examined using a δTolC knockout mutant of S. oneidensis. Possible roles for the uncharacterised proteins were identified using comparative bioinformatics. We demonstrate that employing an insoluble extracellular electron acceptor requires multiple proteins involved in cell surface properties. All MS and processed data are available via ProteomeXchange with identifier PXD004090.
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Affiliation(s)
- Gregory J S Fowler
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Ana G Pereira-Medrano
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Stephen Jaffe
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Grzegorz Pasternak
- Bristol Robotics Laboratory, Universities of Bristol and of the West of England, , Frenchay Campus, Bristol, UK
| | - Trong Khoa Pham
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Pablo Ledezma
- Bristol Robotics Laboratory, Universities of Bristol and of the West of England, , Frenchay Campus, Bristol, UK
| | - Simon T E Hall
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Ioannis A Ieropoulos
- Bristol Robotics Laboratory, Universities of Bristol and of the West of England, , Frenchay Campus, Bristol, UK
| | - Phillip C Wright
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK. .,Faculty of Science, Agriculture & Engineering, Newcastle University, Devonshire Building, Newcastle upon Tyne, UK.
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24
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Lian Y, Yang Y, Guo J, Wang Y, Li X, Fang Y, Gan L, Xu M. Electron acceptor redox potential globally regulates transcriptomic profiling in Shewanella decolorationis S12. Sci Rep 2016; 6:31143. [PMID: 27503002 PMCID: PMC4977559 DOI: 10.1038/srep31143] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/12/2016] [Indexed: 11/09/2022] Open
Abstract
Electron acceptor redox potential (EARP) was presumed to be a determining factor for microbial metabolism in many natural and engineered processes. However, little is known about the potentially global effects of EARP on bacteria. In this study, we compared the physiological and transcriptomic properties of Shewanella decolorationis S12 respiring with different EARPs in microbial electrochemical systems to avoid the effects caused by the other physicochemical properties of real electron acceptor. Results showed that the metabolic activities of strain S12 were nonlinear responses to EARP. The tricarboxylic acid cycle for central carbon metabolism was down-regulated while glyoxylate shunt was up-regulated at 0.8 V compared to 0.2 and -0.2 V, which suggested that EARP is an important but not the only determinant for metabolic pathways of strain S12. Moreover, few cytochrome c genes were differentially expressed at different EARPs. The energy intensive flagella assembly and assimilatory sulfur metabolism pathways were significantly enriched at 0.8 V, which suggested strain S12 had stronger electrokinesis behavior and oxidative stress-response at high EARP. This study provides the first global information of EARP regulations on microbial metabolism, which will be helpful for understanding microorganism respiration.
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Affiliation(s)
- Yingli Lian
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Yonggang Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Jun Guo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Yan Wang
- Science and Technology Library of Guangdong Province, Guangzhou 510070, China
| | - Xiaojing Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Yun Fang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Lixia Gan
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
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25
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Abstract
Aim: Sequential window acquisition of all theoretical fragment-ion spectra (SWATH) has recently emerged as a powerful high resolution mass spectrometric data independent acquisition technique. In the present work, the potential and challenges of an integrated strategy based on LC-SWATH/MS for simultaneous drug metabolism and metabolomics studies was investigated. Methodology: The richness of SWATH data allows numerous data analysis approaches, including: detection of metabolites by prediction; metabolite detection by mass defect filtering; quantification from high-resolution MS precursor chromatograms or fragment chromatograms. Multivariate analysis can be applied to the data from the full scan or SWATH windows and allows changes in endogenous metabolites as well as xenobiotic metabolites, to be detected. Principal component variable grouping detects intersample variable correlation and groups variables with similar profiles which simplifies interpretation and highlights related ions and fragments. Principal component variable grouping can extract product ion spectra from the data collected by fragmenting a wide precursor ion window. Conclusion: It was possible to characterize 28 vinpocetine metabolites in urine, mostly mono- and di-hydroxylated forms, and detect endogenous metabolite expression changes in urine after the administration of a single dose of a model drug (vinpocetine) to rats.
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White GF, Edwards MJ, Gomez-Perez L, Richardson DJ, Butt JN, Clarke TA. Mechanisms of Bacterial Extracellular Electron Exchange. Adv Microb Physiol 2016; 68:87-138. [PMID: 27134022 DOI: 10.1016/bs.ampbs.2016.02.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The biochemical mechanisms by which microbes interact with extracellular soluble metal ions and insoluble redox-active minerals have been the focus of intense research over the last three decades. The process presents two challenges to the microorganism. Firstly, electrons have to be transported at the cell surface, which in Gram-negative bacteria presents an additional problem of electron transfer across the ~6nm of the outer membrane. Secondly, the electrons must be transferred to or from the terminal electron acceptors or donors. This review covers the known mechanisms that bacteria use to transport electrons across the cell envelope to external electron donors/acceptors. In Gram-negative bacteria, electron transfer across the outer membrane involves the use of an outer membrane β-barrel and cytochrome. These can be in the form of a porin-cytochrome protein, such as Cyc2 of Acidithiobacillus ferrooxidans, or a multiprotein porin-cytochrome complex like MtrCAB of Shewanella oneidensis MR-1. For mineral-respiring organisms, there is the additional challenge of transferring the electrons from the cell to mineral surface. For the strict anaerobe Geobacter sulfurreducens this requires electron transfer through conductive pili to associated cytochrome OmcS that directly reduces Fe(III)oxides, while the facultative anaerobe S. oneidensis MR-1 accomplishes mineral reduction through direct membrane contact, contact through filamentous extensions and soluble flavin shuttles, all of which require the outer membrane cytochromes MtrC and OmcA in addition to secreted flavin.
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Affiliation(s)
- G F White
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - M J Edwards
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - L Gomez-Perez
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - D J Richardson
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - J N Butt
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - T A Clarke
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom.
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Li WW, Yu HQ. Electro-assisted groundwater bioremediation: fundamentals, challenges and future perspectives. BIORESOURCE TECHNOLOGY 2015; 196:677-684. [PMID: 26227572 DOI: 10.1016/j.biortech.2015.07.074] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 07/20/2015] [Accepted: 07/21/2015] [Indexed: 06/04/2023]
Abstract
Bioremediation is envisaged as an important way to abate groundwater contamination, but the need for chemical addition and limited bioavailability of electron donors/acceptors or contaminants hamper its application. As a promising means to enhance such processes, electrochemical system has drawn considerable attention, as it offers distinct advantages in terms of environmental benignity, controllability and treatment efficiency. Meanwhile, there are also potential risks and considerable engineering challenges for its practical application. This review provides a first comprehensive introduction of this emerging technology, discusses its potential applications and current challenges, identifies the knowledge gaps, and outlooks the future opportunities to bring it to field application. The need for a better understanding on the microbiology under electrochemical stimulation and the future requirements on process monitoring, modeling and evaluation protocols and field investigations are highlighted.
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Affiliation(s)
- Wen-Wei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China.
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Yu L, Yuan Y, Chen S, Zhuang L, Zhou S. Direct uptake of electrode electrons for autotrophic denitrification by Thiobacillus denitrificans. Electrochem commun 2015. [DOI: 10.1016/j.elecom.2015.08.025] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Kouzuma A, Kasai T, Hirose A, Watanabe K. Catabolic and regulatory systems in Shewanella oneidensis MR-1 involved in electricity generation in microbial fuel cells. Front Microbiol 2015; 6:609. [PMID: 26136738 PMCID: PMC4468914 DOI: 10.3389/fmicb.2015.00609] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 06/02/2015] [Indexed: 12/12/2022] Open
Abstract
Shewanella oneidensis MR-1 is a facultative anaerobe that respires using a variety of inorganic and organic compounds. MR-1 is also capable of utilizing extracellular solid materials, including anodes in microbial fuel cells (MFCs), as electron acceptors, thereby enabling electricity generation. As MFCs have the potential to generate electricity from biomass waste and wastewater, MR-1 has been extensively studied to identify the molecular systems that are involved in electricity generation in MFCs. These studies have demonstrated the importance of extracellular electron-transfer (EET) pathways that electrically connect the quinone pool in the cytoplasmic membrane to extracellular electron acceptors. Electricity generation is also dependent on intracellular catabolic pathways that oxidize electron donors, such as lactate, and regulatory systems that control the expression of genes encoding the components of catabolic and electron-transfer pathways. In addition, recent findings suggest that cell-surface polymers, e.g., exopolysaccharides, and secreted chemicals, which function as electron shuttles, are also involved in electricity generation. Despite these advances in our knowledge on the EET processes in MR-1, further efforts are necessary to fully understand the underlying intra- and extracellular molecular systems for electricity generation in MFCs. We suggest that investigating how MR-1 coordinates these systems to efficiently transfer electrons to electrodes and conserve electrochemical energy for cell proliferation is important for establishing the biological basis for MFCs.
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Affiliation(s)
- Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences , Hachioji, Japan
| | - Takuya Kasai
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences , Hachioji, Japan
| | - Atsumi Hirose
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences , Hachioji, Japan
| | - Kazuya Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences , Hachioji, Japan
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Guo W, Luo S, He Z, Feng X. 13C pathway analysis of biofilm metabolism of Shewanella oneidensis MR-1. RSC Adv 2015. [DOI: 10.1039/c5ra05573c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Biofilm metabolism ofShewanellawas analyzedvia13C tracing experiments for the first time.
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Affiliation(s)
- Weihua Guo
- Department of Biological Systems Engineering
- Virginia Polytechnic Institute and State University
- Blacksburg
- USA
| | - Shuai Luo
- Department of Civil and Environmental Engineering
- Virginia Polytechnic Institute and State University
- Blacksburg
- USA
| | - Zhen He
- Department of Civil and Environmental Engineering
- Virginia Polytechnic Institute and State University
- Blacksburg
- USA
| | - Xueyang Feng
- Department of Biological Systems Engineering
- Virginia Polytechnic Institute and State University
- Blacksburg
- USA
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