1
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Defeat undefeatable: ionic liquids as novel antimicrobial agents. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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2
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Grewal J, Khare SK, Drewniak L, Pranaw K. Recent perspectives on microbial and ionic liquid interactions with implications for biorefineries. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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3
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Fu Y, Wang F, Wang Z, Mei Z, Jiang X, Schäffer A, Virta M, Tiedje JM. Application of magnetic biochar/quaternary phosphonium salt to combat the antibiotic resistome in livestock wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 811:151386. [PMID: 34742956 DOI: 10.1016/j.scitotenv.2021.151386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
The overuse and misuse of antibiotics in animal breeding for disease treatment and growth enhancement have been major drivers of the occurrence, diffusion, and accumulation of antibiotic resistance genes (ARGs) in wastewater. Strategies to combat ARG dissemination are pressingly needed for human and ecological safety. To achieve this goal, a biochar-based polymer, magnetic biochar/quaternary phosphonium salt (MBQ), was applied in livestock wastewater and displayed a high performance in bacterial deactivation and ARG decrease. Efficient antibacterial effects were achieved by both MBQ and quaternary phosphonium salt; however, the abundance and fold change of ARGs in the MBQ treatment indicated a more powerful ARG dissemination control than quaternary phosphonium salt. The application of MBQ evidently reduced the microbial diversity and may primarily be responsible for altering the ARG profiles in wastewater. Network, redundancy, and variation partitioning analyses were further employed to reveal that the microbial community and the presence of mobile genetic elements were two critical factors shaping the pattern of the antibiotic resistome in livestock wastewater. Considered together, these findings extend the application field of biochar and have important implications for reducing ARG dissemination risks in livestock wastewater.
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Affiliation(s)
- Yuhao Fu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Microbiology, University of Helsinki, Helsinki 00014, Finland
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ziquan Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhi Mei
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Andreas Schäffer
- RWTH Aachen University, Institute for Environmental Research, Aachen 52074, Germany
| | - Marko Virta
- Department of Microbiology, University of Helsinki, Helsinki 00014, Finland
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA
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4
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Xylan Deconstruction by Thermophilic Thermoanaerobacterium bryantii Hemicellulases Is Stimulated by Two Oxidoreductases. Catalysts 2022. [DOI: 10.3390/catal12020182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Thermoanaerobacterium bryantii strain mel9T is a thermophilic bacterium isolated from a waste pile of a corn-canning factory. The genome of T. bryantii mel9T was sequenced and a hemicellulase gene cluster was identified. The cluster encodes seven putative enzymes, which are likely an endoxylanase, an α-glucuronidase, two oxidoreductases, two β-xylosidases, and one acetyl xylan esterase. These genes were designated tbxyn10A, tbagu67A, tbheoA, tbheoB, tbxyl52A, tbxyl39A, and tbaxe1A, respectively. Only TbXyn10A released reducing sugars from birchwood xylan, as shown by thin-layer chromatography analysis. The five components of the hemicellulase cluster (TbXyn10A, TbXyl39A, TbXyl52A, TbAgu67A, and TbAxe1A) functioned in synergy to hydrolyze birchwood xylan. Surprisingly, the two putative oxidoreductases increased the enzymatic activities of the gene products from the xylanolytic gene cluster in the presence of NADH and manganese ions. The two oxidoreductases were therefore named Hemicellulase-Enhancing Oxidoreductases (HEOs). All seven enzymes were thermophilic and acted in synergy to degrade xylans at 60 °C. Except for TbXyn10A, the other enzymes encoded by the gene cluster were conserved with high amino acid identities (85–100%) in three other Thermoanaerobacterium species. The conservation of the gene cluster is, therefore, suggestive of an important role of these enzymes in xylan degradation by these bacteria. The mechanism for enhancement of hemicellulose degradation by the HEOs is under investigation. It is anticipated, however, that the discovery of these new actors in hemicellulose deconstruction will have a significant impact on plant cell wall deconstruction in the biofuel industry.
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5
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Banerjee D, Eng T, Sasaki Y, Srinivasan A, Oka A, Herbert RA, Trinh J, Singan VR, Sun N, Putnam D, Scown CD, Simmons B, Mukhopadhyay A. Genomics Characterization of an Engineered Corynebacterium glutamicum in Bioreactor Cultivation Under Ionic Liquid Stress. Front Bioeng Biotechnol 2021; 9:766674. [PMID: 34869279 PMCID: PMC8637627 DOI: 10.3389/fbioe.2021.766674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/27/2021] [Indexed: 12/04/2022] Open
Abstract
Corynebacterium glutamicum is an ideal microbial chassis for production of valuable bioproducts including amino acids and next generation biofuels. Here we resequence engineered isopentenol (IP) producing C. glutamicum BRC-JBEI 1.1.2 strain and assess differential transcriptional profiles using RNA sequencing under industrially relevant conditions including scale transition and compare the presence vs absence of an ionic liquid, cholinium lysinate ([Ch][Lys]). Analysis of the scale transition from shake flask to bioreactor with transcriptomics identified a distinct pattern of metabolic and regulatory responses needed for growth in this industrial format. These differential changes in gene expression corroborate altered accumulation of organic acids and bioproducts, including succinate, acetate, and acetoin that occur when cells are grown in the presence of 50 mM [Ch][Lys] in the stirred-tank reactor. This new genome assembly and differential expression analysis of cells grown in a stirred tank bioreactor clarify the cell response of an C. glutamicum strain engineered to produce IP.
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Affiliation(s)
- Deepanwita Banerjee
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Thomas Eng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yusuke Sasaki
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Aparajitha Srinivasan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Asun Oka
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, United States
| | - Robin A Herbert
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jessica Trinh
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Vasanth R Singan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ning Sun
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, United States
| | - Dan Putnam
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Corinne D Scown
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Energy Analysis and Environmental Impacts Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Blake Simmons
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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6
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Beil S, Markiewicz M, Pereira CS, Stepnowski P, Thöming J, Stolte S. Toward the Proactive Design of Sustainable Chemicals: Ionic Liquids as a Prime Example. Chem Rev 2021; 121:13132-13173. [PMID: 34523909 DOI: 10.1021/acs.chemrev.0c01265] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The tailorable and often unique properties of ionic liquids (ILs) drive their implementation into a broad variety of seminal technologies. The modular design of ILs allows in this context a proactive selection of structures that favor environmental sustainability─ideally without compromising their technological performance. To achieve this objective, the whole life cycle must be taken into account and various aspects considered simultaneously. In this review, we discuss how the structural design of ILs affects their environmental impacts throughout all stages of their life cycles and scrutinize the available data in order to point out knowledge gaps that need further research activities. The design of more sustainable ILs starts with the selection of the most beneficial precursors and synthesis routes, takes their technical properties and application specific performance into due account, and considers its environmental fate particularly in terms of their (eco)toxicity, biotic and abiotic degradability, mobility, and bioaccumulation potential. Special emphasis is placed on reported structure-activity relationships and suggested mechanisms on a molecular level that might rationalize the empirically found design criteria.
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Affiliation(s)
- Stephan Beil
- Institute of Water Chemistry, TU Dresden, 01062 Dresden, Germany
| | - Marta Markiewicz
- Institute of Water Chemistry, TU Dresden, 01062 Dresden, Germany
| | - Cristina Silva Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Piotr Stepnowski
- Department of Environmental Analysis, Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Jorg Thöming
- Chemical Process Engineering, University of Bremen, Leobener Straße 6, 28359 Bremen, Germany
| | - Stefan Stolte
- Institute of Water Chemistry, TU Dresden, 01062 Dresden, Germany
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7
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Jeremias G, Jesus F, Ventura SPM, Gonçalves FJM, Asselman J, Pereira JL. New insights on the effects of ionic liquid structural changes at the gene expression level: Molecular mechanisms of toxicity in Daphnia magna. JOURNAL OF HAZARDOUS MATERIALS 2021; 409:124517. [PMID: 33199138 DOI: 10.1016/j.jhazmat.2020.124517] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/18/2020] [Accepted: 11/05/2020] [Indexed: 06/11/2023]
Abstract
Knowledge on the molecular basis of ionic liquids' (ILs) ecotoxicity is critical for the development of these designer solvents as their structure can be engineered to simultaneously meet functionality performance and environmental safety. The molecular effects of ILs were investigated by using RNA-sequencing following Daphnia magna exposure to imidazolium- and cholinium-based ILs: 1-ethyl-3-methylimidazolium chloride ([C2mim]Cl), 1-dodecyl-3-methylimidazolium chloride ([C12mim]Cl) and cholinium chloride ([Chol]Cl)-; the selection allowing to compare different families and cation alkyl chains. ILs shared mechanisms of toxicity focusing e.g. cellular membrane and cytoskeleton, oxidative stress, energy production, protein biosynthesis, DNA damage, disease initiation. [C2mim]Cl and [C12mim]Cl were the least and the most toxic ILs at the transcriptional level, denoting the role of the alkyl chain as a driver of ILs toxicity. Also, it was reinforced that [Chol]Cl is not devoid of environmental hazardous potential regardless of its argued biological compatibility. Unique gene expression signatures could also be identified for each IL, enlightening specific mechanisms of toxicity.
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Affiliation(s)
- Guilherme Jeremias
- Department of Biology & CESAM - Centre for Environmental and Marine Studies, University of Aveiro, Portugal
| | - Fátima Jesus
- Department of Biology & CESAM - Centre for Environmental and Marine Studies, University of Aveiro, Portugal
| | - Sónia P M Ventura
- Department of Chemistry & CICECO - Aveiro Institute of Materials, University of Aveiro, Portugal
| | - Fernando J M Gonçalves
- Department of Biology & CESAM - Centre for Environmental and Marine Studies, University of Aveiro, Portugal
| | - Jana Asselman
- Blue Growth Research Lab, Ghent University, Bluebridge Building, Ostend Science Park 1, 8400 Ostend, Belgium
| | - Joana L Pereira
- Department of Biology & CESAM - Centre for Environmental and Marine Studies, University of Aveiro, Portugal.
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8
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Popescu R, Filimon MN, Vlad DC, Verdes D, Moatar A, Moise G, Guran K, Caraba IV, Ciochina LP, Pinzaru I, Dehelean CA, Dumitrescu G. Antiproliferative and antibacterial potential of tetrahexylammonium bromide-based ionic liquids. Exp Ther Med 2021; 22:672. [PMID: 33986837 PMCID: PMC8112146 DOI: 10.3892/etm.2021.10104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/16/2021] [Indexed: 12/27/2022] Open
Abstract
Ionic liquids (ILs) exhibit cytotoxic effects on prokaryotic and eukaryotic cells. In this study, the antibacterial and antiproliferative activities of tetrahexylammonium bromide-based ILs were investigated. In order to evaluate the therapeutic potential of these ionic liquids, firstly microbiological assay using both Gram-positive and Gram-negative bacteria were conducted by employing Disk-Diffusion and 2,3,5-triphenyltetrazolium chlorine (TTC) methods to assess the antimicrobial effects. Likewise, the antitumor effects on 2D and 3D cell culture systems were assessed using the human colon cancer Caco-2 cell line and cytotoxic activity was assessed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and Alamar blue assays. Results obtained showed that [CH3(CH2)5]4N(Br) possesses an antibacterial potential, particularly in the case of two bacteria, S. aureus (Gram+) and H. influenzae (Gram-). Preliminary screening of antiproliferative activity showed moderate activity, except for the concentration of 10 mM. Furthermore, regarding the effect of [CH3(CH2)5]4N(Br) on tumor cell aggregation, positive outcomes were noted. [CH3(CH2)5]4N(Br) presents promising and under-explored potential to improve antibacterial or anticancer therapies.
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Affiliation(s)
- Roxana Popescu
- Faculty of Medicine, 'Victor Babes' University of Medicine and Pharmacy of Timisoara, 300041 Timisoara, Romania.,ANAPATMOL Research Center, 'Victor Babes' University of Medicine and Pharmacy of Timisoara, 300041 Timisoara, Romania
| | - Marioara Nicoleta Filimon
- ANAPATMOL Research Center, 'Victor Babes' University of Medicine and Pharmacy of Timisoara, 300041 Timisoara, Romania.,Faculty of Chemistry, Biology, Geography, West University of Timisoara, 300115 Timisoara, Romania
| | - Daliborca Cristina Vlad
- Faculty of Medicine, 'Victor Babes' University of Medicine and Pharmacy of Timisoara, 300041 Timisoara, Romania
| | - Doina Verdes
- Faculty of Medicine, 'Victor Babes' University of Medicine and Pharmacy of Timisoara, 300041 Timisoara, Romania.,ANAPATMOL Research Center, 'Victor Babes' University of Medicine and Pharmacy of Timisoara, 300041 Timisoara, Romania
| | - Aurica Moatar
- Faculty of Medicine, 'Victor Babes' University of Medicine and Pharmacy of Timisoara, 300041 Timisoara, Romania
| | - Georgiana Moise
- Faculty of Medicine, 'Victor Babes' University of Medicine and Pharmacy of Timisoara, 300041 Timisoara, Romania
| | - Kristine Guran
- Faculty of Medicine, 'Victor Babes' University of Medicine and Pharmacy of Timisoara, 300041 Timisoara, Romania
| | - Ion Valeriu Caraba
- Faculty of Bioengineering of Animal Resources, 'Regele Mihai I al României' Banat University of Agricultural Sciences and Veterinary Medicine, 300645 Timisoara, Romania
| | - Liliana Petculescu Ciochina
- Faculty of Bioengineering of Animal Resources, 'Regele Mihai I al României' Banat University of Agricultural Sciences and Veterinary Medicine, 300645 Timisoara, Romania
| | - Iulia Pinzaru
- Faculty of Pharmacy, 'Victor Babes' University of Medicine and Pharmacy of Timisoara, 300041 Timisoara, Romania
| | - Cristina Adriana Dehelean
- Faculty of Pharmacy, 'Victor Babes' University of Medicine and Pharmacy of Timisoara, 300041 Timisoara, Romania
| | - Gabi Dumitrescu
- ANAPATMOL Research Center, 'Victor Babes' University of Medicine and Pharmacy of Timisoara, 300041 Timisoara, Romania.,Faculty of Bioengineering of Animal Resources, 'Regele Mihai I al României' Banat University of Agricultural Sciences and Veterinary Medicine, 300645 Timisoara, Romania
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9
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Kurata A, Aoki D, Fukuta Y, Kamimura T, Onishi T, Kishimoto N, Uegaki K. Transcriptome analysis of ionic-liquid tolerant Bacillus amyloliquefaciens CMW1 and identification of a novel efflux pump. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1885995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Atsushi Kurata
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Nara, Japan
| | - Daichi Aoki
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Nara, Japan
| | - Yoshihumi Fukuta
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Nara, Japan
| | - Taichi Kamimura
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Nara, Japan
| | - Taiki Onishi
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Nara, Japan
| | - Noriaki Kishimoto
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Nara, Japan
| | - Koichi Uegaki
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Nara, Japan
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10
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Wang X, Chen Z, Mu Q, Wu X, Zhang J, Mao D, Luo Y, Alvarez PJJ. Ionic Liquid Enriches the Antibiotic Resistome, Especially Efflux Pump Genes, Before Significantly Affecting Microbial Community Structure. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:4305-4315. [PMID: 31944684 DOI: 10.1021/acs.est.9b04116] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
An expanding list of chemicals may permeabilize bacterial cells and facilitate horizontal gene transfer (HGT), which enhances propagation of antibiotic resistance genes (ARGs) in the environment. Previous studies showed that 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]), an ionic liquid, can facilitate HGT of some ARGs among bacteria. However, the dynamic response of a wider range of ARGs and associated mobile genetic elements (MGEs) in different environments is unknown. Here, we used metagenomic tools to study shifts of the resistome and microbiome in both sediments and freshwater microcosms exposed to [BMIm][PF6]. Exposure for 16 h to 0.1 or 1.0 g/L significantly enriched more than 207 ARG subtypes primarily encoding efflux pumps in freshwater microcosms as well as cultivable antibiotic-resistant bacteria. This resistome enrichment was attributed to HGT facilitated by MGEs (428 plasmids, 61 integron-integrase genes, and 45 gene cassettes were enriched) as well as to HGT-related functional genes. Interestingly, resistome enrichment occurred fast (within 16 h) after [BMIm][PF6] exposure, before any significant changes in bacterial community structure. Similar ARG enrichment occurred in sediment microcosms exposed to [BMIm][PF6] for 28 d, and this longer exposure affected the microbial community structure (e.g., Proteobacteria abundance increased significantly). Overall, this study suggests that [BMIm][PF6] releases could rapidly enrich the antibiotic resistome in receiving environments by increasing HGT and fortuitously selecting for efflux pump genes, thus contributing to ARG propagation.
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Affiliation(s)
- Xiaolong Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Zeyou Chen
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Quanhua Mu
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Xinyan Wu
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Jingjing Zhang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Pedro J J Alvarez
- Dept of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
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11
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Onyeabor M, Martinez R, Kurgan G, Wang X. Engineering transport systems for microbial production. ADVANCES IN APPLIED MICROBIOLOGY 2020; 111:33-87. [PMID: 32446412 DOI: 10.1016/bs.aambs.2020.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The rapid development in the field of metabolic engineering has enabled complex modifications of metabolic pathways to generate a diverse product portfolio. Manipulating substrate uptake and product export is an important research area in metabolic engineering. Optimization of transport systems has the potential to enhance microbial production of renewable fuels and chemicals. This chapter comprehensively reviews the transport systems critical for microbial production as well as current genetic engineering strategies to improve transport functions and thus production metrics. In addition, this chapter highlights recent advancements in engineering microbial efflux systems to enhance cellular tolerance to industrially relevant chemical stress. Lastly, future directions to address current technological gaps are discussed.
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Affiliation(s)
- Moses Onyeabor
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Rodrigo Martinez
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Gavin Kurgan
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Xuan Wang
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.
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12
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Sivapragasam M, Moniruzzaman M, Goto M. An Overview on the Toxicological Properties of Ionic Liquids toward Microorganisms. Biotechnol J 2020; 15:e1900073. [PMID: 31864234 DOI: 10.1002/biot.201900073] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 11/21/2019] [Indexed: 12/27/2022]
Abstract
Ionic liquids (ILs), a class of materials with unique physicochemical properties, have been used extensively in the fields of chemical engineering, biotechnology, material sciences, pharmaceutics, and many others. Because ILs are very polar by nature, they can migrate into the environment with the possibility of inclusion in the food chain and bioaccumulation in living organisms. However, the chemical natures of ILs are not quintessentially biocompatible. Therefore, the practical uses of ILs must be preceded by suitable toxicological assessments. Among different methods, the use of microorganisms to evaluate IL toxicity provides many advantages including short generation time, rapid growth, and environmental and industrial relevance. This article reviews the recent research progress on the toxicological properties of ILs toward microorganisms and highlights the computational prediction of various toxicity models.
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Affiliation(s)
- Magaret Sivapragasam
- Biotechnology Department, QUEST International University Perak, 30250, Ipoh, Perak, Malaysia
| | - Muhammad Moniruzzaman
- Chemical Engineering Department, Universiti Teknologi PETRONAS, 32610, Seri Iskandar, Perak, Malaysia.,Center of Researches in Ionic Liquids (CORIL), Universiti Teknologi PETRONAS, 32610, Seri Iskandar, Perak, Malaysia
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Fukuoka, 819-0395, Japan.,Center for Future Chemistry, Kyushu University, Fukuoka, 819-0395, Japan
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13
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Pal S, Sar A, Dam B. Moderate halophilic bacteria, but not extreme halophilic archaea can alleviate the toxicity of short-alkyl side chain imidazolium-based ionic liquids. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 184:109634. [PMID: 31520950 DOI: 10.1016/j.ecoenv.2019.109634] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 08/26/2019] [Accepted: 09/01/2019] [Indexed: 06/10/2023]
Abstract
Imidazolium-based ionic liquids (IL) with short-alkyl side chain such as 1-ethyl-3-methyl-imidazolium chloride ([Emim]Cl) and 1-butyl-3-methyl-imidazolium chloride ([Bmim]Cl) has immense application potential including in lignocellulosic bioenergy production. But they are toxic to most microorganisms, and those isolated from different environments as IL-tolerant have salt tolerance capabilities. This study evaluates the relationship between salt and [Emim]Cl tolerance of microorganisms using different salinity sediments (2-19%) and brines (35%) of India's largest inland hypersaline lake, Sambhar in Rajasthan as the model system. While samples with 2% and 35% salinities do not yield any [Emim]Cl (100 mM) tolerant colonies, others have 6-50% colonies tolerant to the IL. Similar trend was observed with 50 mM [Bmim]Cl. Moderate halophilic isolates of genera Halomonas and Bacillus (growth in 0.7-3.0 M NaCl) isolated from the sediments could grow in as high as 375 mM [Emim]Cl, or 125 mM [Bmim]Cl facilitated by higher synthesis, and uptake of organic osmolytes; and up to 1.7-fold increased activity of active efflux pumps. [Bmim]Cl was more toxic than [Emim]Cl in all performed experiments. [Emim]Cl-adapted cells could trounce IL-induced stress. Interestingly, enrichment with 100 mM [Emim]Cl resulted in increase of IL-tolerant colonies in all sediments including the one with 2% salinity. However, the salt saturated brines (35%) do not yield any such colony even after repeated incubations. Extreme halophilic archaea, Natronomonas (growth in 3.0-4.0 M NaCl) isolated from such brines, were exceedingly sensitive to even 5 mM [Emim]Cl, or 1 mM [Bmim]Cl. Two additional extremophilic archaea, namely Haloferax and Haladaptatus were also sensitive to the tested ILs. Archaeal sensitivity is possibly due to the competitive interaction of [Emim]+ with their acidic proteome (15.4-17.5% aspartic and glutamic acids, against 10.7-12.9% in bacteria) that they maintain to stabilize the high amount of K+ ion accumulated by salt-in strategy. Thus, general salt adaptation strategies of moderate halophilic bacteria help them to restrain toxicity of these ILs, but extremophilic archaea are highly sensitive and demands meticulous use of these solvents to prevent environmental contamination.
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Affiliation(s)
- Srikanta Pal
- Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India
| | - Abhijit Sar
- Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India
| | - Bomba Dam
- Microbiology Laboratory, Department of Botany (DST-FIST & UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India.
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Zhang S, Chang S, Xiao P, Qiu S, Ye Y, Li L, Yan H, Guo S, Duan J. Enzymatic in situ saccharification of herbal extraction residue by a medicinal herbal-tolerant cellulase. BIORESOURCE TECHNOLOGY 2019; 287:121417. [PMID: 31076294 DOI: 10.1016/j.biortech.2019.121417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
Herbel-tolerant strains exhibit considerable environmental and commercial values not only due to their harmless treatment of herbal-extraction residues (HERs) but also because of their use in preparing high-quality cellulase cocktails. In this study, three typical HERs were evaluated for enzymatic in situ saccharification performance. A HERs-tolerance fungus, identified as Penicillium oxalicum G2, can grow in 1.5% (w/v) Radix isatidis residues (RIR), thereby exhibiting the highest FPase (2.2 U/mL), carboxymethyl cellulase (13.3 U/mL), and β-glucosidase (4.6 U/mL) activities. The most effective production of cellulase cocktail was achieved via orthogonal experiment in a system with pH 6.0, 30 °C, and 96 h. Cellulase cocktail from P. oxalicum G2 can directly saccharify the extraction RIR, thereby achieving a maximum reducing sugar yield of 7.2 mg/mL, which is 1.7-fold higher than those of commercial cellulases. Results illustrate the potential of P. oxalicum G2 for enzymatic in situ saccharification.
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Affiliation(s)
- Sen Zhang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources and Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Siyuan Chang
- School of Biology and Environment, Nanjing Polytechnic Institute, 625 Geguan Road, Nanjing 210048, Jiangsu, China; School of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhunan Road, Nanjing 211816, Jiangsu, China
| | - Ping Xiao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources and Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Shouzhe Qiu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources and Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yin Ye
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources and Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Lizhi Li
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources and Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Hui Yan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources and Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Sheng Guo
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources and Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Jinao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources and Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China.
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15
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Walker C, Ryu S, Trinh CT. Exceptional solvent tolerance in Yarrowia lipolytica is enhanced by sterols. Metab Eng 2019; 54:83-95. [DOI: 10.1016/j.ymben.2019.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/24/2019] [Accepted: 03/11/2019] [Indexed: 12/11/2022]
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Guanidine Riboswitch-Regulated Efflux Transporters Protect Bacteria against Ionic Liquid Toxicity. J Bacteriol 2019; 201:JB.00069-19. [PMID: 30988034 DOI: 10.1128/jb.00069-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/09/2019] [Indexed: 11/20/2022] Open
Abstract
Plant cell walls contain a renewable, nearly limitless supply of sugar that could be used to support microbial production of commodity chemicals and biofuels. Imidazolium ionic liquid (IIL) solvents are among the best reagents for gaining access to the sugars in this otherwise recalcitrant biomass. However, the sugars from IIL-treated biomass are inevitably contaminated with residual IILs that inhibit growth in bacteria and yeast, blocking biochemical production by these organisms. IIL toxicity is, therefore, a critical roadblock in many industrial biosynthetic pathways. Although several IIL-tolerant (IILT) bacterial and yeast isolates have been identified in nature, few genetic mechanisms have been identified. In this study, we identified two IILT Bacillus isolates as well as a spontaneous IILT Escherichia coli lab strain that are tolerant to high levels of two widely used IILs. We demonstrate that all three IILT strains contain one or more pumps of the small multidrug resistance (SMR) family, and two of these strains contain mutations that affect an adjacent regulatory guanidine riboswitch. Furthermore, we show that the regulation of E. coli sugE by the guanidine II riboswitch can be exploited to promote IIL tolerance by the simple addition of guanidine to the medium. Our results demonstrate the critical role that transporter genes play in IIL tolerance in their native bacterial hosts. The study presented here is another step in engineering IIL tolerance into industrial strains toward overcoming this key gap in biofuels and industrial biochemical production processes.IMPORTANCE This study identifies bacteria that are tolerant to ionic liquid solvents used in the production of biofuels and industrial biochemicals. For industrial microbiology, it is essential to find less-harmful reagents and microbes that are resistant to their cytotoxic effects. We identified a family of small multidrug resistance efflux transporters, which are responsible for the tolerance of these strains. We also found that this resistance can be caused by mutations in the sequences of guanidine-specific riboswitches that regulate these efflux pumps. Extending this knowledge, we demonstrated that guanidine itself can promote ionic liquid tolerance. Our findings will inform genetic engineering strategies that improve conversion of cellulosic sugars into biofuels and biochemicals in processes where low concentrations of ionic liquids surpass bacterial tolerance.
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Eng T, Demling P, Herbert RA, Chen Y, Benites V, Martin J, Lipzen A, Baidoo EEK, Blank LM, Petzold CJ, Mukhopadhyay A. Restoration of biofuel production levels and increased tolerance under ionic liquid stress is enabled by a mutation in the essential Escherichia coli gene cydC. Microb Cell Fact 2018; 17:159. [PMID: 30296937 PMCID: PMC6174563 DOI: 10.1186/s12934-018-1006-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/26/2018] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Microbial production of chemicals from renewable carbon sources enables a sustainable route to many bioproducts. Sugar streams, such as those derived from biomass pretreated with ionic liquids (IL), provide efficiently derived and cost-competitive starting materials. A limitation to this approach is that residual ILs in the pretreated sugar source can be inhibitory to microbial growth and impair expression of the desired biosynthetic pathway. RESULTS We utilized laboratory evolution to select Escherichia coli strains capable of robust growth in the presence of the IL, 1-ethyl-3-methyl-imidizolium acetate ([EMIM]OAc). Whole genome sequencing of the evolved strain identified a point mutation in an essential gene, cydC, which confers tolerance to two different classes of ILs at concentrations that are otherwise growth inhibitory. This mutation, cydC-D86G, fully restores the specific production of the bio-jet fuel candidate D-limonene, as well as the biogasoline and platform chemical isopentenol, in growth medium containing ILs. Similar amino acids at this position in cydC, such as cydC-D86V, also confer tolerance to [EMIM]OAc. We show that this [EMIM]OAc tolerance phenotype of cydC-D86G strains is independent of its wild-type function in activating the cytochrome bd-I respiratory complex. Using shotgun proteomics, we characterized the underlying differential cellular responses altered in this mutant. While wild-type E. coli cannot produce detectable amounts of either product in the presence of ILs at levels expected to be residual in sugars from pretreated biomass, the engineered cydC-D86G strains produce over 200 mg/L D-limonene and 350 mg/L isopentenol, which are among the highest reported titers in the presence of [EMIM]OAc. CONCLUSIONS The optimized strains in this study produce high titers of two candidate biofuels and bioproducts under IL stress. Both sets of production strains surpass production titers from other IL tolerant mutants in the literature. Our application of laboratory evolution identified a gain of function mutation in an essential gene, which is unusual in comparison to other published IL tolerant mutants.
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Affiliation(s)
- Thomas Eng
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Philipp Demling
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, 52074 Aachen, Germany
| | - Robin A. Herbert
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Veronica Benites
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Joel Martin
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, 94598 USA
| | - Anna Lipzen
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, 94598 USA
| | - Edward E. K. Baidoo
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Lars M. Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, 52074 Aachen, Germany
| | - Christopher J. Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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18
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Higgins DA, Young MKM, Tremaine M, Sardi M, Fletcher JM, Agnew M, Liu L, Dickinson Q, Peris D, Wrobel RL, Hittinger CT, Gasch AP, Singer SW, Simmons BA, Landick R, Thelen MP, Sato TK. Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast. Genetics 2018; 210:219-234. [PMID: 30045857 PMCID: PMC6116967 DOI: 10.1534/genetics.118.301161] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/23/2018] [Indexed: 01/20/2023] Open
Abstract
Imidazolium ionic liquids (IILs) have a range of biotechnological applications, including as pretreatment solvents that extract cellulose from plant biomass for microbial fermentation into sustainable bioenergy. However, residual levels of IILs, such as 1-ethyl-3-methylimidazolium chloride ([C2C1im]Cl), are toxic to biofuel-producing microbes, including the yeast Saccharomyces cerevisiae. S. cerevisiae strains isolated from diverse ecological niches differ in genomic sequence and in phenotypes potentially beneficial for industrial applications, including tolerance to inhibitory compounds present in hydrolyzed plant feedstocks. We evaluated >100 genome-sequenced S. cerevisiae strains for tolerance to [C2C1im]Cl and identified one strain with exceptional tolerance. By screening a library of genomic DNA fragments from the [C2C1im]Cl-tolerant strain for improved IIL tolerance, we identified SGE1, which encodes a plasma membrane multidrug efflux pump, and a previously uncharacterized gene that we named ionic liquid tolerance 1 (ILT1), which encodes a predicted membrane protein. Analyses of SGE1 sequences from our panel of S. cerevisiae strains together with growth phenotypes implicated two single nucleotide polymorphisms (SNPs) that associated with IIL tolerance and sensitivity. We confirmed these phenotypic effects by transferring the SGE1 SNPs into a [C2C1im]Cl-sensitive yeast strain using CRISPR/Cas9 genome editing. Further studies indicated that these SNPs affect Sge1 protein stability and cell surface localization, influencing the amount of toxic IILs that cells can pump out of the cytoplasm. Our results highlight the general potential for discovering useful biotechnological functions from untapped natural sequence variation and provide functional insight into emergent SGE1 alleles with reduced capacities to protect against IIL toxicity.
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Affiliation(s)
- Douglas A Higgins
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, California 94550
| | - Megan K M Young
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Mary Tremaine
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Maria Sardi
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Jenna M Fletcher
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Margaret Agnew
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Lisa Liu
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Quinn Dickinson
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - David Peris
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Russell L Wrobel
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Chris Todd Hittinger
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Audrey P Gasch
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Steven W Singer
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, California 94720
| | - Blake A Simmons
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, California 94550
| | - Robert Landick
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53726
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53726
| | - Michael P Thelen
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, California 94550
| | - Trey K Sato
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
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Long X, Tian J, Liao X, Tian Y. Adaptations of Bacillus shacheensis HNA-14 required for long-term survival under osmotic challenge: a multi-omics perspective. RSC Adv 2018; 8:27525-27536. [PMID: 35540019 PMCID: PMC9083893 DOI: 10.1039/c8ra05472j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 07/26/2018] [Indexed: 01/28/2023] Open
Abstract
Genomic sequence, transcriptomic, metabolomic and fatty acid analyses of strain HNA-14 were performed to understand the mechanism of salt tolerance for long-term survival. The results indicated that strain HNA-14 has different osmotic resistance mechanisms for long-term survival and short-term salt stress. The cells mainly synthesized compatible solutes to resist osmotic pressure when cultured under nutrient deficient conditions, while they can slow down the synthesis rate and uptake from the environment when cultured under a nutritionally rich environment. Also, the amounts of branched and unsaturated fatty acids in the cell membrane are maintained to a high degree (>50%) to maintain the fluidity of the cell membrane; when the cells are cultured in a high osmotic environment for long-term survival, they may increase the content of branched fatty acids and phosphoric fatty acids to increase the fluidity of the cell membrane to resist the high osmotic pressure.
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Affiliation(s)
- Xiufeng Long
- Department of Biomass and Leather Engineering, Sichuan University Chengdu 610065 PR China
| | - Jiewei Tian
- Department of Biomass and Leather Engineering, Sichuan University Chengdu 610065 PR China
| | - Xuepin Liao
- Department of Biomass and Leather Engineering, Sichuan University Chengdu 610065 PR China
- National Engineering Laboratory for Clean Technology of Leather Manufacture, Sichuan University Chengdu 610065 PR China
| | - Yongqiang Tian
- Department of Biomass and Leather Engineering, Sichuan University Chengdu 610065 PR China
- National Engineering Laboratory for Clean Technology of Leather Manufacture, Sichuan University Chengdu 610065 PR China
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20
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Egorova KS, Ananikov VP. Ionic liquids in whole-cell biocatalysis: a compromise between toxicity and efficiency. Biophys Rev 2018; 10:881-900. [PMID: 29313188 PMCID: PMC5988618 DOI: 10.1007/s12551-017-0389-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/13/2017] [Indexed: 12/11/2022] Open
Abstract
Comparison of chemical catalysis by metal complexes, enzymatic catalysis and whole-cell biocatalysis shows well-addressed advantages of the latter approach. However, a critical limitation in the practical applications originates from the high sensitivity of microorganisms to the toxic effects of organic solvents. In the present review, we consider toxic solvent properties of ionic liquid/water systems towards the development of efficient applications in practical organic transformations.
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Affiliation(s)
- Ksenia S Egorova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, Moscow, 119991, Russia
| | - Valentine P Ananikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, Moscow, 119991, Russia.
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21
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Jia X, Hua J, Liu L, Xu Z, Li Y. Phenotypic characterization of pathogenic Cronobacter spp. strains. Microb Pathog 2018; 121:232-237. [PMID: 29800699 DOI: 10.1016/j.micpath.2018.05.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/15/2018] [Accepted: 05/22/2018] [Indexed: 01/14/2023]
Abstract
BACKGROUND Cronobacter species are Gram-negative opportunistic foodborne pathogens that may cause enterocolitis, bacteremia and meningitis in neonates and premature neonates. Lipopolysaccharide (LPS) serves as the major component of the outer membrane of cell, is a potential virulence factor for Cronobacter. METHODS Given the potential importance of this molecule in infection and virulence, SDS-PAGE of LPS, MS and TLC characterization of phospholipids and phenotypic characterization of Cronobacter spp. strains were carried out. RESULT The phospholipids from Cronobacter yielded four major peaks at m/z 719.9, 733.9, 747.9 and 773.9 in the spectrum. All Cronobacter showed O-antigen bands except C. muytjensii ATCC 51329. When Cronobacter defect O-antigen, the outer membrane permeability and cell surface hydrophobicities are increased. All Cronobacter are able to grow under pH 5.0 condition and able to grow under 6% NaCl concentration. C. dublinensis DSM 18705 has a higher infection rate to Caco-2 cells than other Cronobacter. CONCLUSION Invasion of pathogens into a host cell is critical component to an infectious case. And C. dublinensis DSM 18705 has a higher infection rate to Caco-2 cells than other Cronobacter.
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Affiliation(s)
- Xiangyin Jia
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Jingjing Hua
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Lu Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Zhenbo Xu
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640, China; Department of Microbial Pathogenesis, University of Maryland, Baltimore, 21201, USA; Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Guangzhou, 510640, China.
| | - Yanyan Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.
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22
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Designing tailored microbial and enzymatic response in ionic liquids for lignocellulosic biorefineries. Biophys Rev 2018; 10:911-913. [PMID: 29687273 DOI: 10.1007/s12551-018-0418-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 04/08/2018] [Indexed: 01/08/2023] Open
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23
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Mai NL, Koo YM. Whole-Cell Biocatalysis in Ionic Liquids. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 168:105-132. [PMID: 30488166 DOI: 10.1007/10_2018_77] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The use of whole-cell biocatalysis in ionic liquid (IL)-containing systems has attracted increasing attention in recent years. Compared to bioreactions catalyzed by isolated enzymes, the major advantage of using whole cells in biocatalytic processes is that the cells provide a natural intracellular environment for the enzymes to function with in situ cofactor regeneration. To date, the applications of whole-cell biocatalysis in IL-containing systems have focused on the production of valuable compounds, mainly through reduction, oxidation, hydrolysis, and transesterification reactions. The interaction mechanisms between the ILs and biocatalysts in whole-cell biocatalysis offer the possibility to effectively integrate ILs with biotransformation. This chapter discusses these interaction mechanisms between ILs and whole-cell catalysts. In addition, examples of whole-cell catalyzed reactions with ILs will also be discussed. Graphical Abstract.
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Affiliation(s)
- Ngoc Lan Mai
- Department of Biological Engineering, Inha University, Incheon, South Korea
| | - Yoon-Mo Koo
- Department of Biological Engineering, Inha University, Incheon, South Korea.
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24
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Orellana R, Chaput G, Markillie LM, Mitchell H, Gaffrey M, Orr G, DeAngelis KM. Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium. PLoS One 2017; 12:e0186440. [PMID: 29049419 PMCID: PMC5648182 DOI: 10.1371/journal.pone.0186440] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/02/2017] [Indexed: 12/11/2022] Open
Abstract
The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors. Enterobacter lignolyticus SCF1 is a facultative anaerobic Gammaproteobacteria isolated from tropical rain forest soil collected in El Yunque forest, Puerto Rico under anoxic growth conditions with lignin as sole carbon source. Whole transcriptome analysis of SCF1 during E.lignolyticus SCF1 lignin degradation was conducted on cells grown in the presence (0.1%, w/w) and the absence of lignin, where samples were taken at three different times during growth, beginning of exponential phase, mid-exponential phase and beginning of stationary phase. Lignin-amended cultures achieved twice the cell biomass as unamended cultures over three days, and in this time degraded 60% of lignin. Transcripts in early exponential phase reflected this accelerated growth. A complement of laccases, aryl-alcohol dehydrogenases, and peroxidases were most up-regulated in lignin amended conditions in mid-exponential and early stationary phases compared to unamended growth. The association of hydrogen production by way of the formate hydrogenlyase complex with lignin degradation suggests a possible value added to lignin degradation in the future.
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Affiliation(s)
- Roberto Orellana
- Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Gina Chaput
- Microbiology Department, University of Massachusetts Amherst, Amherst, United States of America
| | - Lye Meng Markillie
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Hugh Mitchell
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Matt Gaffrey
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Galya Orr
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Kristen M. DeAngelis
- Microbiology Department, University of Massachusetts Amherst, Amherst, United States of America
- * E-mail:
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25
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1-Ethyl-3-methylimidazolium tolerance and intracellular lipid accumulation of 38 oleaginous yeast species. Appl Microbiol Biotechnol 2017; 101:8621-8631. [DOI: 10.1007/s00253-017-8506-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 08/09/2017] [Accepted: 08/23/2017] [Indexed: 10/18/2022]
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26
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Kurata A, Shimizu S, Shiraishi Y, Abe M, Naito N, Shimada M, Kishimoto N. Degradation of ionic liquids by a UV/H 2O 2 process and CMCase from novel ionic liquid-tolerant alkaliphilic Nocardiopsis sp. SSC4. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1335613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Atsushi Kurata
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Japan
| | - Shota Shimizu
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Japan
| | - Yutaro Shiraishi
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Japan
| | - Mihoko Abe
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Japan
| | - Nobutoshi Naito
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Japan
| | - Mihoko Shimada
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Japan
| | - Noriaki Kishimoto
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara City, Japan
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27
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Egorova KS, Gordeev EG, Ananikov VP. Biological Activity of Ionic Liquids and Their Application in Pharmaceutics and Medicine. Chem Rev 2017; 117:7132-7189. [PMID: 28125212 DOI: 10.1021/acs.chemrev.6b00562] [Citation(s) in RCA: 906] [Impact Index Per Article: 129.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ionic liquids are remarkable chemical compounds, which find applications in many areas of modern science. Because of their highly tunable nature and exceptional properties, ionic liquids have become essential players in the fields of synthesis and catalysis, extraction, electrochemistry, analytics, biotechnology, etc. Apart from physical and chemical features of ionic liquids, their high biological activity has been attracting significant attention from biochemists, ecologists, and medical scientists. This Review is dedicated to biological activities of ionic liquids, with a special emphasis on their potential employment in pharmaceutics and medicine. The accumulated data on the biological activity of ionic liquids, including their antimicrobial and cytotoxic properties, are discussed in view of possible applications in drug synthesis and drug delivery systems. Dedicated attention is given to a novel active pharmaceutical ingredient-ionic liquid (API-IL) concept, which suggests using traditional drugs in the form of ionic liquid species. The main aim of this Review is to attract a broad audience of chemical, biological, and medical scientists to study advantages of ionic liquid pharmaceutics. Overall, the discussed data highlight the importance of the research direction defined as "Ioliomics", studies of ions in liquids in modern chemistry, biology, and medicine.
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Affiliation(s)
- Ksenia S Egorova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Leninsky prospect 47, Moscow 119991, Russia
| | - Evgeniy G Gordeev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Leninsky prospect 47, Moscow 119991, Russia
| | - Valentine P Ananikov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Leninsky prospect 47, Moscow 119991, Russia.,Department of Chemistry, Saint Petersburg State University , Stary Petergof 198504, Russia
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Cancemi P, Buttacavoli M, D'Anna F, Feo S, Fontana RM, Noto R, Sutera A, Vitale P, Gallo G. The effects of structural changes on the anti-microbial and anti-proliferative activities of diimidazolium salts. NEW J CHEM 2017. [DOI: 10.1039/c6nj03904a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Anti-microbial and anti-proliferative activities of diimidazolium salts have been analyzed as a function of the main changes in their structural features.
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Affiliation(s)
- Patrizia Cancemi
- Dipartimento STEBICEF
- Sezione di Biologia Cellulare
- Viale delle Scienze
- 90128 Palermo
- Italy
| | - Miriam Buttacavoli
- Dipartimento STEBICEF
- Sezione di Biologia Cellulare
- Viale delle Scienze
- 90128 Palermo
- Italy
| | - Francesca D'Anna
- Dipartimento STEBICEF
- Sezione di Chimica
- Viale delle Scienze
- 90128 Palermo
- Italy
| | - Salvatore Feo
- Dipartimento STEBICEF
- Sezione di Biologia Cellulare
- Viale delle Scienze
- 90128 Palermo
- Italy
| | - Rosa Maria Fontana
- Dipartimento STEBICEF
- Sezione di Biologia Cellulare
- Viale delle Scienze
- 90128 Palermo
- Italy
| | - Renato Noto
- Dipartimento STEBICEF
- Sezione di Chimica
- Viale delle Scienze
- 90128 Palermo
- Italy
| | - Alberto Sutera
- Dipartimento STEBICEF
- Sezione di Biologia Cellulare
- Viale delle Scienze
- 90128 Palermo
- Italy
| | - Paola Vitale
- Dipartimento STEBICEF
- Sezione di Chimica
- Viale delle Scienze
- 90128 Palermo
- Italy
| | - Giuseppe Gallo
- Dipartimento STEBICEF
- Sezione di Biologia Cellulare
- Viale delle Scienze
- 90128 Palermo
- Italy
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29
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Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis. mSystems 2016; 1:mSystems00120-16. [PMID: 27981239 PMCID: PMC5155067 DOI: 10.1128/msystems.00120-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/15/2016] [Indexed: 01/12/2023] Open
Abstract
Pretreatment using ionic liquids (IL) is a promising approach for the conversion of lignocellulose to biofuels. Because IL can be inhibitory to enzymes and microorganisms involved in downstream hydrolysis and fermentation steps, discovery of IL-tolerant organisms and enzymes is critical for advancing this technology. Employing metatranscriptomics in the analysis of IL-enriched cultures facilitated tracking of dynamic changes in a complex microbial community at the level of gene transcription and doing so with genome resolution. Specific organisms were discovered that could simultaneously tolerate a moderate IL concentration and transcribe a diverse array of cellulolytic enzymes. Gene sequences of cellulolytic enzymes and efflux pumps from those same organisms were also identified, providing important resources for future research on engineering IL-tolerant organisms and enzymes. Ionic liquid (IL) pretreatment is a promising approach for the conversion of lignocellulose to biofuels. The toxicity of residual IL, however, negatively impacts the performance of industrial enzymes and microorganisms in hydrolysis and fermentation. In this study, a thermophilic microbial community was cultured on switchgrass amended with various levels of the ionic liquid 1-ethyl-3-methylimidazolium acetate. Changes in the microbial community composition and transcription of genes relevant to IL tolerance and lignocellulose hydrolysis were quantified. Increasing the level of IL to 0.1% (wt) led to increased levels of relative abundance and transcription in organisms of the phylum Firmicutes. Interestingly, IL concentrations of up to 1% (wt) also resulted in greater xylanase transcription and enzyme activity as well as increased transcription of endoglucanase, beta-glucosidase, and IL tolerance genes compared to communities without IL. IL levels above 1% (wt) resulted in decreased enzyme activity and transcription of genes involved in lignocellulose hydrolysis. The results indicate that moderate levels of IL select for thermophilic microorganisms that not only tolerate IL but also effectively hydrolyze lignocellulose from switchgrass. Discovery of IL-tolerant organisms and enzymes is critical for the development of biological processes that convert IL-pretreated biomass to biofuels and chemicals. Employing metatranscriptomic analysis of enrichment cultures can facilitate the discovery of microorganisms and enzymes that may be active in the presence of toxic compounds such as ionic liquids. IMPORTANCE Pretreatment using ionic liquids (IL) is a promising approach for the conversion of lignocellulose to biofuels. Because IL can be inhibitory to enzymes and microorganisms involved in downstream hydrolysis and fermentation steps, discovery of IL-tolerant organisms and enzymes is critical for advancing this technology. Employing metatranscriptomics in the analysis of IL-enriched cultures facilitated tracking of dynamic changes in a complex microbial community at the level of gene transcription and doing so with genome resolution. Specific organisms were discovered that could simultaneously tolerate a moderate IL concentration and transcribe a diverse array of cellulolytic enzymes. Gene sequences of cellulolytic enzymes and efflux pumps from those same organisms were also identified, providing important resources for future research on engineering IL-tolerant organisms and enzymes.
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30
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Zou W, Li X, Lai Z, Zhang X, Hu X, Zhou Q. Graphene Oxide Inhibits Antibiotic Uptake and Antibiotic Resistance Gene Propagation. ACS APPLIED MATERIALS & INTERFACES 2016; 8:33165-33174. [PMID: 27934199 DOI: 10.1021/acsami.6b09981] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Antibiotics and antibiotic resistance genes (ARGs) in the natural environment have become substantial threats to the ecosystem and public health. Effective strategies to control antibiotics and ARG contaminations are emergent. A novel carbon nanomaterial, graphene oxide (GO), has attracted a substantial amount of attention in environmental fields. This study discovered the inhibition effects of GO on sulfamethoxazole (SMZ) uptake for bacteria and ARG transfer among microorganisms. GO promoted the penetration of SMZ from intracellular to extracellular environments by increasing the cell membrane permeability. In addition, the formation of a GO-SMZ complex reduced the uptake of SMZ in bacteria. Moreover, GO decreased the abundance of the sulI and intI genes by approximately 2-3 orders of magnitude, but the global bacterial activity was not obviously inhibited. A class I integron transfer experiment showed that the transfer frequency was up to 55-fold higher in the control than that of the GO-treated groups. Genetic methylation levels were not significant while sulI gene replication was inhibited. The biological properties of ARGs were altered due to the GO-ARG noncovalent combination, which was confirmed using multiple spectral analyses. This work suggests that GO can potentially be applied for controlling ARG contamination via inhibiting antibiotic uptake and ARG propagation.
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Affiliation(s)
- Wei Zou
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University , Tianjin 300071, China
| | - Xiaokang Li
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University , Tianjin 300071, China
| | - Ziyang Lai
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University , Tianjin 300071, China
| | - Xingli Zhang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University , Tianjin 300071, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University , Tianjin 300071, China
| | - Qixing Zhou
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University , Tianjin 300071, China
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31
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Forget A, Arya N, Randriantsilefisoa R, Miessmer F, Buck M, Ahmadi V, Jonas D, Blencowe A, Shastri VP. Nonwoven Carboxylated Agarose-Based Fiber Meshes with Antimicrobial Properties. Biomacromolecules 2016; 17:4021-4026. [DOI: 10.1021/acs.biomac.6b01401] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aurelien Forget
- Future
Industries Institute, University of South Australia, Mawson
Lakes 5095, South Australia, Australia
- Institute
for Macromolecular Chemistry, University of Freiburg, 79104, Freiburg, Germany
| | - Neha Arya
- Institute
for Macromolecular Chemistry, University of Freiburg, 79104, Freiburg, Germany
- Helmholtz Virtual
Institute on Multifunctional Biomaterials for Medicine, Kantstraße 5514513, Teltow, Germany
| | | | - Florian Miessmer
- Institute
for Macromolecular Chemistry, University of Freiburg, 79104, Freiburg, Germany
| | - Marion Buck
- Department
of Environmental Health Science, Universitätklinikum Freiburg, Freiburg 79106, Germany
| | - Vincent Ahmadi
- Institute
for Macromolecular Chemistry, University of Freiburg, 79104, Freiburg, Germany
| | - Daniel Jonas
- Department
of Environmental Health Science, Universitätklinikum Freiburg, Freiburg 79106, Germany
| | - Anton Blencowe
- School
of Pharmacy and Medical Sciences, University of South Australia, Mawson
Lakes 5095, South Australia, Australia
| | - V. Prasad Shastri
- Institute
for Macromolecular Chemistry, University of Freiburg, 79104, Freiburg, Germany
- Helmholtz Virtual
Institute on Multifunctional Biomaterials for Medicine, Kantstraße 5514513, Teltow, Germany
- BIOSS−Centre
for Biological Signaling Studies, University of Freiburg, 79104, Freiburg, Germany
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32
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Yu C, Simmons BA, Singer SW, Thelen MP, VanderGheynst JS. Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts. Appl Microbiol Biotechnol 2016; 100:10237-10249. [PMID: 27838839 DOI: 10.1007/s00253-016-7955-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 11/26/2022]
Abstract
Chemical and physical pretreatment of biomass is a critical step in the conversion of lignocellulose to biofuels and bioproducts. Ionic liquid (IL) pretreatment has attracted significant attention due to the unique ability of certain ILs to solubilize some or all components of the plant cell wall. However, these ILs inhibit not only the enzyme activities but also the growth and productivity of microorganisms used in downstream hydrolysis and fermentation processes. While pretreated biomass can be washed to remove residual IL and reduce inhibition, extensive washing is costly and not feasible in large-scale processes. IL-tolerant microorganisms and microbial communities have been discovered from environmental samples and studies begun to elucidate mechanisms of IL tolerance. The discovery of IL tolerance in environmental microbial communities and individual microbes has lead to the proposal of molecular mechanisms of resistance. In this article, we review recent progress on discovering IL-tolerant microorganisms, identifying metabolic pathways and mechanisms of tolerance, and engineering microorganisms for IL tolerance. Research in these areas will yield new approaches to overcome inhibition in lignocellulosic biomass bioconversion processes and increase opportunities for the use of ILs in biomass pretreatment.
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Affiliation(s)
- Chaowei Yu
- Department of Biological and Agricultural Engineering, University of California, One Shields Ave., Davis, CA, 95616, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Michael P Thelen
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biosciences Division, Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA
| | - Jean S VanderGheynst
- Department of Biological and Agricultural Engineering, University of California, One Shields Ave., Davis, CA, 95616, USA.
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
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33
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Kurata A, Senoo H, Ikeda Y, Kaida H, Matsuhara C, Kishimoto N. Properties of an ionic liquid-tolerant Bacillus
amyloliquefaciens CMW1 and its extracellular protease. Extremophiles 2016; 20:415-24. [DOI: 10.1007/s00792-016-0832-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 04/25/2016] [Indexed: 10/21/2022]
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34
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Alves PC, Hartmann DO, Núñez O, Martins I, Gomes TL, Garcia H, Galceran MT, Hampson R, Becker JD, Silva Pereira C. Transcriptomic and metabolomic profiling of ionic liquid stimuli unveils enhanced secondary metabolism in Aspergillus nidulans. BMC Genomics 2016; 17:284. [PMID: 27072538 PMCID: PMC4830055 DOI: 10.1186/s12864-016-2577-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/08/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The inherent potential of filamentous fungi, especially of Ascomycota, for producing diverse bioactive metabolites remains largely silent under standard laboratory culture conditions. Innumerable strategies have been described to trigger their production, one of the simplest being manipulation of the growth media composition. Supplementing media with ionic liquids surprisingly enhanced the diversity of extracellular metabolites generated by penicillia. This finding led us to evaluate the impact of ionic liquids' stimuli on the fungal metabolism in Aspergillus nidulans and how it reflects on the biosynthesis of secondary metabolites (SMs). RESULTS Whole transcriptional profiling showed that exposure to 0.7 M cholinium chloride or 1-ethyl-3-methylimidazolium chloride dramatically affected expression of genes encoding both primary and secondary metabolism. Both ionic liquids apparently induced stress responses and detoxification mechanisms but response profiles to each stimulus were unique. Primary metabolism was up-regulated by choline, but down-regulated by 1-ethyl-3-methylimidazolium chloride; both stimulated production of acetyl-CoA (key precursor to numerous SMs) and non proteinogenic amino acids (building blocks of bioactive classes of SMs). In total, twenty one of the sixty six described backbone genes underwent up-regulation. Accordingly, differential analysis of the fungal metabolome showed that supplementing growth media with ionic liquids resulted in ca. 40 differentially accumulated ion masses compared to control conditions. In particular, it stimulated production of monodictyphenone and orsellinic acid, otherwise cryptic. Expression levels of genes encoding corresponding polyketide biosynthetic enzymes (i.e. backbone genes) increased compared to control conditions. The corresponding metabolite extracts showed increased cell polarity modulation potential in an ex vivo whole tissue assay (The lial Live Targeted Epithelia; theLiTE™). CONCLUSIONS Ionic liquids, a diverse class of chemicals composed solely of ions, can provide an unexpected means to further resolve the diversity of natural compounds, guiding discovery of fungal metabolites with clinical potential.
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Affiliation(s)
- Paula C Alves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Diego O Hartmann
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Oscar Núñez
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, E-08028, Barcelona, Spain.,Serra Hunter Fellow, Generalitat de Catalunya, Barcelona, Spain
| | - Isabel Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Teresa L Gomes
- Thelial Technologies S.A., Parque Tecnológico de Cantanhede, Nucleo 04 Lote 3, 3060-197, Cantanhede, Portugal
| | - Helga Garcia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Maria Teresa Galceran
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, E-08028, Barcelona, Spain
| | - Richard Hampson
- Thelial Technologies S.A., Parque Tecnológico de Cantanhede, Nucleo 04 Lote 3, 3060-197, Cantanhede, Portugal
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Cristina Silva Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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Hartmann DO, Petkovic M, Silva Pereira C. Ionic Liquids as Unforeseen Assets to Fight Life-Threatening Mycotic Diseases. Front Microbiol 2016; 7:111. [PMID: 26903990 PMCID: PMC4744837 DOI: 10.3389/fmicb.2016.00111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 01/22/2016] [Indexed: 11/13/2022] Open
Abstract
Ionic liquids discovery has celebrated 100 years. They consist solely of ions, one of which is typically organic and asymmetrical. Remarkable physical and chemical properties stirred their use as alternative solvents in many chemical processes. The recent demonstration of their occurrence in nature might boost their interest in biological sciences. In the search of mechanistic understandings of ionic liquids’ ecotoxicological impacts in fungi, we have analyzed the proteome, transcriptome, and metabolome responses to this chemical stress. Data illuminated new hypotheses that altered our research path – exploit ionic liquids as tools for the discovery of pathways and metabolites that may impact fungal development and pathogenicity. As we get closer to solve the primary effects of each ionic liquid family and their specific gene targets, the vision of developing antifungal ionic liquids and/or materials, by taking advantage of elegant progresses in this field, might become a reality. Task-designed formulations may improve the performance of conventional antifungal drugs, build functional coatings for reducing allergens production, or aid in the recovery of antifungal plant polymers. The frontier research in this cross-disciplinary field may provide us unforeseen means to address the global concern of mycotic diseases. Pathogenic and opportunistic fungi are responsible for numerous infections, killing annually nearly 1.5 million immunocompromised individuals worldwide, a similar rate to malaria or tuberculosis. This perspective will review our major findings and current hypotheses, contextualizing how they might bring us closer to efficient strategies to prevent and fight mycotic diseases.
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Affiliation(s)
- Diego O Hartmann
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Marija Petkovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Cristina Silva Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
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36
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Sriariyanun M, Tantayotai P, Yasurin P, Pornwongthong P, Cheenkachorn K. Production, purification and characterization of an ionic liquid tolerant cellulase from Bacillus sp. isolated from rice paddy field soil. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2015.11.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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37
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Biocatalysts for biomass deconstruction from environmental genomics. Curr Opin Chem Biol 2015; 29:18-25. [DOI: 10.1016/j.cbpa.2015.06.032] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 06/30/2015] [Accepted: 06/30/2015] [Indexed: 01/23/2023]
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38
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Wang Q, Lu Q, Mao D, Cui Y, Luo Y. The horizontal transfer of antibiotic resistance genes is enhanced by ionic liquid with different structure of varying alkyl chain length. Front Microbiol 2015; 6:864. [PMID: 26379641 PMCID: PMC4550778 DOI: 10.3389/fmicb.2015.00864] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 08/07/2015] [Indexed: 01/24/2023] Open
Abstract
Antibiotic resistance genes (ARGs) have become a global health concern. In our previous study, an ionic liquid (IL) 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]) had been proven to facilitate the dissemination of ARGs in the environment. However, enhanced alkyl group chain length or the substitution of alkyl groups with the cation ring corresponded with increased antimicrobial effects. In this study, we investigated how different structures of ILs with 4, 6, and 8 C atoms in the longer alkyl chain on the imidazolium cations facilitated the dissemination of ARGs. The promotion of plasmid RP4 transfer frequency decreased with [CnMIM][BF4] increasing the alkyl chain length from 4 carbon atoms to 8 carbon atoms on the imidazolium cations, which is observed with [BMIM][BF4] (n = 4, 5.9 fold) > HMIM][BF4] (n = 6, 2.2 fold) > [OMIM][BF4] (n = 8, 1.7 fold). This illustrates that [CnMIM][BF4] with increasing the alkyl chain length exert decreasing ability in facilitating plasmid RP4 horizontal transfer, which is possibly related to IL-structure dependent toxicity. The IL-structure dependent plasmid RP4 transfer frequency was attributable to bacterial cell membrane permeability weaken with increasing alkyl chain length of [CnMIM][PF4], which was evidenced by flow cytometry. In freshwater microcosm, [CnMIm][BF4] promoted the relative abundance of the sulI and intI genes for 4.6 folds, aphA and traF for 5.2 folds higher than the untreated groups, promoting the propagation of ARGs in the aquatic environment. This is the first report that ILs with different structure of varying alkyl chain length facilitate horizontal transfer of plasmid RP4 which is widely distributed in the environment, and thus add the adverse effects of the environmental risk of ILs.
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Affiliation(s)
- Qing Wang
- School of Environmental Science and Engineering, Tianjin UniversityTianjin, China
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai UniversityTianjin, China
| | - Qian Lu
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai UniversityTianjin, China
| | - Daqing Mao
- School of Environmental Science and Engineering, Tianjin UniversityTianjin, China
| | - Yuxiao Cui
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai UniversityTianjin, China
| | - Yi Luo
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai UniversityTianjin, China
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Identification of Oxygen-Responsive Transcripts in the Silage Inoculant Lactobacillus buchneri CD034 by RNA Sequencing. PLoS One 2015; 10:e0134149. [PMID: 26230316 PMCID: PMC4521753 DOI: 10.1371/journal.pone.0134149] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 07/06/2015] [Indexed: 11/19/2022] Open
Abstract
The Lactobacillus buchneri CD034 strain, known to improve the ensiling process of green fodder and the quality of the silage itself was transcriptionally analyzed by sequencing of transcriptomes isolated under anaerobic vs. aerobic conditions. L. buchneri CD034 was first cultivated under anaerobic conditions and then shifted to aerobic conditions by aeration with 21% oxygen. Cultivations already showed that oxygen was consumed by L. buchneri CD034 after aeration of the culture while growth of L. buchneri CD034 was still observed. RNA sequencing data revealed that irrespective of the oxygen status of the culture, the most abundantly transcribed genes are required for basic cell functions such as protein biosynthesis, energy metabolism and lactic acid fermentation. Under aerobic conditions, 283 genes were found to be transcriptionally up-regulated while 198 genes were found to be down-regulated (p-value < 0.01). Up-regulated genes i. a. play a role in oxygen consumption via oxidation of pyruvate or lactate (pox, lctO). Additionally, genes encoding proteins required for decomposition of reactive oxygen species (ROS) such as glutathione reductase or NADH peroxidase were also found to be up-regulated. Genes related to pH homeostasis and redox potential balance were found to be down-regulated under aerobic conditions. Overall, genes required for lactic acid fermentation were hardly affected by the growth conditions applied. Genes identified to be differentially transcribed depending on the aeration status of the culture are suggested to specify the favorable performance of the strain in silage formation.
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Wang Q, Mao D, Luo Y. Ionic Liquid Facilitates the Conjugative Transfer of Antibiotic Resistance Genes Mediated by Plasmid RP4. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:8731-8740. [PMID: 26120784 DOI: 10.1021/acs.est.5b01129] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The dissemination and propagation of antibiotic resistance genes (ARGs) is an emerging global health concern. In our previous study, the ionic liquid (IL) 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]) had been proven to facilitate the dissemination of ARGs via horizontal gene transfer. In this study, we further confirm that this compound facilitates the horizontal transfer of plasmid RP4 through a conjugation mechanism and not by natural transformation. The mechanisms for [BMIm][PF6] promoting conjugative transfer are attributable to enhancing the mRNA expression levels of conjugative and global regulatory genes, as well as by inhibiting the genes that are responsible for the vertical transfer of cell growth. [BMIm][PF6] significantly enhanced the expression of the outer membrane porin proteins (OMPs) OmpC and OmpA and the corresponding mRNA expression levels of ompC and ompA genes in recipient bacteria, which contributed to pore formation and increased cell membrane permeability. The increased expression of pilin and pili allowed the donor pilus to attach to and access the recipient cells, thereby assisting cell-to-cell contact to facilitate the conjugative transfer of plasmid RP4. To the best of our knowledge, this is the first insightful exploration of [BMIm][PF6] facilitating the conjugative transfer of ARGs mediated by plasmid RP4 and of several other ILs with different cations or anions that are capable of promoting plasmid transfer. It is therefore suggested that the application of some ILs in industrial processes should be carefully evaluated before their bulk emission into the environment.
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Affiliation(s)
- Qing Wang
- ‡College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Daqing Mao
- †School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Yi Luo
- ‡College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
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Wang Q, Mao D, Mu Q, Luo Y. Enhanced horizontal transfer of antibiotic resistance genes in freshwater microcosms induced by an ionic liquid. PLoS One 2015; 10:e0126784. [PMID: 25951456 PMCID: PMC4423773 DOI: 10.1371/journal.pone.0126784] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/07/2015] [Indexed: 12/22/2022] Open
Abstract
The spread and propagation of antibiotic resistance genes (ARGs) is a worldwide public health concern. Ionic liquids (ILs), considered as "environmentally friendly" replacements for industrial organic solvents, have been widely applied in modern industry. However, few data have been collected regarding the potential ecological and environmental risks of ILs, which are important for preparing for their potential discharge into the environment. In this paper, the IL 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]) (0.001-5.0 g/L) was tested for its effects on facilitating ARGs horizontal transfer mediated by plasmid RP4 in freshwater microcosms. In the horizontal transfer microcosms, the transfer frequency of plasmid RP4 was significantly enhanced (60-fold higher than untreated groups) by the IL [BMIm][PF6] (1.0 g/L). Meanwhile, two strains of opportunistic pathogen Acinetobacter spp. and Salmonella spp. were isolated among the transconjugants, illustrating plasmid RP4 mediated horizontal transfer of ARGs occurred in pathogen. This could increase the risk of ARGs dissemination to human pathogens and pose great threat to public health. The cause that [BMIm[PF6] enhanced the transfer frequency of plasmid RP4 was proposed by suppressed cell membrane barrier and enhanced cell membrane permeability, which was evidenced by flow cytometry (FCM). This is the first report that some ILs facilitate horizontal transfer of plasmid RP4 which is widely distributed in the environment and thus add the adverse effects of the environmental risk of ILs.
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Affiliation(s)
- Qing Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Daqing Mao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Quanhua Mu
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
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cAMP receptor protein (CRP)-mediated resistance/tolerance in bacteria: mechanism and utilization in biotechnology. Appl Microbiol Biotechnol 2015; 99:4533-43. [DOI: 10.1007/s00253-015-6587-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 03/31/2015] [Accepted: 04/03/2015] [Indexed: 02/05/2023]
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Xu J, Wang X, Hu L, Xia J, Wu Z, Xu N, Dai B, Wu B. A novel ionic liquid-tolerant Fusarium oxysporum BN secreting ionic liquid-stable cellulase: consolidated bioprocessing of pretreated lignocellulose containing residual ionic liquid. BIORESOURCE TECHNOLOGY 2015; 181:18-25. [PMID: 25625459 DOI: 10.1016/j.biortech.2014.12.080] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 12/22/2014] [Accepted: 12/23/2014] [Indexed: 06/04/2023]
Abstract
In this study, microbial communities from chemicals polluted microhabitats were cultured with the addition of imidazolium-based ionic liquid (IL) to enrich for IL-tolerant microbes. A strain of Fusarium oxysporum BN producing cellulase from these enrichments was capable of growing in 10% (w/v) 1-ethyl-3-methylimidazolium phosphinate, much higher than the normal IL concentrations in the lignocellulose regenerated from ILs. Cellulase secreted by the strain showed high resistance to ILs based on phosphate and sulfate radicals, evidencing of a high conformational stability in relevant media. Gratifyingly, F. oxysporum BN can directly convert IL-pretreated rice straw to bioethanol via consolidated bioprocessing (I-CBP). At optimum fermentation condition, a maximum ethanol yield of 0.125 g ethanol g(-1) of rice straw was finally obtained, corresponding to 64.2% of the theoretical yield.
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Affiliation(s)
- Jiaxing Xu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiangxi Road, Huaian 223300, China
| | - Xinfeng Wang
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiangxi Road, Huaian 223300, China; Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huaian 223300, China
| | - Lei Hu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiangxi Road, Huaian 223300, China
| | - Jun Xia
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiangxi Road, Huaian 223300, China
| | - Zhen Wu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiangxi Road, Huaian 223300, China
| | - Ning Xu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiangxi Road, Huaian 223300, China
| | - Benlin Dai
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiangxi Road, Huaian 223300, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing 210000, China.
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Simultaneous saccharification and fermentation of cellulose in ionic liquid for efficient production of α-ketoglutaric acid by Yarrowia lipolytica. Appl Microbiol Biotechnol 2015; 99:4237-44. [PMID: 25783627 DOI: 10.1007/s00253-015-6521-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 03/01/2015] [Accepted: 03/02/2015] [Indexed: 01/06/2023]
Abstract
Ionic liquids (ILs) are benign solvents that are highly effective for biomass pretreatment. However, their applications for scale-up biorefinery are limited due to multiple expensive IL recovery and separation steps that are required. To overcome this limitation, it is very critical to develop a compatible enzymatic and microbial biocatalyst system to carry the simultaneous saccharification and fermentation in IL environments (SSF-IL). While enzymatic biocatalysts have been demonstrated to be compatible with various IL environments, it is challenging to develop microbial biocatalysts that can thrive and perform efficient biotransformation under the same conditions (pH and temperature). In this study, we harnessed the robust metabolism of Yarrowia lipolytica as a microbial platform highly compatible with the IL environments such as 1-ethyl-3-methylimidazolium acetate ([EMIM][OAc]). We optimized the enzymatic and microbial biocatalyst system using commercial cellulases and demonstrated the capability of Y. lipolytica to convert cellulose into high-value organics such as α-ketoglutaric acid (KGA) in the SSF-IL process at relatively low temperature 28 °C and high pH 6.3. We showed that SSF-IL not only enhanced the enzymatic saccharification but also produced KGA up to 92% of the maximum theoretical yield.
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Abstract
One out of 10 microorganisms from extreme locations was adapted to the presence of common families of ionic liquids, which have lately emerged as “contaminants on the horizon”.
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Affiliation(s)
- M. S. Álvarez
- Department of Chemical Engineering
- University of Vigo
- Vigo
- Spain
| | - A. Rodríguez
- Department of Chemical Engineering
- University of Vigo
- Vigo
- Spain
| | - M. A. Sanromán
- Department of Chemical Engineering
- University of Vigo
- Vigo
- Spain
| | - F. J. Deive
- Department of Chemical Engineering
- University of Vigo
- Vigo
- Spain
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Woo HL, Ballor NR, Hazen TC, Fortney JL, Simmons B, Davenport KW, Goodwin L, Ivanova N, Kyrpides NC, Mavromatis K, Woyke T, Jansson J, Kimbrel J, DeAngelis KM. Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2. Stand Genomic Sci 2014; 9:19. [PMID: 25566348 PMCID: PMC4273726 DOI: 10.1186/1944-3277-9-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 11/03/2014] [Indexed: 11/10/2022] Open
Abstract
In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated Klebsiella sp. strain BRL6-2 on minimal media with alkali lignin as the sole carbon source. This organism was isolated anaerobically from tropical forest soils collected from the Bisley watershed at the Ridge site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are characterized by cycles of iron oxidation and reduction. Genome sequencing was targeted because of its ability to grow on lignin anaerobically and lignocellulolytic activity via in vitro enzyme assays. The genome of Klebsiella sp. strain BRL6-2 is 5.80 Mbp with no detected plasmids, and includes a relatively small arsenal of genes encoding lignocellulolytic carbohydrate active enzymes. The genome revealed four putative peroxidases including glutathione and DyP-type peroxidases, and a complete protocatechuate pathway encoded in a single gene cluster. Physiological studies revealed Klebsiella sp. strain BRL6-2 to be relatively stress tolerant to high ionic strength conditions. It grows in increasing concentrations of ionic liquid (1-ethyl-3-methyl-imidazolium acetate) up to 73.44 mM and NaCl up to 1.5 M.
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Affiliation(s)
- Hannah L Woo
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA ; Department of Civil & Environmental Engineering, The University of Tennessee, Knoxville, TN, USA
| | - Nicholas R Ballor
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA
| | - Terry C Hazen
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA ; Department of Civil & Environmental Engineering, The University of Tennessee, Knoxville, TN, USA ; Department of Microbiology, The University of Tennessee, Knoxville, TN, USA ; Department of Earth & Planetary Sciences, The University of Tennessee, Knoxville, TN, USA
| | - Julian L Fortney
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA ; Department of Civil & Environmental Engineering, The University of Tennessee, Knoxville, TN, USA
| | - Blake Simmons
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA ; Sandia National Lab, Livermore, CA, USA
| | | | | | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Janet Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jeff Kimbrel
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA ; Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Sitepu IR, Shi S, Simmons BA, Singer SW, Boundy-Mills K, Simmons CW. Yeast tolerance to the ionic liquid 1-ethyl-3-methylimidazolium acetate. FEMS Yeast Res 2014; 14:1286-94. [DOI: 10.1111/1567-1364.12224] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 10/17/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Irnayuli R. Sitepu
- Department of Food Science and Technology; University of California; Davis CA USA
- Forestry Research and Development Agency (FORDA); The Ministry of Forestry; Bogor Indonesia
| | - Shuang Shi
- Department of Food Science and Technology; University of California; Davis CA USA
| | - Blake A. Simmons
- Deconstruction Division; Joint BioEnergy Institute; Emeryville CA USA
- Biological and Materials Sciences Center; Sandia National Laboratories; Livermore CA USA
| | - Steven W. Singer
- Deconstruction Division; Joint BioEnergy Institute; Emeryville CA USA
- Earth Sciences Division; Lawrence Berkeley National Laboratory; Berkeley CA USA
| | - Kyria Boundy-Mills
- Department of Food Science and Technology; University of California; Davis CA USA
| | - Christopher W. Simmons
- Department of Food Science and Technology; University of California; Davis CA USA
- Deconstruction Division; Joint BioEnergy Institute; Emeryville CA USA
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Draft Genome Sequence of the Ionic Liquid-Tolerant Bacterium Bacillus amyloliquefaciens CMW1. GENOME ANNOUNCEMENTS 2014; 2:2/5/e01051-14. [PMID: 25323721 PMCID: PMC4200159 DOI: 10.1128/genomea.01051-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome sequence of an ionic liquid-tolerant bacterium, Bacillus amyloliquefaciens CMW1, which is newly isolated from a Japanese fermented soybean paste. The genome sequence will allow for a characterization of the molecular mechanism of its ionic liquid tolerance.
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Frederix M, Hütter K, Leu J, Batth TS, Turner WJ, Rüegg TL, Blanch HW, Simmons BA, Adams PD, Keasling JD, Thelen MP, Dunlop MJ, Petzold CJ, Mukhopadhyay A. Development of a native Escherichia coli induction system for ionic liquid tolerance. PLoS One 2014; 9:e101115. [PMID: 24983352 PMCID: PMC4077768 DOI: 10.1371/journal.pone.0101115] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 06/03/2014] [Indexed: 01/15/2023] Open
Abstract
The ability to solubilize lignocellulose makes certain ionic liquids (ILs) very effective reagents for pretreating biomass prior to its saccharification for biofuel fermentation. However, residual IL in the aqueous sugar solution can inhibit the growth and function of biofuel-producing microorganisms. In E. coli this toxicity can be partially overcome by the heterologous expression of an IL efflux pump encoded by eilA from Enterobacter lignolyticus. In the present work, we used microarray analysis to identify native E. coli IL-inducible promoters and develop control systems for regulating eilA gene expression. Three candidate promoters, PmarR', PydfO', and PydfA', were selected and compared to the IPTG-inducible PlacUV5 system for controlling expression of eilA. The PydfA' and PmarR' based systems are as effective as PlacUV5 in their ability to rescue E. coli from typically toxic levels of IL, thereby eliminating the need to use an IPTG-based system for such tolerance engineering. We present a mechanistic model indicating that inducible control systems reduce target gene expression when IL levels are low. Selected-reaction monitoring mass spectrometry analysis revealed that at high IL concentrations EilA protein levels were significantly elevated under the control of PydfA' and PmarR' in comparison to the other promoters. Further, in a pooled culture competition designed to determine fitness, the strain containing pPmarR'-eilA outcompeted strains with other promoter constructs, most significantly at IL concentrations above 150 mM. These results indicate that native promoters such as PmarR' can provide effective systems for regulating the expression of heterologous genes in host engineering and simplify the development of industrially useful strains.
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Affiliation(s)
- Marijke Frederix
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Kimmo Hütter
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jessica Leu
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Tanveer S. Batth
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - William J. Turner
- School of Engineering, University of Vermont, Burlington, Vermont, United States of America
| | - Thomas L. Rüegg
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Botanical Institute, University of Basel, Basel, Switzerland
- Biology and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Harvey W. Blanch
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Chemistry, College of Chemistry, University of California, Berkeley, California, United States of America
| | - Blake A. Simmons
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Biological and Materials Science Center, Sandia National Laboratories, Livermore, California, United States of America
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jay D. Keasling
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Chemistry, College of Chemistry, University of California, Berkeley, California, United States of America
- Department of Chemical & Biomolecular Engineering, College of Chemistry, University of California, Berkeley, California, United States of America
| | - Michael P. Thelen
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Biology and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Mary J. Dunlop
- School of Engineering, University of Vermont, Burlington, Vermont, United States of America
| | - Christopher J. Petzold
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
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50
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Abstract
Engineering the microbial transformation of lignocellulosic biomass is essential to developing modern biorefining processes that alleviate reliance on petroleum-derived energy and chemicals. Many current bioprocess streams depend on the genetic tractability of Escherichia coli with a primary emphasis on engineering cellulose/hemicellulose catabolism, small molecule production, and resistance to product inhibition. Conversely, bioprocess streams for lignin transformation remain embryonic, with relatively few environmental strains or enzymes implicated. Here we develop a biosensor responsive to monoaromatic lignin transformation products compatible with functional screening in E. coli. We use this biosensor to retrieve metagenomic scaffolds sourced from coal bed bacterial communities conferring an array of lignin transformation phenotypes that synergize in combination. Transposon mutagenesis and comparative sequence analysis of active clones identified genes encoding six functional classes mediating lignin transformation phenotypes that appear to be rearrayed in nature via horizontal gene transfer. Lignin transformation activity was then demonstrated for one of the predicted gene products encoding a multicopper oxidase to validate the screen. These results illuminate cellular and community-wide networks acting on aromatic polymers and expand the toolkit for engineering recombinant lignin transformation based on ecological design principles.
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