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Zhang H, Zhao Z, Guan W, Zhong Y, Wang Y, Zhou Q, Liu F, Luo Q, Liu J, Ni J, He N, Guo D, Li L, Xing Q. Nano-Selenium inhibited antibiotic resistance genes and virulence factors by suppressing bacterial selenocompound metabolism and chemotaxis pathways in animal manure. Ecotoxicol Environ Saf 2023; 263:115277. [PMID: 37499390 DOI: 10.1016/j.ecoenv.2023.115277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023]
Abstract
Numerous antibiotic resistance genes (ARGs) and virulence factors (VFs) found in animal manure pose significant risks to human health. However, the effects of graphene sodium selenite (GSSe), a novel chemical nano-Selenium, and biological nano-Selenium (BNSSe), a new bioaugmentation nano-Se, on bacterial Se metabolism, chemotaxis, ARGs, and VFs in animal manure remain unknown. In this study, we investigated the effects of GSSe and BNSSe on ARGs and VFs expression in broiler manure using high-throughput sequencing. Results showed that BNSSe reduced Se pressure during anaerobic fermentation by inhibiting bacterial selenocompound metabolism pathways, thereby lowering manure Selenium pollution. Additionally, the expression levels of ARGs and VFs were lower in the BNSSe group compared to the Sodium Selenite and GSSe groups, as BNSSe inhibited bacterial chemotaxis pathways. Co-occurrence network analysis identified ARGs and VFs within the following phyla Bacteroidetes (genera Butyricimonas, Odoribacter, Paraprevotella, and Rikenella), Firmicutes (genera Lactobacillus, Candidatus_Borkfalkia, Merdimonas, Oscillibacter, Intestinimonas, and Megamonas), and Proteobacteria (genera Desulfovibrio). The expression and abundance of ARGs and VFs genes were found to be associated with ARGs-VFs coexistence. Moreover, BNSSe disruption of bacterial selenocompound metabolism and chemotaxis pathways resulted in less frequent transfer of ARGs and VFs. These findings indicate that BNSSe can reduce ARGs and VFs expression in animal manure by suppressing bacterial selenocompound metabolism and chemotaxis pathways.
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Affiliation(s)
- Haibo Zhang
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Zhigang Zhao
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Weikun Guan
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Yuhong Zhong
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Yang Wang
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Qilong Zhou
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Fuyu Liu
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Qi Luo
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Junyi Liu
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Jian Ni
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Ning He
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Dongsheng Guo
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Lizhi Li
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China.
| | - Qingfeng Xing
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China.
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2
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Zhang H, Guan W, Shu J, Yu S, Xiong Y, Liu G, Zhong Y, Chen J, Zhao Z, He N, Xing Q, Guo D, Li L, Hongbing O. Graphene nano zinc oxide reduces the expression and release of antibiotic resistance-related genes and virulence factors in animal manure. Sci Total Environ 2023; 881:163520. [PMID: 37061060 DOI: 10.1016/j.scitotenv.2023.163520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/22/2023] [Accepted: 04/11/2023] [Indexed: 06/01/2023]
Abstract
Animal manure contains many antibiotic resistance genes (ARGs) and virulence factors (VFs), posing significant health threats to humans. However, the effects of graphene nano zinc oxide (GZnONP), a zinc bioaugmentation substitute, on bacterial chemotaxis, ARGs, and VFs in animal manure remain scanty. Herein, the effect of GZnONP on the in vivo anaerobic expression of ARGs and VFs in cattle manure was assessed using high-throughput sequencing. Results showed that GZnONP inhibited bacterial chemotaxis by reducing the zinc pressure under anaerobic fermentation, altering the microbial community structure. The expression of ARGs was significantly lower in GZnONP than in zinc oxide and nano zinc oxide (ZnONP) groups. The expression of VFs was lower in the GZnONP than in the zinc oxide and ZnONP groups by 9.85 % and 13.46 %, respectively. Co-occurrence network analysis revealed that ARGs and VFs were expressed by the Spirochaetes phylum, Paraprevotella genus, and Treponema genus et al. The ARGs-VFs coexistence was related to the expression/abundance of ARGs and VFs genes. GZnONP reduces the abundance of certain bacterial species by disrupting chemotaxis, minimizing the transfer of ARGs and VFs. These findings suggest that GZnONP, a bacterial chemotaxis suppressor, effectively reduces the expression and release of ARGs and VFs in animal manure.
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Affiliation(s)
- Haibo Zhang
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Weikun Guan
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Jun Shu
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Sen Yu
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Yingmin Xiong
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Gao Liu
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Yuhong Zhong
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Jia Chen
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Zhigang Zhao
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Ning He
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Qingfeng Xing
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Dongsheng Guo
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Lizhi Li
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China.
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Tan JKP, Tan CP, Nurzaman SG. An Embodied Intelligence-Based Biologically Inspired Strategy for Searching a Moving Target. Artif Life 2022; 28:348-368. [PMID: 35881682 DOI: 10.1162/artl_a_00375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacterial chemotaxis in unicellular Escherichia coli, the simplest biological creature, enables it to perform effective searching behaviour even with a single sensor, achieved via a sequence of "tumbling" and "swimming" behaviours guided by gradient information. Recent studies show that suitable random walk strategies may guide the behaviour in the absence of gradient information. This article presents a novel and minimalistic biologically inspired search strategy inspired by bacterial chemotaxis and embodied intelligence concept: a concept stating that intelligent behaviour is a result of the interaction among the "brain," body morphology including the sensory sensitivity tuned by the morphology, and the environment. Specifically, we present bacterial chemotaxis inspired searching behaviour with and without gradient information based on biological fluctuation framework: a mathematical framework that explains how biological creatures utilize noises in their behaviour. Via extensive simulation of a single sensor mobile robot that searches for a moving target, we will demonstrate how the effectiveness of the search depends on the sensory sensitivity and the inherent random walk strategies produced by the brain of the robot, comprising Ballistic, Levy, Brownian, and Stationary search. The result demonstrates the importance of embodied intelligence even in a behaviour inspired by the simplest creature.
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Affiliation(s)
| | - Chee Pin Tan
- Monash University Malaysia, School of Engineering, Advanced Engineering Platform.
| | - Surya G Nurzaman
- Monash University Malaysia, School of Engineering, Advanced Engineering Platform.
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Zan S, Wang J, Wang F, Li Z, Du M, Cai Y. A novel degradation mechanism of naphthenic acids by marine Pseudoalteromonas sp. J Hazard Mater 2022; 424:127534. [PMID: 34879524 DOI: 10.1016/j.jhazmat.2021.127534] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Naphthenic acids (NAs) are a persistent toxic organic pollutant that occur in different environment worldwide and cause serious threat to the ecosystem and public health. However, knowledge on the behavior and fate of NAs in marine environments still remains unknown. In this study, the degradation mechanism of NAs (cyclohexylacetic acid, CHAA) was investigated using an common indigenous marine Pseudoalteromonas sp. The results showed that CHAA could be degraded completely under aerobic condition, but could not be utilized directly under anaerobic condition. Interestingly, transcriptome and key enzyme activity results showed the CHAA degradation pathway induced under aerobic condition could still work in anaerobic condition. The degradation was activated by acetyl-CoA transferase and sequentially formed the corresponding cyclohexene, alcohol, and ketone with the assistance of related enzymes, and finally cleaved by hydroxymethylglutarate-CoA lyase. Besides, there was a positive correlation between chemotaxis and aerobic degradation genes (r = 0.976, P < 0.05), the chemotaxis would enhance bacterium movement and NAs biodegradation. It is proposed that bacterium could translocate to NAs and accomplish biodegradation from aerobic to anaerobic environments, which was a new anaerobic degradation pathway of NAs. This study provides new insights into the fate of NAs and other organic contaminants in marine environment.
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Affiliation(s)
- Shuaijun Zan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
| | - Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
| | - Fengbo Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
| | - Zelong Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
| | - Miaomiao Du
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
| | - Yingxue Cai
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
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5
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Boyeldieu A, Ali Chaouche A, Méjean V, Jourlin-Castelli C. Combining two optimized and affordable methods to assign chemoreceptors to a specific signal. Anal Biochem 2021; 620:114139. [PMID: 33621526 DOI: 10.1016/j.ab.2021.114139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/20/2021] [Accepted: 02/12/2021] [Indexed: 01/01/2023]
Abstract
Chemotaxis allows bacteria to detect specific compounds and move accordingly. This pathway involves signal detection by chemoreceptors (MCPs). Attributing a chemoreceptor to a ligand is difficult because there is a lot of redundancy in the MCPs that recognize a single ligand. We propose a methodology to define which chemoreceptors bind a given ligand. First, an MCP is overproduced to increase sensitivity to the ligand(s) it recognizes, thus promoting accumulation of cells around an agarose plug containing a low attractant concentration. Second, the ligand-binding domain (LBD) of the chemoreceptor is fused to maltose-binding protein (MBP), which facilitates purification and provides a control for a thermal shift assay (TSA). An increase in the melting temperature of the LBD in the presence of the ligand indicates that the chemoreceptor directly binds it. We showed that overexpression of two Shewanella oneidensis chemoreceptors (SO_0987 and SO_1056) promoted swimming toward an agarose plug containing a low concentration of chromate. The LBD of each of the two chemoreceptors was fused to MBP. A TSA revealed that only the LBD from SO_1056 had its melting temperature increased by chromate. In conclusion, we describe an efficient approach to define chemoreceptor-ligand pairs before undertaking more-sophisticated biochemical and structural studies.
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Affiliation(s)
- Anne Boyeldieu
- Aix Marseille Univ, CNRS, BIP UMR 7281, IMM, IM2B, Marseille, France
| | | | - Vincent Méjean
- Aix Marseille Univ, CNRS, BIP UMR 7281, IMM, IM2B, Marseille, France
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Song X, Hou M, Tu J, Xue M, Shao Y, Jiang H, Liu H, Xue T, Wang G, Qi K. Outer membrane proteins YbjX and PagP co-regulate motility in Escherichia coli via the bacterial chemotaxis pathway. Res Vet Sci 2019; 125:279-284. [PMID: 31326704 DOI: 10.1016/j.rvsc.2019.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/25/2019] [Accepted: 07/10/2019] [Indexed: 02/08/2023]
Abstract
Mutation of the PhoP/Q two-component system decreases the expression of ybjX and pagP encoding outer membrane proteins, and mutation of ybjX or pagP attenuates avian pathogenic Escherichia coli (APEC) pathogenicity. However, whether ybjX/pagP mutation (double-deletion mutant) has a synergistic effect on pathogenicity remains unknown. Herein, electrophoresis mobility shift assay (EMSA) experiments showed that the PhoP/Q system regulated ybjX and pagP transcription indirectly. The APECΔybjX/pagP mutant strain, constructed using the Red recombination method, exhibited reduced invasion of chicken embryo fibroblast (DF-1) cells, but had no effect on virulence in a chicken model. Using RNA sequencing to identify differential mRNAs in APECΔybjXΔpagP and native strains, we revealed up-regulation of genes involved in the bacterial chemotaxis pathway. The ybjX/pagP mutant strain displayed significantly increased motility, suggesting that double deletion of ybjX and pagP enhances motility via the bacterial chemotaxis pathway.
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Affiliation(s)
- Xiangjun Song
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Manman Hou
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Jian Tu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Mei Xue
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Ying Shao
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Huyan Jiang
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Hongmei Liu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Ting Xue
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Guijun Wang
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Kezong Qi
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China.
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Stalla D, Akkaladevi N, White TA, Hazelbauer GL. Spatial Restrictions in Chemotaxis Signaling Arrays: A Role for Chemoreceptor Flexible Hinges across Bacterial Diversity. Int J Mol Sci 2019; 20:ijms20122989. [PMID: 31248079 PMCID: PMC6628036 DOI: 10.3390/ijms20122989] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/15/2019] [Accepted: 06/17/2019] [Indexed: 01/02/2023] Open
Abstract
The chemotactic sensory system enables motile bacteria to move toward favorable environments. Throughout bacterial diversity, the chemoreceptors that mediate chemotaxis are clustered into densely packed arrays of signaling complexes. In these arrays, rod-shaped receptors are in close proximity, resulting in limited options for orientations. A recent geometric analysis of these limitations in Escherichia coli, using published dimensions and angles, revealed that in this species, straight chemoreceptors would not fit into the available space, but receptors bent at one or both of the recently-documented flexible hinges would fit, albeit over a narrow window of shallow bend angles. We have now expanded our geometric analysis to consider variations in receptor length, orientation and placement, and thus to species in which those parameters are known to be, or might be, different, as well as to the possibility of dynamic variation in those parameters. The results identified significant limitations on the allowed combinations of chemoreceptor dimensions, orientations and placement. For most combinations, these limitations excluded straight chemoreceptors, but allowed receptors bent at a flexible hinge. Thus, our analysis identifies across bacterial diversity a crucial role for chemoreceptor flexible hinges, in accommodating the limitations of molecular crowding in chemotaxis core signaling complexes and their arrays.
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Affiliation(s)
- David Stalla
- Electron Microscopy Core Facility, W117 Veterinary Medicine Building, 1600 East Rollins St., University of Missouri, Columbia, MO 65211, USA.
| | - Narahari Akkaladevi
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, MO 65211, USA.
| | - Tommi A White
- Electron Microscopy Core Facility, W117 Veterinary Medicine Building, 1600 East Rollins St., University of Missouri, Columbia, MO 65211, USA.
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, MO 65211, USA.
| | - Gerald L Hazelbauer
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, MO 65211, USA.
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Chen D, Liu SJ, Du W. Chemotactic screening of imidazolinone-degrading bacteria by microfluidic SlipChip. J Hazard Mater 2019; 366:512-519. [PMID: 30562663 DOI: 10.1016/j.jhazmat.2018.12.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/19/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
The group of imidazolinone herbicides, widely used for weed control, is hazardous to some sensitive rotational crops. Thus, rapid elimination of imidazolinones from contaminated soil is significant for the environment. Biodegradation studies have demonstrated the ability of chemotaxis to enhance the biodegradation of pollutants. In this study, we used our newly developed SlipChip device for chemotactic sorting and a microfluidic streak plate device for bacterial cultivation as a new pipeline for screening imidazolinone degraders. The degradation efficiencies of an enrichment consortium and a chemotaxis consortium were determined by HPLC-MS/MS. Both consortia degraded all tested imidazolinones, with the highest efficiency (71.8%) for imazethapyr, and the chemotaxis consortium degraded these compounds approximately 10% more efficiently than the enrichment consortium. Moreover, the community diversities of the enrichment consortium and the chemotaxis consortium were analyzed by 16S rRNA gene amplicon sequencing. The results indicated that members of genus Ochrobactrum primarily contribute to the degradation of imidazolinones. This work proved that chemotaxis toward biodegradable pollutants increases their bioavailability and enhances the biodegradation rate. It also provided a new way to screen effective pollutant degraders and can be applied for the selective isolation of other chemotactic species from environmental samples.
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Affiliation(s)
- Dongwei Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 100049, China.
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9
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Balaraman P, Plettner E. Chemotaxis by Pseudomonas putida (ATCC 17453) towards camphor involves cytochrome P450 cam (CYP101A1). Biochim Biophys Acta Gen Subj 2018; 1863:304-312. [PMID: 30391161 DOI: 10.1016/j.bbagen.2018.10.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 11/29/2022]
Abstract
The camphor-degrading microorganism, Pseudomonas putida strain ATCC 17453, is an aerobic, gram-negative soil bacterium that uses camphor as its sole carbon and energy source. The genes responsible for the catabolic degradation of camphor are encoded on the extra-chromosomal CAM plasmid. A monooxygenase, cytochrome P450cam, mediates hydroxylation of camphor to 5-exo-hydroxycamphor as the first and committed step in the camphor degradation pathway, requiring a dioxygen molecule (O2) from air. Under low O2 levels, P450cam catalyzes the production of borneol via an unusual reduction reaction. We have previously shown that borneol downregulates the expression of P450cam. To understand the function of P450cam and the consequences of down-regulation by borneol under low O2 conditions, we have studied chemotaxis of camphor induced and non-induced P. putida strain ATCC 17453. We have tested camphor, borneol, oxidized camphor metabolites and known bacterial attractants (d)-glucose, (d) - and (l)-glutamic acid for their elicitation chemotactic behavior. In addition, we have used 1-phenylimidazole, a P450cam inhibitor, to investigate if P450cam plays a role in the chemotactic ability of P. putida in the presence of camphor. We found that camphor, a chemoattractant, became toxic and chemorepellent when P450cam was inhibited. We have also evaluated the effect of borneol on chemotaxis and found that the bacteria chemotaxed away from camphor in the presence of borneol. This is the first report of the chemotactic behaviour of P. putida ATCC 17453 and the essential role of P450cam in this process.
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Affiliation(s)
- Priyadarshini Balaraman
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Erika Plettner
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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10
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Abstract
We undertake a detailed mathematical analysis of a recent nonlinear ordinary differential equation (ODE) model describing the chemotactic signalling cascade within an Escherichia coli cell. The model includes a detailed description of the cell signalling cascade and an average approximation of the receptor activity. A steady-state stability analysis reveals the system exhibits one positive real steady state which is shown to be asymptotically stable. Given the occurrence of a negative feedback between phosphorylated CheB (CheB-P) and the receptor state, we ask under what conditions the system may exhibit oscillatory-type behaviour. A detailed analysis of parameter space reveals that whilst variation in kinetic rate parameters within known biological limits is unlikely to lead to such behaviour, changes in the total concentration of the signalling proteins do. We postulate that experimentally observed overshoot behaviour can actually be described by damped oscillatory dynamics and consider the relationship between overshoot amplitude, total cell protein concentration and the magnitude of the external ligand stimulus. Model reductions in the full ODE model allow us to understand the link between phosphorylation events and the negative feedback between CheB-P and receptor methylation, as well as elucidate why some mathematical models exhibit overshoot and others do not. Our paper closes by discussing intercell variability of total protein concentration as a means of ensuring the overall survival of a population as cells are subjected to different environments.
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Affiliation(s)
- Matthew P Edgington
- Department of Mathematics and Statistics, University of Reading, Whiteknights, PO Box 220, Reading, RG6 6AX, UK.,The Pirbright Institute, Ash Road, Woking, Surrey, GU24 0NF, UK
| | - Marcus J Tindall
- Department of Mathematics and Statistics, University of Reading, Whiteknights, PO Box 220, Reading, RG6 6AX, UK. .,Institute for Cardiovascular and Metabolic Research, University of Reading, Whiteknights, PO Box 218, Reading, RG6 6AA, UK.
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11
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Solari J, Anquez F, Scherer KM, Shimizu TS. Bacterial Chemoreceptor Imaging at High Spatiotemporal Resolution Using Photoconvertible Fluorescent Proteins. Methods Mol Biol 2018; 1729:203-31. [PMID: 29429094 DOI: 10.1007/978-1-4939-7577-8_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
We describe two methods for high-resolution fluorescence imaging of the positioning and mobility of E. coli chemoreceptors fused to photoconvertible fluorescent proteins. Chemoreceptors such as Tar and Tsr are transmembrane proteins expressed at high levels (thousands of copies per cell). Together with their cognate cytosolic signaling proteins, they form clusters on the plasma membrane. Theoretical models imply that the size of these clusters is an important parameter for signaling, and recent PALM imaging has revealed a broad distribution of cluster sizes. We describe experimental setups and protocols for PALM imaging in fixed cells with ~10 nm spatial precision, which allows analysis of cluster-size distributions, and localized-photoactivation single-particle tracking (LPA-SPT) in live cells at ~10 ms temporal resolution, which allows for analysis of cluster mobility.
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12
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Liew CW, Hynson RM, Ganuelas LA, Shah-Mohammadi N, Duff AP, Kojima S, Homma M, Lee LK. Solution structure analysis of the periplasmic region of bacterial flagellar motor stators by small angle X-ray scattering. Biochem Biophys Res Commun 2017; 495:1614-1619. [PMID: 29197577 DOI: 10.1016/j.bbrc.2017.11.194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 11/28/2017] [Indexed: 01/18/2023]
Abstract
The bacterial flagellar motor drives the rotation of helical flagellar filaments to propel bacteria through viscous media. It consists of a dynamic population of mechanosensitive stators that are embedded in the inner membrane and activate in response to external load. This entails assembly around the rotor, anchoring to the peptidoglycan layer to counteract torque from the rotor and opening of a cation channel to facilitate an influx of cations, which is converted into mechanical rotation. Stator complexes are comprised of four copies of an integral membrane A subunit and two copies of a B subunit. Each B subunit includes a C-terminal OmpA-like peptidoglycan-binding (PGB) domain. This is thought to be linked to a single N-terminal transmembrane helix by a long unstructured peptide, which allows the PGB domain to bind to the peptidoglycan layer during stator anchoring. The high-resolution crystal structures of flagellar motor PGB domains from Salmonella enterica (MotBC2) and Vibrio alginolyticus (PomBC5) have previously been elucidated. Here, we use small-angle X-ray scattering (SAXS). We show that unlike MotBC2, the dimeric conformation of the PomBC5 in solution differs to its crystal structure, and explore the functional relevance by characterising gain-of-function mutants as well as wild-type constructs of various lengths. These provide new insight into the conformational diversity of flagellar motor PGB domains and experimental verification of their overall topology.
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Affiliation(s)
- C W Liew
- School of Medical Sciences, The University of New South Wales, Australia
| | - R M Hynson
- Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - L A Ganuelas
- School of Medical Sciences, The University of New South Wales, Australia
| | - N Shah-Mohammadi
- Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia; Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - A P Duff
- Australian Nuclear and Science Technology Organisation, Lucas Heights, New South Wales, Australia
| | - S Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Nagoya 464-8602, Japan
| | - M Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Nagoya 464-8602, Japan
| | - L K Lee
- School of Medical Sciences, The University of New South Wales, Australia; Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.
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Giverso C, Verani M, Ciarletta P. Emerging morphologies in round bacterial colonies: comparing volumetric versus chemotactic expansion. Biomech Model Mechanobiol 2016; 15:643-61. [PMID: 26296713 DOI: 10.1007/s10237-015-0714-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/27/2015] [Indexed: 10/23/2022]
Abstract
Biological experiments performed on living bacterial colonies have demonstrated the microbial capability to develop finger-like shapes and highly irregular contours, even starting from an homogeneous inoculum. In this work, we study from the continuum mechanics viewpoint the emergence of such branched morphologies in an initially circular colony expanding on the top of a Petri dish coated with agar. The bacterial colony expansion, based on either a source term, representing volumetric mitotic processes, or a nonconvective mass flux, describing chemotactic expansion, is modeled at the continuum scale. We demonstrate that the front of the colony is always linearly unstable, having similar dispersion curves to the ones characterizing branching instabilities. We also perform finite element simulations, which not only prove the emergence of branching, but also highlight dramatic differences between the two mechanisms of colony expansion in the nonlinear regime. Furthermore, the proposed combination of analytical and numerical analysis allowed studying the influence of different model parameters on the selection of specific patterns. A very good agreement has been found between the resulting simulations and the typical structures observed in biological assays. Finally, this work provides a new interpretation of the emergence of branched patterns in living aggregates, depicted as the results of a complex interplay among chemical, mechanical and size effects.
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14
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Yan Z, Bouwer EJ, Hilpert M. Coupled effects of chemotaxis and growth on traveling bacterial waves. J Contam Hydrol 2014; 164:138-152. [PMID: 24984293 DOI: 10.1016/j.jconhyd.2014.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 06/04/2014] [Accepted: 06/11/2014] [Indexed: 06/03/2023]
Abstract
Traveling bacterial waves are capable of improving contaminant remediation in the subsurface. It is fairly well understood how bacterial chemotaxis and growth separately affect the formation and propagation of such waves. However, their interaction is not well understood. We therefore perform a modeling study to investigate the coupled effects of chemotaxis and growth on bacterial migration, and examine their effects on contaminant remediation. We study the waves by using different initial electron acceptor concentrations for different bacteria and substrate systems. Three types of traveling waves can occur: a chemotactic wave due to the biased movement of chemotactic bacteria resulting from metabolism-generated substrate concentration gradients; a growth/decay/motility wave due to a dynamic equilibrium between bacterial growth, decay and random motility; and an integrated wave due to the interaction between bacterial chemotaxis and growth. Chemotaxis hardly enhances the bacterial propagation if it is too weak to form a chemotactic wave or its wave speed is less than half of the growth/decay/motility wave speed. However, chemotaxis significantly accelerates bacterial propagation once its wave speed exceeds the growth/decay/motility wave speed. When convection occurs, it speeds up the growth/decay/motility wave but slows down or even eliminates the chemotactic wave due to the dispersion. Bacterial survival proves particularly important for bacterial propagation. Therefore we develop a conceptual model to estimate the speed of growth/decay/motility waves.
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Affiliation(s)
- Zhifeng Yan
- Department of Geography and Environmental Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Edward J Bouwer
- Department of Geography and Environmental Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Markus Hilpert
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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15
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Abstract
Flagellar motion has been an active area of study right from the discovery of bacterial chemotaxis in 1882. During chemotaxis, E. coli moves with the help of helical flagella in an aquatic environment. Helical flagella are rotated in clockwise or counterclockwise direction using reversible flagellar motors situated at the base of each flagellum. The swimming of E. coli is characterized by a low Reynolds number that is unique and time reversible. The random motion of E. coli is influenced by the viscosity of the fluid and the Brownian motion of molecules of fluid, chemoattractants, and chemorepellants. This paper reviews the literature about the physics involved in the propulsion mechanism of E. coli. Starting from the resistive-force theory, various theories on flagellar hydrodynamics are critically reviewed. Expressions for drag force, elastic force and velocity of flagellar elements are derived. By taking the elastic nature of flagella into account, linear and nonlinear equations of motions are derived and their solutions are presented.
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