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Wang T, Hua C, Deng X. c-di-GMP signaling in Pseudomonas syringae complex. Microbiol Res 2023; 275:127445. [PMID: 37450986 DOI: 10.1016/j.micres.2023.127445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
The Pseudomonas syringae Complex is one of the model phytopathogenic bacteria for exploring plant-microbe interactions, causing devastating plant diseases and economic losses worldwide. The ubiquitous second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) plays an important role in the 'lifestyle switch' from single motile cells to biofilm formation and modulates bacterial behavior, thus influencing virulence in Pseudomonas and other bacterial species. However, less is known about the role of c-di-GMP in the P. syringae complex, in which c-di-GMP levels are controlled by diguanylate cyclases (DGCs) and phosphodiesterases (PDEs), such as Chp8, BifA and WspR. Deletion the chemotaxis receptor PscA also influences c-di-GMP levels, suggesting a cross-talk between chemotaxis and c-di-GMP pathways. Another transcription factor, FleQ, plays a dual role (positive or negative) in regulating cellulose synthesis as a c-di-GMP effector, whereas the transcription factor AmrZ regulates local c-di-GMP levels by inhibiting the DGC enzyme AdcA and the PDE enzyme MorA. Our recent research demonstrated that an increase in the c-di-GMP concentration increased biofilm development, siderophore biosynthesis and oxidative stress tolerance, while it decreased the siderophore content, bacterial motility and type III secretion system activity in P. syringae complex. These findings show that c-di-GMP intricately controls virulence in P. syringae complex, indicating that adjusting c-di-GMP levels may be a valuable tactic for defending plants against pathogens. This review highlights recent research on metabolic enzymes, regulatory mechanisms and the phenotypic consequences of c-di-GMP signaling in the P. syringae.
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Affiliation(s)
- Tingting Wang
- Department of Biomedicine, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Canfeng Hua
- Department of Biomedicine, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Xin Deng
- Department of Biomedicine, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China; Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Hong Kong SAR, China; Tung Research Centre, City University of Hong Kong, Hong Kong SAR, China; Chengdu Research Institute, City University of Hong Kong, Chengdu, China.
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2
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Li F, Meng X, Wang X, Ji C, Wu H. Graphene-triphenyl phosphate (TPP) co-exposure in the marine environment: Interference with metabolism and immune regulation in mussel Mytilus galloprovincialis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 227:112904. [PMID: 34655885 DOI: 10.1016/j.ecoenv.2021.112904] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Both immune regulation and endocrine systems are great challenges to marine organisms, and effective protocols for determining these adverse outcome pathways are limited, especially in vivo. The increasing usage of graphene nanomaterials can lead to the frequent exposure to marine organisms. Triphenyl phosphate (TPP), an organophosphate flame retardant, is frequently detected in natural environments. In this study, the combined toxic effects of co-exposure to graphene and TPP was investigated in Mytilus galloprovincialis using computational toxicology and multi-omics technology. Noticeably, graphene could disturb the membrane stability and increase the tissue accumulation of TPP. The adsorption behavior of TPP on graphene could inhibit the surface activity of graphene. In the digestive gland, transcriptomics analysis revealed the down-regulated genes in graphene + TPP treatment, including glyceraldehyde-3-phosphate dehydrogenase (GAPDH), sorbitol dehydrogenase (SORD), glutathione s-transferase mu 3 (GSTM3) and 4-aminobutyrate aminotransferase (ABAT), were mainly associated with oxidative stress and energy metabolism. Moreover, metabolic responses indicated that graphene + TPP could cause disturbances in energy metabolism and osmotic regulation marked by differentially altered ATP, glucose and taurine in mussels. These data underline the need for further knowledge on the potential interactions of nanomaterials with existing contaminants in marine organisms.
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Affiliation(s)
- Fei Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai 264003, PR China; Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China.
| | - Xiangjing Meng
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai 264003, PR China; Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xiaoqing Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai 264003, PR China; Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Chenglong Ji
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai 264003, PR China; Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Huifeng Wu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai 264003, PR China; Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China.
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3
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Ding H, Chen L, Hong Z, Yu X, Wang Z, Feng J. Network pharmacology-based identification of the key mechanism of quercetin acting on hemochromatosis. Metallomics 2021; 13:6271328. [PMID: 33960370 DOI: 10.1093/mtomcs/mfab025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 04/21/2021] [Accepted: 04/24/2021] [Indexed: 02/07/2023]
Abstract
Hemochromatosis is an iron overload disease, which lacks nutritional intervention strategies. This study explored the protective effect of quercetin on hemochromatosis and its possible mechanism through network pharmacology. We used Online Mendelian Inheritance in Man to screen the disease targets of hemochromatosis, and further constructed a potential protein interaction network through STITCH. The above-mentioned targets revealed by Gene enrichment analysis have played a significant role in ferroptosis, mineral absorption, basal cell carcinoma, and related signal pathways. Besides, the drug likeness of quercetin obtained by Comparative Toxicogenomics Database was evaluated by Traditional Chinese Medicine Systems Pharmacology, and potential drug targets identified by PharmMapper and similar compounds identified by PubChem were selected for further research. Moreover, gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed the relationship between quercetin and glycosylation. Furthermore, we performed experiments to verify that the protective effect of quercetin on iron overload cells is to inhibit the production of reactive oxygen species, limit intracellular iron, and degrade glycosaminoglycans. Finally, iron-induced intracellular iron overload caused ferroptosis, and quercetin and fisetin were potential ferroptosis inhibitors. In conclusion, our study revealed the correlation between hemochromatosis and ferroptosis, provided the relationship between the target of quercetin and glycosylation, and verified that quercetin and its similar compounds interfere with iron overload related disease. Our research may provide novel insights for quercetin and its structurally similar compounds as a potential nutritional supplement for iron overload related diseases.
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Affiliation(s)
- Haoxuan Ding
- College of Animal Sciences, Zhejiang University, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou 310058, China
| | - Lingjun Chen
- College of Animal Sciences, Zhejiang University, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou 310058, China
| | - Zuopeng Hong
- Research Center of Zhejiang Weifeng Biotechnology Co., Ltd, Hangzhou 310000, China
| | - Xiaonan Yu
- College of Animal Sciences, Zhejiang University, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou 310058, China
| | - Zhonghang Wang
- College of Animal Sciences, Zhejiang University, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou 310058, China
| | - Jie Feng
- College of Animal Sciences, Zhejiang University, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou 310058, China
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Molina Mora JA, Montero-Manso P, García-Batán R, Campos-Sánchez R, Vilar-Fernández J, García F. A first perturbome of Pseudomonas aeruginosa: Identification of core genes related to multiple perturbations by a machine learning approach. Biosystems 2021; 205:104411. [PMID: 33757842 DOI: 10.1016/j.biosystems.2021.104411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 01/27/2023]
Abstract
Tolerance to stress conditions is vital for organismal survival, including bacteria under specific environmental conditions, antibiotics, and other perturbations. Some studies have described common modulation and shared genes during stress response to different types of disturbances (termed as perturbome), leading to the idea of central control at the molecular level. We implemented a robust machine learning approach to identify and describe genes associated with multiple perturbations or perturbome in a Pseudomonas aeruginosa PAO1 model. Using microarray datasets from the Gene Expression Omnibus (GEO), we evaluated six approaches to rank and select genes: using two methodologies, data single partition (SP method) or multiple partitions (MP method) for training and testing datasets, we evaluated three classification algorithms (SVM Support Vector Machine, KNN K-Nearest neighbor and RF Random Forest). Gene expression patterns and topological features at the systems level were included to describe the perturbome elements. We were able to select and describe 46 core response genes associated with multiple perturbations in P. aeruginosa PAO1 and it can be considered a first report of the P. aeruginosa perturbome. Molecular annotations, patterns in expression levels, and topological features in molecular networks revealed biological functions of biosynthesis, binding, and metabolism, many of them related to DNA damage repair and aerobic respiration in the context of tolerance to stress. We also discuss different issues related to implemented and assessed algorithms, including data partitioning, classification approaches, and metrics. Altogether, this work offers a different and robust framework to select genes using a machine learning approach.
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Affiliation(s)
- Jose Arturo Molina Mora
- Centro de Investigacion en Enfermedades Tropicales (CIET) and Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica.
| | | | - Raquel García-Batán
- Centro de Investigacion en Enfermedades Tropicales (CIET) and Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica.
| | - Rebeca Campos-Sánchez
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San José, Costa Rica.
| | | | - Fernando García
- Centro de Investigacion en Enfermedades Tropicales (CIET) and Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica.
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Shen H, Li C, He M, Huang Y, Wang J, Wang M, Yue B, Zhang X. Immune profiles of male giant panda (Ailuropoda melanoleuca) during the breeding season. BMC Genomics 2021; 22:143. [PMID: 33639852 PMCID: PMC7916315 DOI: 10.1186/s12864-021-07456-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 02/19/2021] [Indexed: 12/13/2022] Open
Abstract
Background The giant panda (Ailuropoda melanoleuca) is a threatened endemic Chinese species and a flagship species of national and global conservation concern. Life history theory proposes that reproduction and immunity can be mutually constraining and interrelated. Knowledge of immunity changes of male giant pandas during the breeding season is limited. Results Here, we researched peripheral blood gene expression profiles associated with immunity. Thirteen captive giant pandas, ranging from 9 to 11 years old, were divided into two groups based on their reproductive status. We identified 318 up-regulated DEGs and 43 down-regulated DEGs, which were enriched in 87 GO terms and 6 KEGG pathways. Additionally, we obtained 45 immune-related genes with altered expression, mostly up-regulated, and identified four hub genes HSPA4, SUGT1, SOD1, and IL1B in PPI analysis. These 45 genes were related to pattern recognition receptors, autophagy, peroxisome, proteasome, natural killer cell, antigen processing and presentation. SUGT1 and IL1B were related to pattern recognition receptors. HSP90AA1 was the most up-regulated gene and is a member of heat shock protein 90 family. HSP90 contributes to the translocation of extracellular antigen. KLRD1 encodes CD94, whose complex is an inhibitor of the cytotoxic activity of NK cells, was down-regulated. IGIP, which has the capability of inducing IgA production by B cells, was down-regulated, suggesting low concentration of IgA in male giant pandas. Our results suggest that most immune-related genes were up-regulated and more related to innate immune than adaptive immune. Conclusions Our results indicated that breeding male giant pandas presented an immunoenhancement in innate immunity, enhanced antigen presentation and processing in cellular immunity compared to non-breeding males. The humoral immunity of male giant pandas may show a tendency to decrease during the breeding season. This study will provide a foundation for further studies of immunity and reproduction in male giant pandas. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07456-x.
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Affiliation(s)
- Haibo Shen
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Ming He
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Jing Wang
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Minglei Wang
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, PR China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, China.
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6
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Sengillo JD, Duker J, Hernandez M, Maestre J, Reyes-Capo D, Patel A, Watane A, Patel NA, Yannuzzi NA, Miller D, Flynn HW. Characterization of Pseudomonas aeruginosa isolates from patients with endophthalmitis using conventional microbiologic techniques and whole genome sequencing. J Ophthalmic Inflamm Infect 2020; 10:25. [PMID: 32984926 PMCID: PMC7520479 DOI: 10.1186/s12348-020-00216-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/04/2020] [Indexed: 11/30/2022] Open
Abstract
Purpose To demonstrate antibiotic susceptibility and genomic virulence factor profiles of Pseudomonas aeruginosa isolates from patients with culture-confirmed endophthalmitis. Methods Clinical isolates from patients diagnosed with pseudomonas endophthalmitis were included. Laboratory antibiotic susceptibility testing and whole genome sequencing was performed on all isolates. Results In the current study, 8 patients had vitreous culture-confirmed endophthalmitis due to P. aeruginosa. All isolates were multi-drug resistant but sensitive to ceftazidime and each fluoroquinolone tested. Whole genome sequencing revealed a total of 179 unique genes. The most common type of virulence genes included those involved in adherence and the secretion system. Seven of 8 (88%) isolates were of the cytoinvasive phenotype (exoST) and no isolates contained exoU. Conclusions P. aeruginosa associated endophthalmitis is often multi-drug resistant and demonstrates a variety of virulence factors with those involved in adherence and the secretion system being the most common.
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Affiliation(s)
- Jesse D Sengillo
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 900 NW 17th Street, Miami, FL, 33136, USA
| | - Jacob Duker
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 900 NW 17th Street, Miami, FL, 33136, USA
| | - Maribel Hernandez
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 900 NW 17th Street, Miami, FL, 33136, USA
| | - Jorge Maestre
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 900 NW 17th Street, Miami, FL, 33136, USA
| | - Daniela Reyes-Capo
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 900 NW 17th Street, Miami, FL, 33136, USA
| | - Annika Patel
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 900 NW 17th Street, Miami, FL, 33136, USA
| | - Arjun Watane
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 900 NW 17th Street, Miami, FL, 33136, USA
| | - Nimesh A Patel
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 900 NW 17th Street, Miami, FL, 33136, USA
| | - Nicolas A Yannuzzi
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 900 NW 17th Street, Miami, FL, 33136, USA
| | - Darlene Miller
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 900 NW 17th Street, Miami, FL, 33136, USA
| | - Harry W Flynn
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 900 NW 17th Street, Miami, FL, 33136, USA.
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Transcriptomic determinants of the response of ST-111 Pseudomonas aeruginosa AG1 to ciprofloxacin identified by a top-down systems biology approach. Sci Rep 2020; 10:13717. [PMID: 32792590 PMCID: PMC7427096 DOI: 10.1038/s41598-020-70581-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that thrives in diverse environments and causes a variety of human infections. Pseudomonas aeruginosa AG1 (PaeAG1) is a high-risk sequence type 111 (ST-111) strain isolated from a Costa Rican hospital in 2010. PaeAG1 has both blaVIM-2 and blaIMP-18 genes encoding for metallo-β-lactamases, and it is resistant to β-lactams (including carbapenems), aminoglycosides, and fluoroquinolones. Ciprofloxacin (CIP) is an antibiotic commonly used to treat P. aeruginosa infections, and it is known to produce DNA damage, triggering a complex molecular response. In order to evaluate the effects of a sub-inhibitory CIP concentration on PaeAG1, growth curves using increasing CIP concentrations were compared. We then measured gene expression using RNA-Seq at three time points (0, 2.5 and 5 h) after CIP exposure to identify the transcriptomic determinants of the response (i.e. hub genes, gene clusters and enriched pathways). Changes in expression were determined using differential expression analysis and network analysis using a top–down systems biology approach. A hybrid model using database-based and co-expression analysis approaches was implemented to predict gene–gene interactions. We observed a reduction of the growth curve rate as the sub-inhibitory CIP concentrations were increased. In the transcriptomic analysis, we detected that over time CIP treatment resulted in the differential expression of 518 genes, showing a complex impact at the molecular level. The transcriptomic determinants were 14 hub genes, multiple gene clusters at different levels (associated to hub genes or as co-expression modules) and 15 enriched pathways. Down-regulation of genes implicated in several metabolism pathways, virulence elements and ribosomal activity was observed. In contrast, amino acid catabolism, RpoS factor, proteases, and phenazines genes were up-regulated. Remarkably, > 80 resident-phage genes were up-regulated after CIP treatment, which was validated at phenomic level using a phage plaque assay. Thus, reduction of the growth curve rate and increasing phage induction was evidenced as the CIP concentrations were increased. In summary, transcriptomic and network analyses, as well as the growth curves and phage plaque assays provide evidence that PaeAG1 presents a complex, concentration-dependent response to sub-inhibitory CIP exposure, showing pleiotropic effects at the systems level. Manipulation of these determinants, such as phage genes, could be used to gain more insights about the regulation of responses in PaeAG1 as well as the identification of possible therapeutic targets. To our knowledge, this is the first report of the transcriptomic analysis of CIP response in a ST-111 high-risk P. aeruginosa strain, in particular using a top-down systems biology approach.
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Meng X, Li F, Wang X, Liu J, Ji C, Wu H. Combinatorial immune and stress response, cytoskeleton and signal transduction effects of graphene and triphenyl phosphate (TPP) in mussel Mytilus galloprovincialis. JOURNAL OF HAZARDOUS MATERIALS 2019; 378:120778. [PMID: 31229880 DOI: 10.1016/j.jhazmat.2019.120778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/08/2019] [Accepted: 06/13/2019] [Indexed: 05/04/2023]
Abstract
Owing to its unique surface properties, graphene can absorb environmental pollutants, thereby affecting their environmental behavior. Triphenyl phosphate (TPP) is a highly produced flame retardant. However, the toxicities of graphene and its combinations with contaminants remain largely unexplored. In this work, we investigated the toxicological effects of graphene and TPP to mussel Mytilus galloprovincialis. Results indicated that graphene could damage the digestive gland tissues, but no significant changes were found in the graphene + TPP co-exposure group. There was a significant decrease in the content of GSH and the activities of GST and CAT in the co-exposure group compared to that in graphene-exposed group. It seemed that the adsorption of TPP on graphene could inhibit the surface activity of graphene and thus reduced its tissue damage and oxidative stress in mussels. Expression levels of stress response (MyD88a), cytoskeleton (MHC1, PMyo and TMyo) and reproductive (CP450 and HSD) genes were up-regulated in the graphene-exposed group, but significantly down-regulated after combined exposure of graphene and TPP. Furthermore, PPI analysis proved that the interactions of HSP90AA1 with UNC45B and FKBP4/5/6/L contributed to the toxicity caused by the combined exposure. Because of the potential toxicity of graphene and TPP, government administrators should consider its risks prior to the widespread environmental exposure.
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Affiliation(s)
- Xiangjing Meng
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Fei Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China.
| | - Xiaoqing Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jialin Liu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China
| | - Chenglong Ji
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China
| | - Huifeng Wu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China.
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9
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de Oliveira AFB, de Souza MR, Benedetti D, Scotti AS, Piazza LS, Garcia ALH, Dias JF, Niekraszewicz LAB, Duarte A, Bauer D, Amaral L, Bassi Branco CL, de Melo Reis É, da Silva FR, da Silva J. Investigation of pesticide exposure by genotoxicological, biochemical, genetic polymorphic and in silico analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 179:135-142. [PMID: 31035247 DOI: 10.1016/j.ecoenv.2019.04.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 03/22/2019] [Accepted: 04/08/2019] [Indexed: 05/07/2023]
Abstract
Soybean farmers are exposed to various types of pesticides that contain in their formulations a combination of chemicals with genotoxic and mutagenic potential. Therefore, the objective of this paper was to evaluate the genetic damages caused by this pesticide exposure to soybean producers in the state of Mato Grosso (Brazil), regarding biochemical, genetic polymorphic and in silico analyses. A total of 148 individuals were evaluated, 76 of which were occupationally exposed and 72 were not exposed at all. The buccal micronucleus cytome assay (BMCyt) detected in the exposed group an increase on DNA damage and cell death. No inhibition of butyrylcholinesterase (BchE) was observed within the exposed group. The detection of inorganic elements was made through the particle-induced X-ray emission technique (PIXE), which revealed higher concentrations of Bromine (Br), Rubidium (Rb) and Lead (Pb) in rural workers. A molecular model using in silico analysis suggests how metal ions can cause both DNA damage and apoptosis in the exposed cells. Analysis of the compared effect of X-ray Repair Cross-complement Protein 1 (XRCC1) and Paraoxonase 1 (PON1) genotypes in the groups demonstrated an increase of binucleated cells (exposed group) and nuclear bud (non-exposed group) in individuals with the XRCC1 Trip/- and PON1 Arg/- genes. There was no significant difference in the telomere (TL) mean value in the exposed group in contrast to the non-exposed group. Our results showed that soybean producers showed genotoxic effect and cell death, which may have been induced by exposure to complex mixtures of agrochemicals and fertilizers. In addition, XRCC1 Arg/Arg could, in some respects, provide protection to individuals.
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Affiliation(s)
- Arielly F B de Oliveira
- Laboratory of Genetic Toxicology, PPGBioSaúde, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Melissa Rosa de Souza
- Laboratory of Genetic Toxicology, PPGBioSaúde, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Danieli Benedetti
- Laboratory of Genetic Toxicology, PPGBioSaúde, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Amanda Souza Scotti
- Laboratory of Genetic Toxicology, PPGBioSaúde, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Luma Smidt Piazza
- Laboratory of Genetic Toxicology, PPGBioSaúde, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Ana Letícia Hilario Garcia
- Laboratory of Genetic Toxicology, PPGBioSaúde, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil; Laboratory of Ecotoxicology, Postgraduate Program in Environmental Quality, University Feevale, Novo Hamburgo, RS, Brazil
| | - Johnny Ferraz Dias
- Ion Implantation Laboratory, Institute of Physics, Federal University of Rio Grande Do Sul, Porto Alegre, RS, Brazil
| | | | - Anaí Duarte
- Ion Implantation Laboratory, Institute of Physics, Federal University of Rio Grande Do Sul, Porto Alegre, RS, Brazil
| | - Dêiverti Bauer
- Ion Implantation Laboratory, Institute of Physics, Federal University of Rio Grande Do Sul, Porto Alegre, RS, Brazil
| | - Livio Amaral
- Ion Implantation Laboratory, Institute of Physics, Federal University of Rio Grande Do Sul, Porto Alegre, RS, Brazil
| | - Carmen Lucia Bassi Branco
- Postgraduate in Health Science, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, MT, Brazil
| | - Érica de Melo Reis
- Postgraduate in Health Science, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, MT, Brazil
| | | | - Juliana da Silva
- Laboratory of Genetic Toxicology, PPGBioSaúde, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil.
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10
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Huang L, Zhang Y, He R, Zuo Z, Luo Z, Xu W, Yan Q. Phenotypic characterization, virulence, and immunogenicity of Pseudomonas plecoglossicida rpoE knock-down strain. FISH & SHELLFISH IMMUNOLOGY 2019; 87:772-777. [PMID: 30776544 DOI: 10.1016/j.fsi.2019.02.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 06/09/2023]
Abstract
Pseudomonas plecoglossicida, a temperature dependent bacterial pathogen in fish, expresses rpoE gene that is sensitive to temperature and probably critical for pathogen virulence and disease development. In this study, the rpoE silence strain rpoE-RNAi-1 was constructed by gene knock-down. The rpoE-RNAi-1 displayed significant changes in biofilm formation, swarming motility, adhesion and virulence. Meanwhile, vaccination of grouper with rpoE-RNAi-1 led to a relative percent survival (RPS) value of 85% after challenged with the wild-type P. plecoglossicida. qRT-PCR assays showed that vaccination with rpoE-RNAi-1 enhanced the expression of immune-related genes, including MHC-I, MHC-II, IgM, and IL-1β, indicating that it was able to induce humoral and cell-mediated immune response in grouper. These results validated the possibility of rpoE as a potential target for constructing P. plecoglossicida live attenuated vaccine.
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Affiliation(s)
- Lixing Huang
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, PR China.
| | - Youyu Zhang
- Institute of Electromagnetics and Acoustics, School of Electronic Science and Engineering, Xiamen University, Xiamen, Fujian, PR China
| | - Rongchao He
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, PR China
| | - Zhenghong Zuo
- School of Life Sciences, Xiamen University, Xiamen, Fujian, PR China
| | - Zhuhua Luo
- Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005, PR China
| | - Wei Xu
- Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005, PR China
| | - Qingpi Yan
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, PR China.
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11
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Lewis RW, Bertsch PM, McNear DH. Nanotoxicity of engineered nanomaterials (ENMs) to environmentally relevant beneficial soil bacteria - a critical review. Nanotoxicology 2019; 13:392-428. [PMID: 30760121 DOI: 10.1080/17435390.2018.1530391] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Deposition of engineered nanomaterials (ENMs) in various environmental compartments is projected to continue rising exponentially. Terrestrial environments are expected to be the largest repository for environmentally released ENMs. Because ENMs are enriched in biosolids during wastewater treatment, agriculturally applied biosolids facilitate ENM exposure of key soil micro-organisms, such as plant growth-promoting rhizobacteria (PGPR). The ecological ramifications of increasing levels of ENM exposure of terrestrial micro-organisms are not clearly understood, but a growing body of research has investigated the toxicity of ENMs to various soil bacteria using a myriad of toxicity end-points and experimental procedures. This review explores what is known regarding ENM toxicity to important soil bacteria, with a focus on ENMs which are expected to accumulate in terrestrial ecosystems at the highest concentrations and pose the greatest potential threat to soil micro-organisms having potential indirect detrimental effects on plant growth. Knowledge gaps in the fundamental understanding of nanotoxicity to bacteria are identified, including the role of physicochemical properties of ENMs in toxicity responses, particularly in agriculturally relevant micro-organisms. Strategies for improving the impact of future research through the implementation of in-depth ENM characterization and use of necessary experimental controls are proposed. The future of nanotoxicological research employing microbial ecoreceptors is also explored, highlighting the need for continued research utilizing bacterial isolates while concurrently expanding efforts to study ENM-bacteria interactions in more complex environmentally relevant media, e.g. soil. Additionally, the particular importance of future work to extensively examine nanotoxicity in the context of bacterial ecosystem function, especially of plant growth-promoting agents, is proposed.
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Affiliation(s)
- Ricky W Lewis
- a Rhizosphere Science Laboratory, Department of Plant and Soil Sciences , University of Kentucky , Lexington , KY , USA
| | - Paul M Bertsch
- a Rhizosphere Science Laboratory, Department of Plant and Soil Sciences , University of Kentucky , Lexington , KY , USA.,b CSIRO Land and Water , Ecosciences Precinct , Brisbane , Australia.,c Center for the Environmental Implications of Nanotechnology (CEINT) , Duke University , Durham , NC , USA
| | - David H McNear
- a Rhizosphere Science Laboratory, Department of Plant and Soil Sciences , University of Kentucky , Lexington , KY , USA
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12
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Anupama R, Lulu S, Madhusmita R, Vino S, Mukherjee A, Babu S. Insights into the interaction of key biofilm proteins in Pseudomonas aeruginosa PAO1 with TiO 2 nanoparticle: An in silico analysis. J Theor Biol 2019; 462:12-25. [PMID: 30391649 DOI: 10.1016/j.jtbi.2018.10.057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 10/27/2022]
Abstract
Pseudomonas aeruginosa is a pathogenic biofilm forming bacteria which exist in wide range of environments such as water, soil and human body. In an earlier study, we used a system biology approach based analysis of biofilm forming genes of P. aeruginosa and their possible role in TiO2 nanoparticle binding. The major protein of P. aeruginosa targeted by TiO2 was found to be KatA, a major catalase required for H2O2 resistance and acute virulence and the direct interacting protein partners of KatA were found to be DnaK, Hfq, RpoA and RpoS. To understand the protein-protein physical interaction characteristic of these key proteins involved in biofilm related processes, homology modeling, docking and molecular dynamic simulation were performed. For all these proteins, physical and chemical properties, amino acid composition, nest and cleft analysis were performed using online tools. The interactions between TiO2NPs-KatA and four protein-protein complexes such as KatA-DnaK, KatA-Hfq, KatA-RpoA and KatA-RpoS were studied. Our results indicate that all four key proteins and TiO2NPs can have stable complexation with KatA. The study has given enough clues to understand the interaction of TiO2NPs with P. aeruginosa biofilm in natural environment. Further investigations could lead to development of TiO2NPs based therapeutic and sanitary interventions to combat this pathogenic bacterium.
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Affiliation(s)
- Rani Anupama
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Sajitha Lulu
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
| | - Rout Madhusmita
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Sundararajan Vino
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
| | - Amitava Mukherjee
- Centre for Nanobiotechnology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
| | - Subramanian Babu
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
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Rani A, Babu S. Environmental proteomic studies: closer step to understand bacterial biofilms. World J Microbiol Biotechnol 2018; 34:120. [PMID: 30022302 DOI: 10.1007/s11274-018-2504-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 07/16/2018] [Indexed: 01/15/2023]
Abstract
Advancement in proteome analytical techniques and the development of protein databases have been helping to understand the physiology and subtle molecular mechanisms behind biofilm formation in bacteria. This review is to highlight how the evolving proteomic approaches have revealed fundamental molecular processes underlying the formation and regulation of bacterial biofilms. Based on the survey of research reports available on differential expression of proteins in biofilms of bacterial from wide range of environments, four important cellular processes viz. metabolism, motility, transport and stress response that contribute to formation of bacterial biofilms are discussed. This review might answer how proteins related to these cellular processes contribute significantly in stabilizing biofilms of different bacteria in diverse environmental conditions.
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Affiliation(s)
- Anupama Rani
- School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - Subramanian Babu
- School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India.
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