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Sun L, Zhang T, Lan X, Zhang N, Wang R, Ma S, Zhao P, Xia Q. High-Throughput Screening of PAM-Flexible Cas9 Variants for Expanded Genome Editing in the Silkworm ( Bombyx mori). INSECTS 2024; 15:241. [PMID: 38667371 PMCID: PMC11050708 DOI: 10.3390/insects15040241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
Genome editing provides novel opportunities for the precise genome engineering of diverse organisms. Significant progress has been made in the development of genome-editing tools for Bombyx mori (B. mori) in recent years. Among these, CRISPR/Cas9, which is currently the most commonly used system in lepidopteran insects, recognizes NGG protospacer adjacent motif (PAM) sequences within the target locus. However, Cas9 lacks the ability to target all gene loci in B. mori, indicating the need for Cas9 variants with a larger editing range. In this study, we developed a high-throughput screening platform to validate Cas9 variants at all possible recognizable and editable PAM sites for target sequences in B. mori. This platform enabled us to identify PAM sites that can be recognized by both xCas9 3.7 and SpCas9-NG variants in B. mori and to assess their editing efficiency. Cas9 shows PAM sites every 13 base pairs in the genome, whereas xCas9 3.7 and SpCas9-NG have an average distance of 3.4 and 3.6 base pairs, respectively, between two specific targeting sites. Combining the two Cas9 variants could significantly expand the targeting range of the genome, accelerate research on the B. mori genome, and extend the high-throughput rapid screening platform to other insects, particularly those lacking suitable NGG PAM sequences.
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Affiliation(s)
- Le Sun
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (L.S.)
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing 400715, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing 400715, China
| | - Tong Zhang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (L.S.)
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing 400715, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing 400715, China
| | - Xinhui Lan
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (L.S.)
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing 400715, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing 400715, China
| | - Na Zhang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (L.S.)
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing 400715, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing 400715, China
| | - Ruolin Wang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (L.S.)
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing 400715, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing 400715, China
| | - Sanyuan Ma
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (L.S.)
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing 400715, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing 400715, China
| | - Ping Zhao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (L.S.)
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing 400715, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing 400715, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (L.S.)
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing 400715, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing 400715, China
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Ma S, Zhang T, Wang R, Wang P, Liu Y, Chang J, Wang A, Lan X, Sun L, Sun H, Shi R, Lu W, Liu D, Zhang N, Hu W, Wang X, Xing W, Jia L, Xia Q. High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism, Bombyx mori. Genome Res 2024; 34:134-144. [PMID: 38191205 PMCID: PMC10903940 DOI: 10.1101/gr.278297.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024]
Abstract
Large-scale genetic mutant libraries are powerful approaches to interrogating genotype-phenotype correlations and identifying genes responsible for certain environmental stimuli, both of which are the central goal of life science study. We produced the first large-scale CRISPR-Cas9-induced library in a nonmodel multicellular organism, Bombyx mori We developed a piggyBac-delivered binary genome editing strategy, which can simultaneously meet the requirements of mixed microinjection, efficient multipurpose genetic operation, and preservation of growth-defect lines. We constructed a single-guide RNA (sgRNA) plasmid library containing 92,917 sgRNAs targeting promoters and exons of 14,645 protein-coding genes, established 1726 transgenic sgRNA lines following microinjection of 66,650 embryos, and generated 300 mutant lines with diverse phenotypic changes. Phenomic characterization of mutant lines identified a large set of genes responsible for visual phenotypic or economically valuable trait changes. Next, we performed pooled context-specific positive screens for tolerance to environmental pollutant cadmium exposure, and identified KWMTBOMO12902 as a strong candidate gene for breeding applications in sericulture industry. Collectively, our results provide a novel and versatile approach for functional B. mori genomics, as well as a powerful resource for identifying the potential of key candidate genes for improving various economic traits. This study also shows the effectiveness, practicality, and convenience of large-scale mutant libraries in other nonmodel organisms.
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Affiliation(s)
- Sanyuan Ma
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China;
| | - Tong Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Ruolin Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Pan Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Yue Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Jiasong Chang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, 030001, China
| | - Aoming Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Xinhui Lan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Le Sun
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Hao Sun
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Run Shi
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Wei Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Dan Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Na Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Wenbo Hu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Xiaogang Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
- China Chongqing Key Laboratory of Chinese Medicine & Health Science, Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China
| | - Weiqing Xing
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Ling Jia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China;
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Gao ZW, Li YY, Li PH, Yang YF, Zhao YH, Yang M, Chen SH, Song ZY, Huang XJ. Synergistic activation of P and orbital coupling effect for ultra-sensitive and selective electrochemical detection of Cd(II) over Fe-doped CoP. JOURNAL OF HAZARDOUS MATERIALS 2024; 463:132842. [PMID: 37907008 DOI: 10.1016/j.jhazmat.2023.132842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 10/12/2023] [Accepted: 10/21/2023] [Indexed: 11/02/2023]
Abstract
Despite significant advancements in the detection of cadmium (Cd(II)) based on nanomaterial adsorbability, limited research has been conducted on ultra-sensitive and selective detection mechanisms, resulting in a lack of guidance for designing efficient interface materials to detect Cd(II). Herein, reductive Fe doping on CoP facilitates an efficient Fe-Co-P electron transfer path, which renders P the electron-rich site and subsequently splits a new orbital peak that matches with that of Cd(II) for excellent electrochemical performance. The sensitivity of Cd(II) was remarkably up to 109.75 μA μM-1 on the Fe-CoP modified electrode with excellent stability and repeatability, surpassing previously reported findings. Meanwhile, the electrode exhibits exceptional selectivity towards Cd(II) ions compared to some bivalent heavy metal ions (HMIs). Moreover, X-ray absorption fine structure (XAFS) analysis reveals the interaction between P and Cd(II), which is further verified via density functional theory (DFT) calculation with the new hybrid peaks resulting from the splitting peak of P atoms coupled with the orbital energy level of Cd(II). Generally, doping engineering for specific active sites and regulation of orbital electrons not only provides valuable insights for the subsequent regulation of electronic configuration but also lays the foundation for customizing highly sensitive and selectivity sensors.
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Affiliation(s)
- Zhi-Wei Gao
- Key Laboratory of Environmental Optics and Technology, And Environmental Materials and Pollution Control Laboratory, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, China; Department of Materials Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Yong-Yu Li
- Key Laboratory of Environmental Optics and Technology, And Environmental Materials and Pollution Control Laboratory, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, China
| | - Pei-Hua Li
- Key Laboratory of Environmental Optics and Technology, And Environmental Materials and Pollution Control Laboratory, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, China
| | - Yuan-Fan Yang
- Key Laboratory of Environmental Optics and Technology, And Environmental Materials and Pollution Control Laboratory, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, China; Department of Materials Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Yong-Huan Zhao
- Key Laboratory of Environmental Optics and Technology, And Environmental Materials and Pollution Control Laboratory, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, China; Department of Materials Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Meng Yang
- Key Laboratory of Environmental Optics and Technology, And Environmental Materials and Pollution Control Laboratory, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, China.
| | - Shi-Hua Chen
- Key Laboratory of Environmental Optics and Technology, And Environmental Materials and Pollution Control Laboratory, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, China; State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem And Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
| | - Zong-Yin Song
- Key Laboratory of Environmental Optics and Technology, And Environmental Materials and Pollution Control Laboratory, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, China.
| | - Xing-Jiu Huang
- Key Laboratory of Environmental Optics and Technology, And Environmental Materials and Pollution Control Laboratory, Institute of Solid State Physics, HFIPS, Chinese Academy of Sciences, Hefei 230031, China; Department of Materials Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
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Sun H, Chen J, Wang R, Liu D, Zhang N, Zhang T, Jia L, Ma S, Xia Q. Genome-wide CRISPR screening reveals key genes and pathways associated with 20-hydroxyecdysone signal transduction in the silkworm (Bombyx mori). INSECT SCIENCE 2024; 31:47-58. [PMID: 37368860 DOI: 10.1111/1744-7917.13237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 06/29/2023]
Abstract
Metamorphosis is a complex developmental process involving multiple pathways and a large number of genes that are regulated by juvenile hormone (JH) and 20-hydroxyecdysone (20E). Despite important progress in understanding various aspects of silkworm biology, the hormone signaling pathway in the silkworm remains poorly understood. Genome-wide screening using clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR-associated protein 9 (Cas9)-based libraries has recently emerged as a novel method for analyzing genome function, enabling further research into essential genes, drug targets, and virus-host interaction. Previously, we constructed a genome-wide CRISPR/Cas9-based library of the silkworm (Bombyx mori) and successfully revealed the genes involved in biotic or abiotic stress factor responses. In this study, we used our silkworm CRISPR library and large-scale genome-wide screening to analyze the key genes in the silkworm 20E signaling pathway and their mechanisms of action. Functional annotation showed that 20E regulates key proteins in processes that mainly occur in the cytoplasm and nucleus. Pathway enrichment analysis showed that 20E can activate phosphorylation and may affect innate immunity, interfere with intracellular nutrition and energy metabolism, and eventually cause cell apoptosis. The screening results were experimentally validated by generating cells with knockout alleles of the relevant genes, which had increased tolerance to 20E. Our findings provide a panoramic overview of signaling in response to 20E in the silkworm, underscoring the utility of genome-wide CRISPR mutant libraries in deciphering hormone signaling pathways and the mechanisms that regulate metamorphosis in insects.
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Affiliation(s)
- Hao Sun
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Biological Science Research Center, Southwest University, Chongqing, China
| | - Jingya Chen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Biological Science Research Center, Southwest University, Chongqing, China
| | - Ruolin Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Biological Science Research Center, Southwest University, Chongqing, China
| | - Dan Liu
- Biological Science Research Center, Southwest University, Chongqing, China
| | - Na Zhang
- Biological Science Research Center, Southwest University, Chongqing, China
| | - Tong Zhang
- Biological Science Research Center, Southwest University, Chongqing, China
| | - Ling Jia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Biological Science Research Center, Southwest University, Chongqing, China
| | - Sanyuan Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Biological Science Research Center, Southwest University, Chongqing, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Biological Science Research Center, Southwest University, Chongqing, China
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Zhao F, Ding X, Liu Z, Yan X, Chen Y, Jiang Y, Chen S, Wang Y, Kang T, Xie C, He M, Zheng J. Application of CRISPR/Cas9-based genome editing in ecotoxicology. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 336:122458. [PMID: 37633433 DOI: 10.1016/j.envpol.2023.122458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
Chemicals are widely used and released into the environment, and their degradation, accumulation, migration, and transformation processes in the environment can pose a threat to the ecosystem. The advancement in analytical methods with high-throughput screening of biomolecules has revolutionized the way toxicologists used to explore the effects of chemicals on organisms. CRISPR/Cas is a newly developed tool, widely used in the exploration of basic science and biologically engineered products given its high efficiency and low cost. For example, it can edit target genes efficiently, and save loss of the crop yield caused by environmental pollution as well as gain a better understanding of the toxicity mechanisms from various chemicals. This review briefly introduces the development history of CRISPR/Cas and summarizes the current application of CRISPR/Cas in ecotoxicology, including its application on improving crop yield and drug resistance towards agricultural pollution, antibiotic pollution and other threats. The benefits by applying the CRISPR/Cas9 system in conventional toxicity mechanism studies are fully demonstrated here together with its foreseeable expansions in other area of ecotoxicology. Finally, the prospects and disadvantages of CRISPR/Cas system in the field of ecotoxicology are also discussed.
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Affiliation(s)
- Fang Zhao
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China; State Environmental Protection Key laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences. Ministry of Environmental Protection, Guangzhou, China; School of Public Health, Guizhou Medical University, Guizhou, China
| | - Xiaofan Ding
- Faculty of Health Sciences, University of Macau, Taipa, Macao SAR, China
| | - Zimeng Liu
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Xiao Yan
- State Environmental Protection Key laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences. Ministry of Environmental Protection, Guangzhou, China
| | - Yanzhen Chen
- Faculty of Health Sciences, University of Macau, Taipa, Macao SAR, China
| | - Yaxin Jiang
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Shunjie Chen
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Yuanfang Wang
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Tingting Kang
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Chun Xie
- School of Public Health, Guizhou Medical University, Guizhou, China
| | - Mian He
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China.
| | - Jing Zheng
- State Environmental Protection Key laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences. Ministry of Environmental Protection, Guangzhou, China
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Huang Y, Zou S, Zhan P, Hao Z, Lu Q, Jing W, Li Y, Xu Y, Wang H. Dinotefuran induces oxidative stress and autophagy on Bombyx mori silk gland: Toxic effects and implications for nontarget organisms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 336:122470. [PMID: 37657723 DOI: 10.1016/j.envpol.2023.122470] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/04/2023] [Accepted: 08/25/2023] [Indexed: 09/03/2023]
Abstract
Dinotefuran, a third-generation neonicotinoid insecticide, is widely utilized in agriculture for pest control; however, its environmental consequences and risks to non-target organisms remain largely unknown. Bombyx mori is an economically important insect and a good toxic detector for environmental assessments. In this study, ultrastructure analysis showed that dinotefuran exposure caused an increase in autophagic vesicles in the silk gland. Dinotefuran exposure triggered elevated levels of oxidative stress in silk glands. Reactive oxygen species, oxidized glutathione disulfide, glutathione peroxidase, the activities of UDP glucuronosyl-transferase and carboxylesterase were induced in the middle silk gland, while malondialdehyde, reactive oxygen species, superoxide dismutase , oxidized glutathione disulfide were increased in the posterior silk gland. Global transcription patterns revealed the physiological responses were induced by dinotefuran. Dinotefuran exposure substantially induced the expression levels of many genes involved in the mTOR and PI3K - Akt signaling pathways in the middle silk gland, whereas many differentially expressed genes involved in fatty acid and pyrimidine metabolism were found in the posterior silk gland. Additionally, functional, ultrastructural, and transcriptomic analysis indicate that dinotefuran exposure induced an increase of autophagy in the silk gland. This study illuminates the toxicity effects of dinotefuran exposure on silkworms and provides new insights into the underlying molecular toxicity mechanisms of dinotefuran to nontarget organisms.
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Affiliation(s)
- Yuxin Huang
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Shiyu Zou
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Pengfei Zhan
- Huzhou Academy of Agricultural Sciences, Huzhou, China
| | - Zhihua Hao
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Qingyu Lu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Wenhui Jing
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yinghui Li
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yusong Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Huabing Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, China.
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Lu Q, Xu S, Hao Z, Li Y, Huang Y, Ying S, Jing W, Zou S, Xu Y, Wang H. Dinotefuran exposure induces autophagy and apoptosis through oxidative stress in Bombyx mori. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131997. [PMID: 37423129 DOI: 10.1016/j.jhazmat.2023.131997] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/18/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
As a third-generation neonicotinoid insecticide, dinotefuran is extensively used in agriculture, and its residue in the environment has potential effects on nontarget organisms. However, the toxic effects of dinotefuran exposure on nontarget organism remain largely unknown. This study explored the toxic effects of sublethal dose of dinotefuran on Bombyx mori. Dinotefuran upregulated reactive oxygen species (ROS) and malondialdehyde (MDA) levels in the midgut and fat body of B. mori. Transcriptional analysis revealed that the expression levels of many autophagy and apoptosis-associated genes were significantly altered after dinotefuran exposure, consistent with ultrastructural changes. Moreover, the expression levels of autophagy-related proteins (ATG8-PE and ATG6) and apoptosis-related proteins (BmDredd and BmICE) were increased, whereas the expression level of an autophagic key protein (sequestosome 1) was decreased in the dinotefuran-exposed group. These results indicate that dinotefuran exposure leads to oxidative stress, autophagy, and apoptosis in B. mori. In addition, its effect on the fat body was apparently greater than that on the midgut. In contrast, pretreatment with an autophagy inhibitor effectively downregulated the expression levels of ATG6 and BmDredd, but induced the expression of sequestosome 1, suggesting that dinotefuran-induced autophagy may promote apoptosis. This study reveals that ROS generation regulates the impact of dinotefuran on the crosstalk between autophagy and apoptosis, laying the foundation for studying cell death processes such as autophagy and apoptosis induced by pesticides. Furthermore, this study provides a comprehensive insight into the toxicity of dinotefuran on silkworm and contributes to the ecological risk assessment of dinotefuran in nontarget organisms.
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Affiliation(s)
- Qingyu Lu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shiliang Xu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhihua Hao
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yinghui Li
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuxin Huang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shuye Ying
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenhui Jing
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shiyu Zou
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yusong Xu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huabing Wang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
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Rafeeq H, Afsheen N, Rafique S, Arshad A, Intisar M, Hussain A, Bilal M, Iqbal HMN. Genetically engineered microorganisms for environmental remediation. CHEMOSPHERE 2023; 310:136751. [PMID: 36209847 DOI: 10.1016/j.chemosphere.2022.136751] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/12/2022] [Accepted: 10/02/2022] [Indexed: 06/16/2023]
Abstract
In the recent era, the increasing persistence of hazardous contaminants is badly affecting the globe in many ways. Due to high environmental contamination, almost every second species on earth facing the worst issue in their survival. Advances in newer remediation approaches may help enhance bioremediation's quality, while conventional procedures have failed to remove hazardous compounds from the environment. Chemical and physical waste cleanup approaches have been used in current circumstances; however, these methods are costly and harmful to the environment. Thus, there has been a rise in the use of bioremediation due to an increase in environmental contamination, which led to the development of genetically engineered microbes (GEMs). It is safer and more cost-effective to use engineered microorganisms rather than alternative methods. GEMs are created by introducing a stronger protein into bacteria through biotechnology or genetic engineering to enhance the desired trait. Biodegradation of oil spills, halobenzoates naphthalenes, toluenes, trichloroethylene, octanes, xylenes etc. has been accomplished using GEMs such bacteria, fungus, and algae. Biotechnologically induced microorganisms are more powerful than naturally occurring ones and may degrade contaminants faster because they can quickly adapt to new pollutants they encounter or co-metabolize. Genetic engineering is a worthy process that will benefit the environment and ultimately the health of our people.
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Affiliation(s)
- Hamza Rafeeq
- Department of Biochemistry, Riphah International University, Faisalabad Campus, Faisalabad, 38000, Pakistan
| | - Nadia Afsheen
- Department of Biochemistry, Riphah International University, Faisalabad Campus, Faisalabad, 38000, Pakistan
| | - Sadia Rafique
- Departement of Pharmacy, Riphah International University, Faisalabad Campus, Faisalabad, 38000, Pakistan
| | - Arooj Arshad
- Department of Biochemistry, University of Agriculture Faisalabad, 38000, Pakistan
| | - Maham Intisar
- Department of Biochemistry, University of Agriculture Faisalabad, 38000, Pakistan
| | - Asim Hussain
- Department of Biochemistry, University of Agriculture Faisalabad, 38000, Pakistan
| | - Muhammad Bilal
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60695 Poznan, Poland.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico.
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9
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The application of genome-wide CRISPR-Cas9 screens to dissect the molecular mechanisms of toxins. Comput Struct Biotechnol J 2022; 20:5076-5084. [PMID: 36187925 PMCID: PMC9489804 DOI: 10.1016/j.csbj.2022.09.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
Many toxins are life-threatening to both animals and humans. However, specific antidotes are not available for most of those toxins. The molecular mechanisms underlying the toxicology of well-known toxins are not yet fully characterized. Recently, the advance in CRISPR-Cas9 technologies has greatly accelerated the process of revealing the toxic mechanisms of some common toxins on hosts from a genome-wide perspective. The high-throughput CRISPR screen has made it feasible to untangle complicated interactions between a particular toxin and its corresponding targeting tissue(s). In this review, we present an overview of recent advances in molecular dissection of toxins’ cytotoxicity by using genome-wide CRISPR screens, summarize the components essential for toxin-specific CRISPR screens, and propose new strategies for future research.
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10
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Ma S, Wang A, Chen X, Zhang T, Xing W, Xia Q. Deep Sequencing Reveals the Comprehensive CRISPR-Cas9 Editing Spectrum in Bombyx mori. CRISPR J 2021; 4:371-380. [PMID: 34042501 DOI: 10.1089/crispr.2021.0003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Application of the clustered regularly interspaced short palindromic repeats associated 9 (CRISPR-Cas9) technology has revolutionized biology by greatly enhancing the ability to introduce mutations into DNA for research and prospective therapeutic purposes. However, the understanding of Cas9 editing outcomes is still limited. Previously, it was considered that Cas9 introduces stochastic insertions or deletions (indels) at the target site. In the current study, we performed in vivo multiplex editing, deep sequencing, and comprehensive analysis of its editing outcomes in Bombyx mori (B. mori). A total of 31161 editing events from 9 single-guide RNA (sgRNA) sites in 16 individuals were generated and analyzed, and we found that Cas9 introduces mutations with some regularity rather than via stochastic indels. The editing efficiency varies with sgRNA sequences, individuals, and orientation. Small deletions account for the vast majority of mutated sequences, followed by a small fraction of substitutions and insertions. The most likely mutations are deletions between two microhomologous sequences or single-base deletions at the cleavage site in the absence of microhomologous pairs. Insertions are formed by diverse mechanisms, including direct acquisition of free genomic fragments, duplication of broken ends, replication of adjacent sequences, or random addition of free nucleotides. The above results indicate that the Cas9 editing spectrum is reproducible and predictable. Thus, our findings enable a deeper understanding of Cas9-mediated mutagenesis and better design of genome editing experiments, as well as elucidate the DNA double-strand break repair processes in B. mori.
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Affiliation(s)
- Sanyuan Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China; Southwest University, Chongqing, China
- Biological Science Research Center, Southwest University, Chongqing, China; and Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing, China
| | - Aoming Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China; Southwest University, Chongqing, China
- Biological Science Research Center, Southwest University, Chongqing, China; and Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing, China
| | - Xiaoxu Chen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China; Southwest University, Chongqing, China
- Biological Science Research Center, Southwest University, Chongqing, China; and Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing, China
| | - Tong Zhang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China; Southwest University, Chongqing, China
- Biological Science Research Center, Southwest University, Chongqing, China; and Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing, China
| | - Weiqing Xing
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China; Southwest University, Chongqing, China
- Biological Science Research Center, Southwest University, Chongqing, China; and Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China; Southwest University, Chongqing, China
- Biological Science Research Center, Southwest University, Chongqing, China; and Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing, China
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