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Ying W, Yunqi Z, Deji L, Jian K, Fusheng Q. Follicular fluid HD-sevs-mir-128-3p is a key molecule in regulating bovine granulosa cells autophagy. Theriogenology 2024; 226:263-276. [PMID: 38954995 DOI: 10.1016/j.theriogenology.2024.06.022] [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: 03/20/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
Follicular fluid (FF) is rich in extracellular vesicles (EVs). EVs carries a variety of miRNA involved in regulating follicular development, the function of cells in follicles, primordial follicular formation, follicular recruitment and selection, follicular atresia, oocyte communication, granulosa cells (GCs) function and luteinization and other biological processes of follicular development. Previous studies in our laboratory have shown that bovine follicular fluid (bFF) high density-small extracellular vesicles (HD-sEVs)-miRNA was enriched in autophagy-related pathways. However, the mechanism of bFF EVs carrying miRNA regulating GCs autophagy is not clear. Thus, this study carried out a series of studies on the previous HD-sEVs sequencing data and miR-128-3p contained in bFF HD-sEVs. A total of 38 differentially expressed genes were detected by RNA-Seq after overexpression of miR-128-3p in bovine GCs (bGCs). Through cell transfection, Western blot (WB) and Immunofluorescence (IF), it was proved that overexpression of miR-128-3p could promote the expression of LC3 (microtubule-associated protein I light chain 3), inhibit p62, promote the number of autophagosome, promote the formation of autophagy lysosome and autophagy flow, and activate bGCs autophagy. MiR-128-3p inhibitor significantly inhibited the expression of LC3 and monodansylcadaverine (MDC) in bGCs, and promoted the expression of autophagy substrate p62, indicating that HD-sEVs-miR-128-3p could activate bGCs autophagy. In addition, through double luciferase assay, bioinformatics analysis, WB and RT-qPCR, it was concluded that bFF HD-sEVs-miR-128-3p could target TFEB (transcription factor EB) and FoxO4 (Forkhead box O4) and activate GCs autophagy.
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Affiliation(s)
- Wang Ying
- Chongqing Key Laboratory of Forage &Herbivore, College of Veterinary Medicine, Southwest University, Beibei, Chongqing, 400715, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhao Yunqi
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Luan Deji
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Kang Jian
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Quan Fusheng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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2
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Fan S, Tang Y, Zhu N, Meng Q, Zhou Y, Zhao Y, Xu J, Gu C, Dai S, Zhu B, Yuan X. Analyzing the defense response mechanism of Atractylodes macrocephala to Fusarium oxysporum through small RNA and degradome sequencing. FRONTIERS IN PLANT SCIENCE 2024; 15:1415209. [PMID: 39104842 PMCID: PMC11298489 DOI: 10.3389/fpls.2024.1415209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 07/08/2024] [Indexed: 08/07/2024]
Abstract
Introduction Fusarium oxysporum is a significant soil-borne fungal pathogen that affects over 100 plant species, including crucial crops like tomatoes, bananas, cotton, cucumbers, and watermelons, leading to wilting, yellowing, growth inhibition, and ultimately plant death. The root rot disease of A. macrocephala, caused by F. oxysporum, is one of the most serious diseases in continuous cropping, which seriously affects its sustainable development. Methods In this study, we explored the interaction between A. macrocephala and F. oxysporum through integrated small RNA (sRNA) and degradome sequencing to uncover the microRNA (miRNA)-mediated defense mechanisms. Results We identified colonization of F. oxysporum in A. macrocephala roots on day 6. Nine sRNA samples were sequenced to examine the dynamic changes in miRNA expression in A. macrocephala infected by F. oxysporum at 0, 6, and 12 days after inoculation. Furthermore, we using degradome sequencing and quantitative real-time PCR (qRT-PCR), validated four miRNA/target regulatory units involved in A. macrocephala-F. oxysporum interactions. Discussion This study provides new insights into the molecular mechanisms underlying A. macrocephala's early defense against F. oxysporum infection, suggesting directions for enhancing resistance against this pathogen.
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Affiliation(s)
- Sen Fan
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yunjia Tang
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, China
| | - Na Zhu
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qingling Meng
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yanguang Zhou
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yujin Zhao
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jingyan Xu
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Chenxian Gu
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Shijie Dai
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Bo Zhu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaofeng Yuan
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
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3
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Niu Y, Zhang Y, Tian W, Wang Y, Liu Y, Ji H, Cai H, Han R, Tian Y, Liu X, Kang X, Li Z. The long noncoding RNA lncMPD2 inhibits myogenesis by targeting the miR-34a-5p/THBS1 axis. Int J Biol Macromol 2024; 275:133688. [PMID: 38971281 DOI: 10.1016/j.ijbiomac.2024.133688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/30/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Long noncoding RNAs (lncRNAs) participate in regulating skeletal muscle development. However, little is known about their role in regulating chicken myogenesis. In this study, we identified a novel lncRNA, lncMPD2, through transcriptome sequencing of chicken myoblasts at different developmental stages. Functionally, gain- and loss-of-function experiments showed that lncMPD2 inhibited myoblast proliferation and differentiation. Mechanistically, lncMPD2 directly bound to miR-34a-5p, and miR-34a-5p promoted myoblasts proliferation and differentiation and inhibited the mRNA and protein expression of its target gene THBS1. THBS1 inhibited myoblast proliferation and differentiation in vitro and delayed muscle regeneration in vivo. Furthermore, rescue experiments showed that lncMPD2 counteracted the inhibitory effects of miR-34a-5p on THBS1 and myogenesis-related gene mRNA and protein expression. In conclusion, lncMPD2 regulates the miR-34a-5p/THBS1 axis to inhibit the proliferation and differentiation of myoblasts and skeletal muscle regeneration. This study provides more insight into the molecular regulatory network of skeletal muscle development, identifying novel potential biomarkers for improving chicken quality and increasing chicken yield. In addition, this study provides a potential goal for breeding strategies that minimize muscle damage in chickens.
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Affiliation(s)
- Yufang Niu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yushi Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Weihua Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yanxing Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yang Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Haigang Ji
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Hanfang Cai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China.
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China.
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4
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Zhang S, Ren Y, Wang S, Song L, Jing Y, Xu T, Kang X, Li Y. EuHDZ25 positively affects rubber biosynthesis by targeting EuFPS1 in Eucommia leaves. Int J Biol Macromol 2024; 272:132707. [PMID: 38825274 DOI: 10.1016/j.ijbiomac.2024.132707] [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: 02/02/2024] [Revised: 05/12/2024] [Accepted: 05/27/2024] [Indexed: 06/04/2024]
Abstract
Eucommia ulmoides is a temperate gum source plant that produces trans-polyisoprene (TPI), also known as Eucommia rubber. The structural configuration and function of TPI offer a new material with important potential for industrial development. In this study, we detected the TPI content in the leaves of diploid and triploid E. ulmoides plants. The average TPI content in the leaves of triploid E. ulmoides was significantly higher than that of diploid. Transcriptome data and weighted gene co-expression network analyses identified a significant positive correlation between the EuFPS1 gene and TPI content. Overexpression of EuFPS1 increased the density of rubber particles and TPI content, indicating its crucial role in TPI biosynthesis. In addition, the expression of EuHDZ25 in E. ulmoides was significantly positively correlated with EuFPS1 expression. Yeast one-hybrid and dual-luciferase assays demonstrated that EuHDZ25 mainly promotes TPI biosynthesis through positive regulation of EuFPS1 expression. The significantly up-regulated expression of EuHDZ25 and its consequent upregulation of EuFPS1 during the biosynthesis of TPI may partially explain the increased TPI content of triploids. This study provides an important theoretical foundation for further exploring the molecular mechanism of secondary metabolites content variation in polyploids and can help to promote the development and utilization of rubber resources.
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Affiliation(s)
- Shuwen Zhang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yongyu Ren
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China
| | - Shun Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Lianjun Song
- Weixian Eucommia National Forest Tree Germplasm Repository, Weixian Forestry Cultivation Base of Superior Species, Hebei, China
| | - Yanchun Jing
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Tingting Xu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xiangyang Kang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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5
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Valentine M, Butruille D, Achard F, Beach S, Brower-Toland B, Cargill E, Hassebrock M, Rinehart J, Ream T, Chen Y. Simultaneous genetic transformation and genome editing of mixed lines in soybean ( Glycine max) and maize ( Zea mays). ABIOTECH 2024; 5:169-183. [PMID: 38974857 PMCID: PMC11224177 DOI: 10.1007/s42994-024-00173-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 06/02/2024] [Indexed: 07/09/2024]
Abstract
Robust genome editing technologies are becoming part of the crop breeding toolbox. Currently, genome editing is usually conducted either at a single locus, or multiple loci, in a variety at one time. Massively parallel genomics platforms, multifaceted genome editing capabilities, and flexible transformation systems enable targeted variation at nearly any locus, across the spectrum of genotypes within a species. We demonstrate here the simultaneous transformation and editing of many genotypes, by targeting mixed seed embryo explants with genome editing machinery, followed by re-identification through genotyping after plant regeneration. Transformation and Editing of Mixed Lines (TREDMIL) produced transformed individuals representing 101 of 104 (97%) mixed elite genotypes in soybean; and 22 of 40 (55%) and 9 of 36 (25%) mixed maize female and male elite inbred genotypes, respectively. Characterization of edited genotypes for the regenerated individuals identified over 800 distinct edits at the Determinate1 (Dt1) locus in samples from 101 soybean genotypes and 95 distinct Brown midrib3 (Bm3) edits in samples from 17 maize genotypes. These results illustrate how TREDMIL can help accelerate the development and deployment of customized crop varieties for future precision breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-024-00173-5.
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Affiliation(s)
- Michelle Valentine
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
| | - David Butruille
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
| | - Frederic Achard
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
| | - Steven Beach
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
| | | | - Edward Cargill
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
| | - Megan Hassebrock
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
| | - Jennifer Rinehart
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
| | - Thomas Ream
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
| | - Yurong Chen
- Bayer Crop Science, 700 Chesterfield Parkway W, Chesterfield, MO 63017 USA
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6
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Chen B, Cai H, Niu Y, Zhang Y, Wang Y, Liu Y, Han R, Liu X, Kang X, Li Z. Whole transcriptome profiling reveals a lncMDP1 that regulates myogenesis by adsorbing miR-301a-5p targeting CHAC1. Commun Biol 2024; 7:518. [PMID: 38698103 PMCID: PMC11066001 DOI: 10.1038/s42003-024-06226-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 04/22/2024] [Indexed: 05/05/2024] Open
Abstract
Myoblast proliferation and differentiation are essential for skeletal muscle development. In this study, we generated the expression profiles of mRNAs, long noncoding RNAs (lncRNAs), and microRNAs (miRNAs) in different developmental stages of chicken primary myoblasts (CPMs) using RNA sequencing (RNA-seq) technology. The dual luciferase reporter system was performed using chicken embryonic fibroblast cells (DF-1), and functional studies quantitative real-time polymerase chain reaction (qPCR), cell counting kit-8 (CCK-8), 5-Ethynyl-2'-deoxyuridine (EdU), flow cytometry cycle, RNA fluorescence in situ hybridization (RNA-FISH), immunofluorescence, and western blotting assay. Our research demonstrated that miR-301a-5p had a targeted binding ability to lncMDP1 and ChaC glutathione-specific gamma-glutamylcyclotransferase 1 (CHAC1). The results revealed that lncMDP1 regulated the proliferation and differentiation of myoblasts via regulating the miR-301a-5p/CHAC1 axis, and CHAC1 promotes muscle regeneration. This study fulfilled the molecular regulatory network of skeletal muscle development and providing an important theoretical reference for the future improvement of chicken meat performance and meat quality.
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Affiliation(s)
- Bingjie Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Hanfang Cai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yufang Niu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yushi Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yanxing Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yang Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China.
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China.
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7
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Zhu X, Zhang J, Pan R, Zhang K, Dai H. CRISPR/Cas12a-mediated entropy-driven electrochemical biosensor for detection of genetically modified maize Mon810. Anal Chim Acta 2024; 1296:342290. [PMID: 38401924 DOI: 10.1016/j.aca.2024.342290] [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: 11/18/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/26/2024]
Abstract
Genetically modified crops (GMOs) have led to significant, if not revolutionary, agricultural advances. The development of GMOs requires necessary regulations, which depend on the detection of GMOs. A sensitive and specific biosensor for the detection of transgenic crops is crucial to improve the detection efficiency of GMOs. Here, we developed a CRISPR/Cas12a-mediated entropy-driven electrochemiluminescence (ECL) biosensor for the sensitive and specific detection of MON810, the world's most widely used transgenic insect-resistant maize. We designed two crRNAs to activate CRISPR/Cas12a, allowing it to cut non-specific single strands, and we modified the DNA tetrahedron (DT) on the surface of the gold electrode to diminish non-specific adsorption. The entropy-driven chain displacement reaction with the target DNA takes place for amplification. After optimization, the biosensor has satisfactory accuracy and selectivity, with a linear range of ECL of 1-106 fM and a limit of detection (LOD) of 3.3 fM by the 3σ method. The biosensor does not require polymerase chain reaction (PCR) amplification or complex sample processing, which dramatically improves transgenic crop detection efficiency. This new biosensor achieves rapid, sensitive, and highly specific detection of transgenic crops, and has great potential for large-scale field detection of transgenic crops.
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Affiliation(s)
- Xia Zhu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jianfeng Zhang
- Beijing Life Science Academy, Changping, 102209, Beijing, China
| | - Ronghui Pan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Kai Zhang
- School of Chemistry and Materials Science, Nanjing University of Information Science and Technology. Nanjing, 210044, China.
| | - Huaxin Dai
- Beijing Life Science Academy, Changping, 102209, Beijing, China.
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8
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Zhao S, Luo J, Tang M, Zhang C, Song M, Wu G, Yan X. Analysis of the Candidate Genes and Underlying Molecular Mechanism of P198, an RNAi-Related Dwarf and Sterile Line. Int J Mol Sci 2023; 25:174. [PMID: 38203344 PMCID: PMC10778984 DOI: 10.3390/ijms25010174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/10/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
The genome-wide long hairpin RNA interference (lhRNAi) library is an important resource for plant gene function research. Molecularly characterizing lhRNAi mutant lines is crucial for identifying candidate genes associated with corresponding phenotypes. In this study, a dwarf and sterile line named P198 was screened from the Brassica napus (B. napus) RNAi library. Three different methods confirmed that eight copies of T-DNA are present in the P198 genome. However, only four insertion positions were identified in three chromosomes using fusion primer and nested integrated polymerase chain reaction. Therefore, the T-DNA insertion sites and copy number were further investigated using Oxford Nanopore Technologies (ONT) sequencing, and it was found that at least seven copies of T-DNA were inserted into three insertion sites. Based on the obtained T-DNA insertion sites and hairpin RNA (hpRNA) cassette sequences, three candidate genes related to the P198 phenotype were identified. Furthermore, the potential differentially expressed genes and pathways involved in the dwarfism and sterility phenotype of P198 were investigated by RNA-seq. These results demonstrate the advantage of applying ONT sequencing to investigate the molecular characteristics of transgenic lines and expand our understanding of the complex molecular mechanism of dwarfism and male sterility in B. napus.
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Affiliation(s)
- Shengbo Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Junling Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Min Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Chi Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Miaoying Song
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Gang Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xiaohong Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (S.Z.); (J.L.); (M.T.); (C.Z.); (M.S.)
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
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9
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Jiang T, Huang J, Li S, Xu Q, Zhang T, Wang X, Chen D. Bioinformatics analysis of carotid vulnerable plaques associated with the SARS-CoV-2 pattern. Gene 2023; 888:147754. [PMID: 37659598 DOI: 10.1016/j.gene.2023.147754] [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: 06/16/2023] [Revised: 08/03/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
The rupture of carotid artery vulnerable plaque plays a critical role in ischemic stroke, and the widely spread new coronavirus in recent years plays a certain role in the development of human carotid artery vulnerable plaque, we screened out 27 differential expression genes (DEGs) of stable plaque and vulnerable plaque associated with the new coronavirus. Through the construction of the protein-protein interaction (PPI) network, the Cathepsin B (CTSB) and Niemann-Pick Disease Type 2 (NPC2) were identified as crucial expression genes, and further, we confirmed the validity of core gene expression in two validation sets. Additionally, we discovered a significant connection between CTSB, NPC2 and 28 different kinds of immune cells in carotid plaque tissue. We screened out 65 target interacting drugs based on 10 differentially expressed genes through online tools and finally verified the high expression of 2 core genes in fragile plaques through clinical sample experiments. These findings imply that two core genes may be novel targets for molecular diagnostics and immunotherapy of vulnerable plaques.
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Affiliation(s)
- Tao Jiang
- Department of Neurosurgery, The Dalian Municipal Central Hospital, Dalian 116033, China; China Medical University, Shenyang, China
| | - Jiaming Huang
- Department of Neurosurgery, The Dalian Municipal Central Hospital, Dalian 116033, China
| | - Shupeng Li
- Department of Neurosurgery, The Dalian Municipal Central Hospital, Dalian 116033, China
| | - Qiushi Xu
- Department of Neurosurgery, The Dalian Municipal Central Hospital, Dalian 116033, China
| | - Tianding Zhang
- Department of Neurosurgery, The Dalian Municipal Central Hospital, Dalian 116033, China
| | - Xianwei Wang
- Department of Neurosurgery, The Dalian Municipal Central Hospital, Dalian 116033, China; China Medical University, Shenyang, China.
| | - Dong Chen
- Department of Neurosurgery, The Dalian Municipal Central Hospital, Dalian 116033, China; China Medical University, Shenyang, China.
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10
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Sun J, Jin L, Li R, Meng X, Jin N, Wang S, Xu Z, Liu Z, Lyu J, Yu J. Effects of Different Forms and Proportions of Nitrogen on the Growth, Photosynthetic Characteristics, and Carbon and Nitrogen Metabolism in Tomato. PLANTS (BASEL, SWITZERLAND) 2023; 12:4175. [PMID: 38140502 PMCID: PMC10748299 DOI: 10.3390/plants12244175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023]
Abstract
Optimal plant growth in many species is achieved when the two major forms of N are supplied at a particular ratio. This study investigated optimal nitrogen forms and ratios for tomato growth using the 'Jingfan 502' tomato variety. Thirteen treatments were applied with varying proportions of nitrate nitrogen (NN), ammonium nitrogen (AN), and urea nitrogen (UN). Results revealed that the combination of AN and UN inhibited tomato growth and photosynthetic capacity. Conversely, the joint application of NN and UN or NN and AN led to a significant enhancement in tomato plant growth. Notably, the T12 (75%UN:25%NN) and T4 (75%NN:25%AN) treatments significantly increased the gas exchange and chlorophyll fluorescence parameters, thereby promoting the accumulation of photosynthetic products. The contents of fructose, glucose, and sucrose were significantly increased by 121.07%, 206.26%, and 94.64% and by 104.39%, 156.42%, and 61.40%, respectively, compared with those in the control. Additionally, AN favored starch accumulation, while NN and UN favored fructose, sucrose, and glucose accumulation. Gene expression related to nitrogen and sugar metabolism increased significantly in T12 and T4, with T12 showing greater upregulation. Key enzyme activity in metabolism also increased notably. In summary, T12 enhanced tomato growth by upregulating gene expression, increasing enzyme activity, and boosting photosynthesis and sugar accumulation. Growers should consider using NN and UN to reduce AN application in tomato fertilization.
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Affiliation(s)
- Jianhong Sun
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (R.L.); (X.M.); (N.J.); (Z.X.); (Z.L.)
| | - Li Jin
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (L.J.); (S.W.)
| | - Ruirui Li
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (R.L.); (X.M.); (N.J.); (Z.X.); (Z.L.)
| | - Xin Meng
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (R.L.); (X.M.); (N.J.); (Z.X.); (Z.L.)
| | - Ning Jin
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (R.L.); (X.M.); (N.J.); (Z.X.); (Z.L.)
| | - Shuya Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (L.J.); (S.W.)
| | - Zhiqi Xu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (R.L.); (X.M.); (N.J.); (Z.X.); (Z.L.)
| | - Zitong Liu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (R.L.); (X.M.); (N.J.); (Z.X.); (Z.L.)
| | - Jian Lyu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (R.L.); (X.M.); (N.J.); (Z.X.); (Z.L.)
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (L.J.); (S.W.)
| | - Jinhua Yu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (R.L.); (X.M.); (N.J.); (Z.X.); (Z.L.)
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (L.J.); (S.W.)
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11
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Tran HT, Schramm C, Huynh MM, Shavrukov Y, Stangoulis JCR, Jenkins CLD, Anderson PA. An accurate, reliable, and universal qPCR method to identify homozygous single insert T-DNA with the example of transgenic rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1221790. [PMID: 37900763 PMCID: PMC10600460 DOI: 10.3389/fpls.2023.1221790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/22/2023] [Indexed: 10/31/2023]
Abstract
Early determination of transgenic plants that are homozygous for a single locus T-DNA insert is highly desirable in most fundamental and applied transgenic research. This study aimed to build on an accurate, rapid, and reliable quantitative real-time PCR (qPCR) method to fast-track the development of multiple homozygous transgenic rice lines in the T1 generation, with low copy number to single T-DNA insert for further analyses. Here, a well-established qPCR protocol, based on the OsSBE4 reference gene and the nos terminator, was optimized in the transgenic Japonica rice cultivar Nipponbare, to distinguish homozygous single-insert plants with 100% accuracy. This method was successfully adapted to transgenic Indica rice plants carrying three different T-DNAs, without any modifications to quickly develop homozygous rice plants in the T1 generation. The accuracy of this qPCR method when applied to transgenic Indica rice approached 100% in 12 putative transgenic lines. Moreover, this protocol also successfully detected homozygous single-locus T-DNA transgenic rice plants with two-transgene T-DNAs, a feature likely to become more popular in future transgenic research. The assay was developed utilizing universal primers targeting common sequence elements of gene cassettes (the nos terminator). This assay could therefore be applied to other transgenic plants carrying the nos terminator. All procedures described here use standardized qPCR reaction conditions and relatively inexpensive dyes, such as SYBR Green, thus the qPCR method could be cost-effective and suitable for lower budget laboratories that are involved in rice transgenic research.
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Affiliation(s)
- Hai Thanh Tran
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | | | | | | | | | | | - Peter A. Anderson
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
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12
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Pradhan M, Baldwin IT, Pandey SP. Argonaute7 (AGO7) optimizes arbuscular mycorrhizal fungal associations and enhances competitive growth in Nicotiana attenuata. THE NEW PHYTOLOGIST 2023; 240:382-398. [PMID: 37532924 DOI: 10.1111/nph.19155] [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: 03/23/2023] [Accepted: 07/02/2023] [Indexed: 08/04/2023]
Abstract
Plants interact with arbuscular mycorrhizal fungi (AMF) and in doing so, change transcript levels of many miRNAs and their targets. However, the identity of an Argonaute (AGO) that modulates this interaction remains unknown, including in Nicotiana attenuata. We examined how the silencing of NaAGO1/2/4/7/and 10 by RNAi influenced plant-competitive ability under low-P conditions when they interact with AMF. Furthermore, the roles of seven miRNAs, predicted to regulate signaling and phosphate homeostasis, were evaluated by transient overexpression. Only NaAGO7 silencing by RNAi (irAGO7) significantly reduced the competitive ability under P-limited conditions, without changes in leaf or root development, or juvenile-to-adult phase transitions. In plants growing competitively in the glasshouse, irAGO7 roots were over-colonized with AMF, but they accumulated significantly less phosphate and the expression of their AMF-specific transporters was deregulated. Furthermore, the AMF-induced miRNA levels were inversely regulated with the abundance of their target transcripts. miRNA overexpression consistently decreased plant fitness, with four of seven-tested miRNAs reducing mycorrhization rates, and two increasing mycorrhization rates. Overexpression of Na-miR473 and Na-miRNA-PN59 downregulated targets in GA, ethylene, and fatty acid metabolism pathways. We infer that AGO7 optimizes competitive ability and colonization by regulating miRNA levels and signaling pathways during a plant's interaction with AMF.
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Affiliation(s)
- Maitree Pradhan
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Shree P Pandey
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
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13
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Liu X, Wu Q, Wu J, Liu J, Zheng F, Yu G, Hu H, Guo Z, Wu S, Li H, Shao W. Microglia-derived exosomal circZNRF1 alleviates paraquat-induced neuronal cell damage via miR-17-5p. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 263:115356. [PMID: 37591128 DOI: 10.1016/j.ecoenv.2023.115356] [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: 04/12/2023] [Revised: 07/19/2023] [Accepted: 08/09/2023] [Indexed: 08/19/2023]
Abstract
Paraquat (PQ) is an environmental poison that causes clinical symptoms similar to those of Parkinson's disease (PD) in vitro and in rodents. It can lead to the activation of microglia and apoptosis of dopaminergic neurons. However, the exact role and mechanism of microglial activation in PQ-induced neuronal degeneration remain unknown. Here, we isolated the microglia-derived exosomes exposed with 0 and 40 μM PQ, which were subsequently co-incubated with PQ-exposed neuronal cells to simulate intercellular communication. First, we found that exosomes released from microglia caused a change in neuronal cell vitality and reversed PQ-induced neuronal apoptosis. RNA sequencing data showed that these activated microglia-derived exosomes carried large amounts of circZNRF1. Moreover, a bioinformatics method was used to study the underlying mechanism of circZNRF1 in regulating PD, and miR-17-5p was predicted to be its target. Second, an increased Bcl2/Bax ratio could play an anti-apoptotic role. Bcl2 was predicted to be a downstream target of miR-17-5p. Our results showed that circZNRF1 plays an anti-apoptotic role by absorbing miR-17-5p and regulating the binding of Bcl2 after exosomes are internalized by dopaminergic neurons. In conclusion, we demonstrated a new intercellular communication mechanism between microglia and neurons, in which circZNRF1 plays a key role in protecting against PQ-induced neuronal apoptosis through miR-17-5p to regulate the biological process of PD. These findings may offer a novel approach to preventing and treating PD.
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Affiliation(s)
- Xu Liu
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Qingqing Wu
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Jingwen Wu
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Jianxi Liu
- College of Environmental and Resource Sciences, College of Carbon Neutral Modern Industry, Fujian Key Laboratory of Pollution Control & Resource Reuse, Fujian Normal University, Fuzhou 350007, China
| | - Fuli Zheng
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Guangxia Yu
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Hong Hu
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Zhenkun Guo
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Siying Wu
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Huangyuan Li
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
| | - Wenya Shao
- Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
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14
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Hua C, Xu Z, Tang N, Xu Y, Zhang Y, Li C. Identification of P450 Candidates Associated with the Biosynthesis of Physalin-Class Compounds in Physalis angulata. Int J Mol Sci 2023; 24:14077. [PMID: 37762378 PMCID: PMC10531436 DOI: 10.3390/ijms241814077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The Physalis genus has long been used as traditional medicine in the treatment of various diseases. Physalins, the characteristic class of compounds in this genus, are major bioactive constituents. To date, the biogenesis of physalins remains largely unknown, except for the recently established knowledge that 24-methyldesmosterol is a precursor of physalin. To identify the genes encoding P450s that are putatively involved in converting 24-methyldesmosterol to physalins, a total of 306 P450-encoding unigenes were retrieved from our recently constructed P. angulata transcriptome. Extensive phylogenetic analysis proposed 21 P450s that might participate in physalin biosynthesis. To validate the candidates, we developed a virus-induced gene silencing (VIGS) system for P. angulata, and four P450 candidates were selected for the VIGS experiments. The reduction in the transcripts of the four P450 candidates by VIGS all led to decreased levels of physalin-class compounds in the P. angulata leaves. Thus, this study provides a number of P450 candidates that are likely associated with the biosynthesis of physalin-class compounds, forming a strong basis to reveal the unknown physalin biosynthetic pathway in the future.
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Affiliation(s)
| | | | | | | | | | - Changfu Li
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai 200444, China; (C.H.); (Z.X.); (N.T.); (Y.X.); (Y.Z.)
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15
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Raruang Y, Omolehin O, Hu D, Wei Q, Promyou S, Parekattil LJ, Rajasekaran K, Cary JW, Wang K, Chen ZY. Targeting the Aspergillus flavus p2c gene through host-induced gene silencing reduces A. flavus infection and aflatoxin contamination in transgenic maize. FRONTIERS IN PLANT SCIENCE 2023; 14:1150086. [PMID: 37229129 PMCID: PMC10203651 DOI: 10.3389/fpls.2023.1150086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/11/2023] [Indexed: 05/27/2023]
Abstract
Aspergillus flavus is an opportunistic fungal pathogen that infects maize and produces aflatoxins. Using biocontrol or developing resistant cultivars to reduce aflatoxin contamination has only achieved limited success. Here, the A. flavus polygalacturonase gene (p2c) was targeted for suppression through host-induced gene silencing (HIGS) to reduce aflatoxin contamination in maize. An RNAi vector carrying a portion of the p2c gene was constructed and transformed into maize B104. Thirteen out of fifteen independent transformation events were confirmed to contain p2c. The T2 generation kernels containing the p2c transgene had less aflatoxin than those without the transgene in six out of eleven events we examined. Homozygous T3 transgenic kernels from four events produced significantly less aflatoxins (P ≤ 0.02) than the kernels from the null or B104 controls under field inoculation conditions. The F1 kernels from the crosses between six elite inbred lines with P2c5 and P2c13 also supported significantly less aflatoxins (P ≤ 0.02) than those from the crosses with null plants. The reduction in aflatoxin ranged from 93.7% to 30.3%. Transgenic leaf (T0 and T3) and kernel tissues (T4) were also found to have significantly higher levels of p2c gene-specific small RNAs. Further, homozygous transgenic maize kernels had significantly less fungal growth (27~40 fold) than the null control kernels 10 days after fungal inoculation in the field. The calculated suppression of p2c gene expression based on RNAseq data was 57.6% and 83.0% in P2c5 and P2c13 events, respectively. These results indicate clearly that the reduced aflatoxin production in the transgenic kernels is due to RNAi-based suppression of p2c expression, which results in reduced fungal growth and toxin production.
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Affiliation(s)
- Yenjit Raruang
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Olanike Omolehin
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Dongfang Hu
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Qijian Wei
- Food and Feed Safety Research Unit, United States Department of Agriculture – Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Surassawadee Promyou
- Faculty of Natural Resources and Agro-Industry, Kasetsart University, Sakonnakhon, Thailand
| | - Lidiya J. Parekattil
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Kanniah Rajasekaran
- Food and Feed Safety Research Unit, United States Department of Agriculture – Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Jeffrey W. Cary
- Food and Feed Safety Research Unit, United States Department of Agriculture – Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Zhi-Yuan Chen
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
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16
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Sharma M, Bhushan S, Sharma D, Kaul S, Dhar MK. A Brief Review of Plant Cell Transfection, Gene Transcript Expression, and Genotypic Integration for Enhancing Compound Production. Methods Mol Biol 2023; 2575:153-179. [PMID: 36301475 DOI: 10.1007/978-1-0716-2716-7_8] [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] [Indexed: 06/16/2023]
Abstract
Plants possess a plethora of important secondary metabolites, which are unique sources of natural pigments, pharmaceutical compounds, food additives, natural pesticides, and other industrial components. The commercial significance of such metabolites/compounds has directed the research toward their production and exploration of methods for enhancement of production. Biotechnological tools are critical in selecting, integrating, multiplying, improving, and analyzing medicinal plants for secondary metabolite production. Out of many techniques that are being explored to enhance secondary metabolite production, "plant cell transfection" is the latest tool to achieve maximum output from the plant source. It is based upon the introduction of foreign DNA into the plant cell relying on physical treatment such as electroporation, cell squeezing, sonoporation, optical transfection nanoparticles, magnetofection, and chemical treatment or biological treatment that depends upon carrier. One of the promising tools that have been exploited is CRISPR-Cas9. Overall, the abovementioned tools focus on the stable transfection of desired gene transcripts. Since the integration and continuous expression of transfected gene of particular trait represents stable transfection of host cell genome, resulting from transfer of required trait to daughter cells ultimately leading to enhanced production of secondary metabolites of interest. This chapter will review a set of biotechnological tools that are candidates for achieving the enhanced bioactive compound production indicated here to be used for drug discovery.
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Affiliation(s)
- Munish Sharma
- Department of Plant Sciences, Central University of Himachal Pradesh, Shahpur, Kangra, Himachal Pradesh, India.
| | - Sakshi Bhushan
- Department of Botany, Central University of Jammu, Jammu, Jammu and Kashmir, India
| | - Deepak Sharma
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Sanjana Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Manoj K Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India
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17
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Guo Y, Zhang K, Geng W, Chen B, Wang D, Wang Z, Tian W, Li H, Zhang Y, Jiang R, Li Z, Tian Y, Kang X, Liu X. Evolutionary analysis and functional characterization reveal the role of the insulin-like growth factor system in a diversified selection of chickens (Gallus gallus). Poult Sci 2022; 102:102411. [PMID: 36587453 PMCID: PMC9816805 DOI: 10.1016/j.psj.2022.102411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/22/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
The insulin-like growth factor (IGF) system plays an indispensable role in embryonic and postnatal development in mammals. However, the effects of the system on growth, carcass, and egg-laying traits, and diversified selection have not been systematically studied in chickens. In the present study, firstly the composition and gene structures of the chicken IGF system were investigated using phylogenetic tree and conserved synteny analysis. Then the effects of the genetic variations in the IGF system genes on breeding of specialized varieties were explored by principal component analysis. In addition, the spatiotemporal expression properties of the genes in this system were analyzed by RT-qPCR and the functions of the genes in egg production performance and growth were explored by association study. Moreover, the effects of IGF-binding proteins 3 (IGFBP3) on skeletal muscle development in chicken were investigated by cell cycle analysis, 5-ethynyl-2'-deoxyuridine (EdU) and Cell Counting Kit-8 (CCK-8) assays. The results showed that the chicken IGF system included 13 members which could be classified into 3 groups based on their amino acid sequences: IGF binding proteins 1 to 5 and 7 (IGFBP1-5 and 7) belonged to the first group; IGF 1 and 2 (IGF1 and IGF2), and IGF 1 and 2 receptor (IGF1R and IGF2R) belonged to the second group; and IGF2 binding proteins 1-3 (IGF2BP1-3) belonged to the third group. The IGF2BP1 and 3, and IGFBP2, 3, and 7 genes likely contributed more to the formation of both the specialized meat-type and egg-type lines, whereas IGFBP1 and 5 likely contributed more to the formation of the egg-type lines. The SNPs in the IGF2BP3 and IGFBP2 and 5 genes were significantly associated with egg number, and SNPs in the IGFBP3 promoter region were significantly associated with body weight, breast muscle weight and leg muscle weight. The IGFBP3 inhibited proliferation but promoted differentiation of chicken primary myoblasts (CPMs). These results provide insights into the roles of the IGF system in the diversified selection of chickens. The SNPs associated with egg-laying performance, growth, and carcass traits could be used as genetic markers for breeding selection of chickens in the future.
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Affiliation(s)
- Yulong Guo
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ke Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Wanzhuo Geng
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Botong Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Dandan Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhang Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Weihua Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China,International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
| | - Yanhua Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China,International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China,International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China,International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China,International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China,International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China; International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China.
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18
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De Saeger J, Park J, Thoris K, De Bruyn C, Chung HS, Inzé D, Depuydt S. IMPLANT: a new technique for transgene copy number estimation in plants using a single end-point PCR reaction. PLANT METHODS 2022; 18:132. [PMID: 36494670 PMCID: PMC9732982 DOI: 10.1186/s13007-022-00965-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Copy number determination is one of the first steps in the characterization of transgenic plant lines. The classical approach to this, Southern blotting, is time-consuming, expensive and requires massive amounts of high-quality genomic DNA. Other PCR-based techniques are either inaccurate, laborious, or expensive. RESULTS Here, we propose a new technique, IMPLANT (Insertion of competitive PCR calibrator for copy number estimation), a competitive PCR-based technique in which the competitor (based on an endogenous gene) is also incorporated in the T-DNA, which then gets integrated in the genome together with the gene of interest. As the number of integrated competitor molecules directly corresponds to the number of transgene copies, the transgene copy number can be determined by a single PCR reaction. We demonstrate that the results of this technique closely correspond with those obtained by segregation analysis in Arabidopsis and digital PCR In rice, indicating that it is a powerful alternative for other techniques for copy number determination. CONCLUSIONS We show that this technique is not only reliable, but is also faster, easier, and cheaper as compared with other techniques. Accurate results are obtained in both Arabidopsis and rice, but this technique can be easily extended to other organisms and as such can be widely adopted in the field of biotechnology.
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Affiliation(s)
- Jonas De Saeger
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon, 406-840, South Korea.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium.
| | - Jihae Park
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon, 406-840, South Korea
- Department of Marine Sciences, Incheon National University, Incheon, 406-840, South Korea
| | - Kai Thoris
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon, 406-840, South Korea
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands
| | - Charlotte De Bruyn
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon, 406-840, South Korea
| | - Hoo Sun Chung
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Stephen Depuydt
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon, 406-840, South Korea
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
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Latif A, Azam S, Shahid N, Javed MR, Haider Z, Yasmeen A, Sadaqat S, Shad M, Husnain T, Rao AQ. Overexpression of the AGL42 gene in cotton delayed leaf senescence through downregulation of NAC transcription factors. Sci Rep 2022; 12:21093. [PMID: 36473939 PMCID: PMC9727159 DOI: 10.1038/s41598-022-25640-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Premature leaf senescence negatively influences the physiology and yield of cotton plants. The conserved IDLNL sequence in the C-terminal region of AGL42 MADS-box determines its repressor potential for the down regulation of senescence-related genes. To determine the delay in premature leaf senescence, Arabidopsis AGL42 gene was overexpressed in cotton plants. The absolute quantification of transgenic cotton plants revealed higher mRNA expression of AGL42 compared to that of the non-transgenic control. The spatial expression of GUS fused with AGL42 and the mRNA level was highest in the petals, abscission zone (flower and bud), 8 days post anthesis (DPA) fiber, fresh mature leaves, and senescenced leaves. The mRNA levels of different NAC senescence-promoting genes were significantly downregulated in AGL42 transgenic cotton lines than those in the non-transgenic control. The photosynthetic rate and chlorophyll content were higher in AGL42 transgenic cotton lines than those in the non-transgenic control. Fluorescence in situ hybridization of the AG3 transgenic cotton line revealed a fluorescent signal on chromosome 1 in the hemizygous form. Moreover, the average number of bolls in the transgenic cotton lines was significantly higher than that in the non-transgenic control because of the higher retention of floral buds and squares, which has the potential to improve cotton fiber yield.
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Affiliation(s)
- Ayesha Latif
- grid.11173.350000 0001 0670 519XCentre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Saira Azam
- grid.11173.350000 0001 0670 519XCentre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Naila Shahid
- grid.11173.350000 0001 0670 519XCentre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Muhammad R. Javed
- grid.411786.d0000 0004 0637 891XDepartment of Bioinformatics and Biotechnology, Government College University Faisalabad, (GCUF), Allama Iqbal Road, Faisalabad, 38000 Pakistan
| | - Zeshan Haider
- grid.411786.d0000 0004 0637 891XDepartment of Bioinformatics and Biotechnology, Government College University Faisalabad, (GCUF), Allama Iqbal Road, Faisalabad, 38000 Pakistan
| | - Aneela Yasmeen
- grid.11173.350000 0001 0670 519XCentre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Sahar Sadaqat
- grid.11173.350000 0001 0670 519XCentre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Mohsin Shad
- grid.11173.350000 0001 0670 519XCentre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Tayyab Husnain
- grid.11173.350000 0001 0670 519XCentre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Abdul Q. Rao
- grid.11173.350000 0001 0670 519XCentre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
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20
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Shahbazi M, Tohidfar M, Aliniaeifard S, Yazdanpanah F, Bosacchi M. Transgenic tobacco co-expressing flavodoxin and betaine aldehyde dehydrogenase confers cadmium tolerance through boosting antioxidant capacity. PROTOPLASMA 2022; 259:965-979. [PMID: 34686944 DOI: 10.1007/s00709-021-01714-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
Excessive heavy metal (HM) levels in soil have become a source of concern due to their adverse effects on human health and the agriculture industry. Soil contamination by HMs leads to an accumulation of reactive oxygen species (ROSs) within the plant cell and disruption of photosynthesis-related proteins. The response of tobacco lines overexpressing flavodoxin (Fld) and betaine aldehyde dehydrogenase (BADH) to cadmium (Cd) toxicity was investigated in this study. PCR results demonstrated the expected amplicon length of each gene in the transgenic lines. Absolute qRT-PCR demonstrates a single copy of T-DNA integration into each transgenic line. Relative qRT-PCR confirmed overexpression of Fld and BADH in transgenic lines. The maximum quantum yield of photosystem II (Fv/Fm) was measured under Cd toxicity stress and revealed that transgenic lines had a higher Fv/Fm than wild-type (WT) plants. Accumulation of proline, glycine betaine (GB), and higher activity of antioxidant enzymes alongside lower levels of malondialdehyde (MDA) and hydrogen peroxide (H2O2) was indicative of a robust antioxidant system in transgenic plants. Therefore, performing a loop in reducing the ROS produced in the photosynthesis electron transport chain and stimulating the ROS scavenger enzyme activity improved the plant tolerance to Cd stress.
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Affiliation(s)
- Mehrdad Shahbazi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, 1983969411, Tehran, Iran
| | - Masoud Tohidfar
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, 1983969411, Tehran, Iran.
| | - Sasan Aliniaeifard
- Photosynthesis Laboratory, Department of Horticulture, Aburaihan Campus, University of Tehran, 1417935840, Tehran, Iran
| | - Farzaneh Yazdanpanah
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, 1983969411, Tehran, Iran
| | - Massimo Bosacchi
- Park at the, Danforth Plant Science Center, KWS Gateway Research Center, LLC, BRDG, Saint Louis, MO, USA
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21
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Fan W, Wang L, Chu J, Li H, Kim EY, Cho J. Tracing Mobile DNAs: From Molecular to Population Scales. FRONTIERS IN PLANT SCIENCE 2022; 13:837378. [PMID: 35178063 PMCID: PMC8843828 DOI: 10.3389/fpls.2022.837378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Transposable elements (TEs, transposons) are mobile DNAs that are prevalent in most eukaryotic genomes. In plants, their mobility has vastly contributed to genetic diversity which is essential for adaptive changes and evolution of a species. Such mobile nature of transposon has been also actively exploited in plant science research by generating genetic mutants in non-model plant systems. On the other hand, transposon mobilization can bring about detrimental effects to host genomes and they are therefore mostly silenced by the epigenetic mechanisms. TEs have been studied as major silencing targets and acted a main feature in the remarkable growth of the plant epigenetics field. Despite the importance of transposon in plant biology and biotechnology, their mobilization and the underlying mechanisms are largely left unanswered. This is mainly because of the sequence repetitiveness of transposons, which makes their detection and analyses difficult and complicated. Recently, some attempts have been made to develop new experimental methods detecting active transposons and their mobilization behavior. These techniques reveal TE mobility in various levels, including the molecular, cellular, organismal and population scales. In this review, we will highlight the novel technical approaches in the study of mobile genetic elements and discuss how these techniques impacted on the advancement of transposon research and broadened our understanding of plant genome plasticity.
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Affiliation(s)
- Wenwen Fan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ling Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Chu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hui Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Eun Yu Kim
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Chinese Academy of Sciences, Shanghai, China
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22
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He QR, Cong M, Yu FH, Ji YH, Yu S, Shi HY, Ding F. Peripheral nerve fibroblasts secrete neurotrophic factors to promote axon growth of motoneurons. Neural Regen Res 2022; 17:1833-1840. [PMID: 35017446 PMCID: PMC8820717 DOI: 10.4103/1673-5374.332159] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Peripheral nerve fibroblasts play a critical role in nerve development and regeneration. Our previous study found that peripheral nerve fibroblasts have different sensory and motor phenotypes. Fibroblasts of different phenotypes can guide the migration of Schwann cells to the same sensory or motor phenotype. In this study, we analyzed the different effects of peripheral nerve-derived fibroblasts and cardiac fibroblasts on motoneurons. Compared with cardiac fibroblasts, peripheral nerve fibroblasts greatly promoted motoneuron neurite outgrowth. Transcriptome analysis results identified 491 genes that were differentially expressed in peripheral nerve fibroblasts and cardiac fibroblasts. Among these, 130 were significantly upregulated in peripheral nerve fibroblasts compared with cardiac fibroblasts. These genes may be involved in axon guidance and neuron projection. Three days after sciatic nerve transection in rats, peripheral nerve fibroblasts accumulated in the proximal and distal nerve stumps, and most expressed brain-derived neurotrophic factor. In vitro, brain-derived neurotrophic factor secreted from peripheral nerve fibroblasts increased the expression of β-actin and F-actin through the extracellular regulated protein kinase and serine/threonine kinase pathways, and enhanced motoneuron neurite outgrowth. These findings suggest that peripheral nerve fibroblasts and cardiac fibroblasts exhibit different patterns of gene expression. Peripheral nerve fibroblasts can promote motoneuron neurite outgrowth.
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Affiliation(s)
- Qian-Ru He
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
| | - Meng Cong
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
| | - Fan-Hui Yu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
| | - Yu-Hua Ji
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
| | - Shu Yu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
| | - Hai-Yan Shi
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
| | - Fei Ding
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
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23
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Kanwar P, Ghosh S, Sanyal SK, Pandey GK. Identification of Gene Copy Number in the Transgenic Plants by Quantitative Polymerase Chain Reaction (qPCR). Methods Mol Biol 2022; 2392:161-171. [PMID: 34773622 DOI: 10.1007/978-1-0716-1799-1_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Transgenic events are defined as exogenous DNA insertion in the genome through genetic transformation. It is a powerful means for the improvement of crop plants and to understand the gene function. Multiple DNA insertion events may occur at one or several chromosomal locations. One of the important tasks, after validation of the transformation of transgenic plants, is the identification of single copy in the transgenic. This means the insertion of exogenous DNA fragment only in a single locus in the genome. Southern blot hybridization is a convincing and reliable method, for estimation of copy number in transgenic lines but it is cumbersome and time-consuming process. One of the other well-known methods is quantitative polymerase chain reactions (qPCR), a simple and rapid method to identify copy number from a population of independent transgenic lines. In comparison to the Southern hybridization method, qPCR is simpler to perform, requires less DNA, lesser time and does not require any labeled probes. This method utilizes specific primers to amplify target transgenes and endogenous reference genes. Designing an appropriate and specific primer pair is a very crucial part of the estimation of the gene copy number. In this chapter, we have illustrated a detailed methodology for identification of the gene copy of the transgenic plants.
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Affiliation(s)
- Poonam Kanwar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Soma Ghosh
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Sibaji K Sanyal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Girdhar K Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India.
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24
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High-Throughput and Accurate Determination of Transgene Copy Number and Zygosity in Transgenic Maize: From DNA Extraction to Data Analysis. Int J Mol Sci 2021; 22:ijms222212487. [PMID: 34830369 PMCID: PMC8619409 DOI: 10.3390/ijms222212487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/10/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
It is vital to develop high-throughput methods to determine transgene copy numbers initially and zygosity during subsequent breeding. In this study, the target sequence of the previously reported endogenous reference gene hmg was analyzed using 633 maize inbred lines, and two SNPs were observed. These SNPs significantly increased the PCR efficiency, while the newly developed hmg gene assay (hmg-taq-F2/R2) excluding these SNPs reduced the efficiency into normal ranges. The TaqMan amplification efficiency of bar and hmg with newly developed primers was calculated as 0.993 and 1.000, respectively. The inter-assay coefficient of variation (CV) values for the bar and hmg genes varied from 1.18 to 2.94%. The copy numbers of the transgene bar using new TaqMan assays were identical to those using dPCR. Significantly, the precision of one repetition reached 96.7% of that of three repetitions of single-copy plants analyzed by simple random sampling, and the actual accuracy reached 95.8%, confirmed by T1 and T2 progeny. With the high-throughput DNA extraction and automated data analysis procedures developed in this study, nearly 2700 samples could be analyzed within eight hours by two persons. The combined results suggested that the new hmg gene assay developed here could be a universal maize reference gene system, and the new assay has high throughput and high accuracy for large-scale screening of maize varieties around the world.
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25
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MiR-29b-1-5p regulates the proliferation and differentiation of chicken primary myoblasts and analysis of its effective targets. Poult Sci 2021; 101:101557. [PMID: 34852967 PMCID: PMC8639469 DOI: 10.1016/j.psj.2021.101557] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/05/2021] [Accepted: 10/14/2021] [Indexed: 12/19/2022] Open
Abstract
Several recent studies investigated the role of the miR-29 family in muscle development. However, only a few studies focused on chicken skeletal muscle. In the present study, cell cycle, 5-ethynyl-2'-deoxyuridine (EdU), cell counting kit-8 (CCK-8), and other assays indicated that miR-29b-1-5p can inhibit the proliferation of chicken primary myoblasts (CPMs); the western blot assay and immunofluorescence detection of MYHC demonstrated that miR-29b-1-5p can promote the differentiation of myoblasts. The functional enrichment analysis revealed that the target genes of miR-29b-1-5p may be involved in muscle tissue development, muscle organ development, and striated muscle tissue development, which are biological processes related to muscle development. The correlation analysis showed that these 6 genes, that is, ankyrin repeat domain 9 (ANKRD9), lactate dehydrogenase A (LDHA), transcription factor 12 (TCF12), FAT atypical cadherin 1 (FAT1), lin-9 homolog (LIN9), and integrin beta 3 binding protein (ITGB3BP), can be used as effective candidate target genes of miR-29b-1-5p. Moreover, miR-29b-1-5p inhibits the expression of ANKRD9 by directly binding the 3'UTR of ANKRD9. Overall, these data indicate that miR-29b-1-5p inhibits the proliferation of primary chicken myoblasts, stimulates their differentiation, and is involved in the process of muscle development and that its effective target gene is ANKRD9. This study identified the molecular mechanism of miR-29b-1-5p in chicken muscle development.
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Cai YM, Dudley QM, Patron NJ. Measurement of Transgene Copy Number in Plants Using Droplet Digital PCR. Bio Protoc 2021; 11:e4075. [PMID: 34327272 PMCID: PMC8292117 DOI: 10.21769/bioprotoc.4075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 11/02/2022] Open
Abstract
Transgenic plants are produced both to investigate gene function and to confer desirable traits into crops. Transgene copy number is known to influence expression levels, and consequently, phenotypes. Similarly, knowledge of transgene zygosity is desirable for making quantitative assessments of phenotype and tracking the inheritance of transgenes in progeny generations. Since the first transgenic plants were produced, several methods for determining copy number have been applied, including Southern blotting, quantitative real-time PCR, and more recently, sequencing methods; however, each method has specific disadvantages, compromising throughput, accuracy, or expense. Digital PCR (dPCR) divides reactions into partitions, converting the exponential, analogue nature of PCR into a linear, digital signal that allows the frequency of occurrence of specific sequences to be accurately estimated. Confidence increases with the number of partitions; therefore, the availability of emulsion technologies that enable reactions to be divided into tens of thousands of nanodroplets allows accurate determination of copy number in what has become known as digital droplet PCR (ddPCR). ddPCR offers similar benefits of low costs and scalability as other PCR techniques but with superior accuracy and reliability. Graphic abstract: Digital PCR (dPCR) divides reactions into partitions, converting the exponential, analogue nature of PCR into a linear, digital signal that allows the frequency of transgene copy number to be accurately assessed.
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Affiliation(s)
- Yao-Min Cai
- Earlham Institute, Norwich Research Park, Colney lane, Norwich, UK
| | | | - Nicola J. Patron
- Earlham Institute, Norwich Research Park, Colney lane, Norwich, UK
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Liu R, Long Q, Zou X, Wang Y, Pei Y. DNA methylation occurring in Cre-expressing cells inhibits loxP recombination and silences loxP-sandwiched genes. THE NEW PHYTOLOGIST 2021; 231:210-224. [PMID: 33742463 DOI: 10.1111/nph.17353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
The low DNA recombination efficiency of site-specific recombinase systems in plants limits their application; however, the underlying mechanism is unknown. We evaluate the gene deletion performance of four recombinase systems (Cre/loxP, Flp/FRT, KD/KDRT and B3/B3RT) in tobacco where the recombinases are under the control of germline-specific promoters. We find that the expression of these recombinases results mostly in gene silencing rather than gene deletion. Using the Cre/loxP system as a model, we reveal that the region flanked by loxP sites (floxed) is hypermethylated, which prevents floxed genes from deletion while silencing the expression of the genes. We further show CG methylation alone in the recombinase binding element of the loxP site is unable to impede gene deletion; instead, CHH methylation in the crossover region is required to inhibit loxP recombination. Our study illustrates the important role of recombinase-induced DNA methylation in the inhibition of site-specific DNA recombination and uncovers the mechanism underlying recombinase-associated gene silence in plants.
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Affiliation(s)
- Ruochen Liu
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Qin Long
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Xiuping Zou
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - You Wang
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Yan Pei
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
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Ren L, Guo L, Kou N, Lv J, Wang Z, Yang K. LncRNA LINC00963 promotes osteogenic differentiation of hBMSCs and alleviates osteoporosis progression by targeting miRNA-760/ETS1 axis. Autoimmunity 2021; 54:313-325. [PMID: 34184952 DOI: 10.1080/08916934.2021.1922890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Although long non-coding RNA LINC00963 has been reported to play a crucial regulatory role in osteoporosis (OP), its specific mechanism has not been well studied. Cell viability of human bone marrow mesenchymal stem cells (hBMSCs) transfected with short hairpin RNA targeting LINC00963 (sh-LINC00963) and negative control (sh-NC) was analysed by cell counting kit-8 (CCK-8) assay. Alkaline phosphatase (ALP) activity in hBMSCs transfected with sh-LINC00963 and sh-NC after induction by osteogenic medium (OM) on day 7 was detected. The protein expression levels of osteocalcin (OCN) and osteopontin (OPN) in hBMSCs transfected with sh-LINC00963 and sh-NC during OM induction on day 3 were detected by western blot. The relationship among LINC00963, miR-760, and E26 transformation specific-1 (ETS1) was determined by bioinformatics analysis, luciferase reporter assay, and RNA-binding protein immunoprecipitation (RIP) assay. A rat model with OP was established to confirm the role of LINC00963 in vivo. The expression level of LINC00963 was much lower in hBMSCs isolated from the discarded femoral head tissues of OP patients compared with that in health patients. Meanwhile, the expression level of LINC00963 was significantly increased and the expression level of miR-760 was decreased in hBMSCs during osteogenic induction. LINC00963 could bind to the 3'-untranslated region (3'-UTR) of miR-760 and negatively regulate the expression of miR-760, then promote the osteogenic differentiation in hBMSCs. ETS1 was identified as a target of miR-760. Moreover, overexpression of LINC00963 obviously reduced bone mineral density (BMD) of the left femur in OP rats and alleviated OP progression in vivo. Our results demonstrated that LINC00963 positively regulated the expression of ETS1 by directly targeting miR-760, and then promoted osteogenic differentiation of hBMSCs in vitro, and also attenuated OP progression in vivo, suggesting that LINC00963 might be a potential therapeutic target for OP.
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Affiliation(s)
- Lirong Ren
- Department of Spine Surgery, The First Affiliated Hospital of Dali University, Dali City, PR China
| | - Limin Guo
- Department of Traumatology, The Second Affiliated Hospital of Kunming Medical University, Kunming City, PR China
| | - Nannan Kou
- Department of Traumatology, The Second Affiliated Hospital of Kunming Medical University, Kunming City, PR China
| | - Jia Lv
- Department of Traumatology, The Second Affiliated Hospital of Kunming Medical University, Kunming City, PR China
| | - Zhihua Wang
- Department of Traumatology, The Second Affiliated Hospital of Kunming Medical University, Kunming City, PR China
| | - Kaishun Yang
- Department of Spine Surgery, The First Affiliated Hospital of Dali University, Dali City, PR China
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Tang H, Shi X, Zhu P, Guo W, Li J, Yan B, Zhang S. Melatonin inhibits gallbladder cancer cell migration and invasion via ERK-mediated induction of epithelial-to-mesenchymal transition. Oncol Lett 2021; 22:609. [PMID: 34188711 PMCID: PMC8227585 DOI: 10.3892/ol.2021.12870] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/19/2021] [Indexed: 12/13/2022] Open
Abstract
Melatonin is a naturally occurring molecule secreted by the pineal gland that exhibits antitumor properties and prevents the development of human cancer. However, little is known regarding the effects of melatonin on gallbladder cancer (GBC) cells. The present study aimed to investigate the role of melatonin on the prevention of GBC cell invasion. The GBC cell line, GBC-SD, was treated with different concentrations of melatonin for different time periods, and the data indicated that melatonin markedly inhibited the invasion of GBC cells. Following treatment of GBC cells with melatonin, the protein levels of the epithelial marker, E-cadherin, significantly increased, while the expression levels of the mesenchymal markers, N-cadherin, Snail and vimentin, notably decreased. In addition, melatonin inhibited the phosphorylation of ERK1/2. Following treatment of the cells with the ERK activator, tert-Butylhydroquinone, the anti-invasive effects of melatonin were reversed by rescuing epithelial-to-mesenchymal transition in GBC cells. Taken together, these results suggest that melatonin inhibits GBC invasiveness by blocking the ERK signaling pathway. Thus, melatonin may be used as a potential novel cancer therapeutic drug for the treatment of GBC.
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Affiliation(s)
- Hongwei Tang
- ZhengZhou Engineering Laboratory of Organ Transplantation Technique and Application, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Henan Engineering Technology Research Center of Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Xiaoyi Shi
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Pengfei Zhu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Jie Li
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Bing Yan
- ZhengZhou Engineering Laboratory of Organ Transplantation Technique and Application, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Henan Engineering Technology Research Center of Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Shuijun Zhang
- ZhengZhou Engineering Laboratory of Organ Transplantation Technique and Application, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Henan Engineering Technology Research Center of Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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Digital PCR (dPCR) and qPCR mediated determination of transgene copy number in the forage legume white clover (Trifolium repens). Mol Biol Rep 2021; 48:3069-3077. [PMID: 33864179 DOI: 10.1007/s11033-021-06354-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
Obtaining data on transgene copy number is an integral step in the generation of transgenic plants. Techniques such as Southern blot, segregation analysis, and quantitative PCR (qPCR) have routinely been used for this task, in a range of species. More recently, use of Digital PCR (dPCR) has become prevalent, with a measurement accuracy higher than qPCR reported. Here, the relative merits of qPCR and dPCR for transgene copy number estimation in white clover were investigated. Furthermore, given that single copy reference genes are desirable for estimating gene copy number by relative quantification, and that no single-copy genes have been reported in this species, a search and evaluation of suitable reference genes in white clover was undertaken. Results demonstrated a higher accuracy of dPCR relative to qPCR for copy number estimation in white clover. Two genes, Pyruvate dehydrogenase (PDH), and an ATP-dependent protease, identified as single-copy genes, were used as references for copy number estimation by relative quantification. Identification of single-copy genes in white clover will enable the application of relative quantification for copy number estimation of other genes or transgenes in the species. The results generated here validate the use of dPCR as a reliable strategy for transgene copy number estimation in white clover, and provide resources for future copy number studies in this species.
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Kumar A, Jaiwal R, Sreevathsa R, Chaudhary D, Jaiwal PK. Transgenic cowpea plants expressing Bacillus thuringiensis Cry2Aa insecticidal protein imparts resistance to Maruca vitrata legume pod borer. PLANT CELL REPORTS 2021; 40:583-594. [PMID: 33471196 DOI: 10.1007/s00299-020-02657-2] [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: 09/17/2020] [Accepted: 12/29/2020] [Indexed: 05/26/2023]
Abstract
Fertile independent transgenic cowpea lines expressing the BtCry2Aa toxin with increased resistance to the most devastating lepidopteran insect pest, Maruca pod borer has been developed for the first time. Cowpea is a staple legume important for food and nutritional security in sub-Saharan Africa and Asia, where its production is limited by the key pest, legume pod borer (Maruca vitrata). Cowpea varieties resistant to M. vitrata are not known, hence, development of Maruca pod borer resistance cowpea through genetic engineering is a promising approach to improve its production. In the present study, transgenic cowpea plants expressing Bacillus thuringiensis Cry2Aa insecticidal protein were developed for the first time using Agrobacterium tumefaciens-mediated transformation of cotyledonary explants. T0 plants recovered from Agrobacterium cocultured explants on medium containing 120 mgl-1 of kanamycin were identified on the basis of the presence of transgenes by PCR, their integration into genome by Southern hybridization and expression of their transcripts by semi quantitative PCR (sqRT-PCR) and quantitative Real-time-PCR (qRT-PCR) and protein by Western blot analysis. The transformation efficiency obtained was 3.47% with 11 independent T0 transgenic lines. The bioefficacy of Cry2Aa protein expressed in randomly selected four T0 plant's leaves and pods was evaluated by feeding Maruca pod borer demonstrated a significant lower damage and a high level of Maruca mortality (more than 90%) for all these Bt lines. The inheritance of transgenes from T0 to T1 progeny plants was demonstrated by PCR analysis. The transgenic plants generated in this study can be used in cowpea breeding program for durable and sustainable legume pod borer resistance.
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Affiliation(s)
- Anil Kumar
- Centre for Biotechnology, M. D. University, Rohtak, 124001, India
| | - Ranjana Jaiwal
- Department of Zoology, M. D. University, Rohtak, 124001, India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, IARI, New Delhi, 110012, India
| | | | - Pawan K Jaiwal
- Centre for Biotechnology, M. D. University, Rohtak, 124001, India.
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Wang F, Zhang Q, Zhang H, Qiao X, Zhang X, Zhang K, Gu X, Wang L, Cui J. MUC16 promotes EOC proliferation by regulating GLUT1 expression. J Cell Mol Med 2021; 25:3031-3040. [PMID: 33543559 PMCID: PMC7957195 DOI: 10.1111/jcmm.16345] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 01/09/2021] [Indexed: 01/24/2023] Open
Abstract
As a common malignancy in females with a higher incidence rate, epithelial ovarian cancer (EOC) is a heterogeneous disease with complexity and diversity in histology and therapeutic response. Although great progress has been made in diagnosis and therapeutic strategies, novel therapeutic strategies are required to improve survival. Although the promoting effect of mucin 16 (MUC16) on tumour progression has been reported, the potential mechanisms remain unclear. In our study, we reported that overexpression of MUC16 was significantly related to cell proliferation and disease progression in EOC. Results from clinical specimen analysis and cell experiment support this conclusion. Patients with a high MUC16 expression usually had a worse prognosis that those with a low expression. Cell proliferation ability was significantly decreased in EOC cell lines when the knockdown of MUC16. Further study shows that the function of MUC16 in cell proliferation is based on the regulation of glucose transporter 1 (GLUT1) expression. MUC16 can control glucose uptake by regulating GLUT1 in EOC cells, thereby promoting glycogen synthesis, so that tumour cells produce more energy for proliferation. This conclusion is based on two findings. First, the significant correlation between MUC16 and GLUT1 was verified by clinical specimen and TCGA data analysis. Then, alteration of MUC16 expression levels can affect the expression of GLUT1 and glucose uptake was also verified. Finally, this conclusion is further verified in vivo by tumour‐bearing mice model. To summarize, our results suggest that MUC16 promotes EOC proliferation and disease progression by regulating GLUT1 expression.
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Affiliation(s)
- Fang Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qing Zhang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hailing Zhang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaogai Qiao
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xia Zhang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ke Zhang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoli Gu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lihong Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinquan Cui
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Yue G, Tang J, Zhang L, Niu H, Li H, Luo S. CD276 suppresses CAR-T cell function by promoting tumor cell glycolysis in esophageal squamous cell carcinoma. J Gastrointest Oncol 2021; 12:38-51. [PMID: 33708423 DOI: 10.21037/jgo-21-50] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background As an immune checkpoint that suppresses antitumor immunity, CD276 is a potential therapeutic target for cancer immunotherapy. However, the role of CD276 in esophageal squamous cell carcinoma (ESCC) has not been thoroughly examined. A greater understanding of the regulatory mechanism of CD276 may improve the clinical response and efficacy of cancer immunotherapy. Methods The expression of CD276 was measured by qRT-PCR, IHC and flow cytometry analysis. T cell infiltration in ESCC was measured by qRT-PCR and immunofluorescence analysis. The regulation function of CD276 in glucose metabolism was examined by metabolism assays, western blotting and small molecule inhibitors. Transfection was used for gene editing. The oncogenic function of CD276 was examined in vivo by CAR-T cell therapy model. Results Based on our findings, CD276 regulated the expression of the PKM2 gene in ESCC. Overexpression of CD276 induced the phosphorylation of PKM2 by the STAT3 signalling pathway to promote glucose metabolism in tumors. The accumulation of lactic acid in the tumor microenvironment has been reported to regulate the immune cells, particularly CD8+ T cells. We further analyzed the effect of CD276 on the function of T cells. Chimeric antigen receptor T cells (CAR-T) targeting human epidermal growth factor receptor 2 (HER2) were used as effector cells to detect the effect of CD276 on immunotherapy. The therapeutic effects of CAR-T cells were markedly limited by CD276 overexpression. Conclusions Our results are the first to show that tumor-derived CD276 supports disease progression. Overexpression of CD276 promoted glucose metabolism in tumor and inhibited the function of CD8+ T cells. Therefore, strategies targeting CD276 might improve the response to cancer immunotherapy of ESCC patients.
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Affiliation(s)
- Guangxing Yue
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Jingwen Tang
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Lihan Zhang
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Hong Niu
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Huahua Li
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Suxia Luo
- Department of Medicine Oncology, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
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Wang XJ, Jiao Y, Ma S, Yang JT, Wang ZX. Whole-Genome Sequencing: An Effective Strategy for Insertion Information Analysis of Foreign Genes in Transgenic Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:573871. [PMID: 33335534 PMCID: PMC7736074 DOI: 10.3389/fpls.2020.573871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/27/2020] [Indexed: 06/12/2023]
Abstract
Molecular characterization is a key step in the risk assessment of genetically modified organisms (GMOs) for regulatory approval. Herein, we describe a method for analyzing copy number, insertion loci, and flanking sequences through whole-genome sequencing (WGS) and bioinformatics. Comprehensive molecular characterization of G2-6 transgenic rice was performed using this pipeline. The results showed that one copy of the foreign gene was inserted into rice chromosome 8. There was no vector backbone insertion but an unexpected insertion and DNA rearrangement at the 3' end of the T-DNA. We also obtained the 5' and 3' flanking sequences of the T-DNA. Our results suggested that the use of a combination of WGS and bioinformatics is an effective strategy for the molecular characterization of GMOs.
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Affiliation(s)
- Xu-jing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences/MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Beijing China
| | - Yue Jiao
- Development Center for Science and Technology/MARA, Beijing, China
| | - Shuo Ma
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences/MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Beijing China
| | - Jiang-tao Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences/MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Beijing China
| | - Zhi-xing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences/MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Beijing China
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Ectopic expression of WsMBP1 from Withania somnifera in transgenic tobacco shows insecticidal activity against teak defoliator Hyblaea puera (Lepidoptera: Hyblaeidae). Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00531-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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36
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Estrada-Rivera M, Hernández-Oñate MÁ, Dautt-Castro M, Gallardo-Negrete JDJ, Rebolledo-Prudencio OG, Uresti-Rivera EE, Arenas-Huertero C, Herrera-Estrella A, Casas-Flores S. IPA-1 a Putative Chromatin Remodeler/Helicase-Related Protein of Trichoderma virens Plays Important Roles in Antibiosis Against Rhizoctonia solani and Induction of Arabidopsis Systemic Disease Resistance. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:808-824. [PMID: 32101077 DOI: 10.1094/mpmi-04-19-0092-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Trichoderma spp. are filamentous fungi that colonize plant roots conferring beneficial effects to plants, either indirectly through the induction of their defense systems or directly through the suppression of phytopathogens in the rhizosphere. Transcriptomic analyses of Trichoderma spp. emerged as a powerful method for identifying the molecular events underlying the establishment of this beneficial relationship. Here, we focus on the transcriptomic response of Trichoderma virens during its interaction with Arabidopsis seedlings. The main response of T. virens to cocultivation with Arabidopsis was the repression of gene expression. The biological processes of transport and metabolism of carbohydrates were downregulated, including a set of cell wall-degrading enzymes putatively relevant for root colonization. Repression of such genes reached their basal levels at later times in the interaction, when genes belonging to the biological process of copper ion transport were induced, a necessary process providing copper as a cofactor for cell wall-degrading enzymes with the auxiliary activities class. RNA-Seq analyses showed the induction of a member of the SNF2 family of chromatin remodelers/helicase-related proteins, which was named IPA-1 (increased protection of Arabidopsis-1). Sequence analyses of IPA-1 showed its closest relatives to be members of the Rad5/Rad16 and SNF2 subfamilies; however, it grouped into a different clade. Although deletion of IPA-1 in T. virens did not affect its growth, the antibiotic activity of Δipa-1 culture filtrates against Rhizoctonia solani diminished but it remained unaltered against Botrytis cinerea. Triggering of the plant defense genes in plants treated with Δipa-1 was higher, showing enhanced resistance against Pseudomonas syringae but not against B. cinerea as compared with the wild type.
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Affiliation(s)
- Magnolia Estrada-Rivera
- IPICYT, División de Biología Molecular, Camino a la presa San José No. 2055, Colonia Lomas 4a sección, C.P. 78216, San Luis Potosí, Mexico
| | - Miguel Ángel Hernández-Oñate
- CONACYT-Centro de Investigación en Alimentación y Desarrollo, Carretera Gustavo Enrique Astiazarán Rosas No. 46, La Victoria, C.P. 83304. Hermosillo, Sonora, Mexico
| | - Mitzuko Dautt-Castro
- IPICYT, División de Biología Molecular, Camino a la presa San José No. 2055, Colonia Lomas 4a sección, C.P. 78216, San Luis Potosí, Mexico
| | - José de Jesús Gallardo-Negrete
- IPICYT, División de Biología Molecular, Camino a la presa San José No. 2055, Colonia Lomas 4a sección, C.P. 78216, San Luis Potosí, Mexico
| | | | - Edith Elena Uresti-Rivera
- Facultad de Ciencias Químicas, Departamento de Inmunología y Biología Celular y Molecular, Universidad Autónoma de San Luis Potosí, Av. Salvador Nava s/n, Zona Universitaria, 78290, San Luis Potosí, Mexico
| | - Catalina Arenas-Huertero
- Facultad de Ciencias, Universidad Autónoma de San Luis Potosí, Av. Chapultepec No. 1570. Priv. del Pedregal 78295, San Luis Potosí, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV-Irapuato, C.P. 36824, Irapuato, Gto., México
| | - Sergio Casas-Flores
- IPICYT, División de Biología Molecular, Camino a la presa San José No. 2055, Colonia Lomas 4a sección, C.P. 78216, San Luis Potosí, Mexico
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Yuan S, Zhang R, Cao Y, Guo J, Xian M, Liu W. New expression system to increase the yield of phloroglucinol. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1764386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Shan Yuan
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Rubing Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong, PR China
| | - Yujin Cao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong, PR China
| | - Jing Guo
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong, PR China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong, PR China
| | - Wei Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong, PR China
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Raruang Y, Omolehin O, Hu D, Wei Q, Han ZQ, Rajasekaran K, Cary JW, Wang K, Chen ZY. Host Induced Gene Silencing Targeting Aspergillus flavus aflM Reduced Aflatoxin Contamination in Transgenic Maize Under Field Conditions. Front Microbiol 2020; 11:754. [PMID: 32411110 PMCID: PMC7201132 DOI: 10.3389/fmicb.2020.00754] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 03/30/2020] [Indexed: 11/13/2022] Open
Abstract
Maize (Zea mays L.) is one of the major crops susceptible to Aspergillus flavus infection and subsequent contamination with aflatoxins, the most potent naturally produced carcinogenic secondary metabolites. This pathogen can pose serious health concerns and cause severe economic losses due to the Food and Drug Administration (FDA) regulations on permissible levels of aflatoxins in food and feed. Although biocontrol has yielded some successes in managing aflatoxin contamination, enhancing crop resistance is still the preferred choice of management for long-term sustainability. Hence, host induced gene silencing (HIGS) strategy was explored in this study. The A. flavus gene aflM encoding versicolorin dehydrogenase, a key enzyme involved in the aflatoxin biosynthetic pathway, was selected as a possible target for suppression through HIGS. An RNAi vector containing a portion of the aflM gene was constructed and introduced into immature B104 maize zygotic embryos through Agrobacterium transformation. PCR analysis of the genomic DNA from T0 leaf tissue confirmed the presence of the transgene in six out of the seven events. The seeds from the lines that showed reduced aflatoxin production in laboratory aflatoxin kernel screening assay (KSA) have been increased from T1 to T4 generation in the past four years. Changes in aflatoxin resistance in these transgenic kernels have been evaluated under both field and laboratory conditions. The T2 generation kernels containing the transgene from two events out of four examined had less aflatoxin (P ≤ 0.01 and P ≤ 0.08) than those without the transgene. Field-inoculated homozygous T3 and T4 transgenic kernels also revealed lower levels of aflatoxins (P ≤ 0.04) than kernels from the null (segregated non-transgenic samples) or B104 controls. A similar result was observed when the harvested T3 and T4 homozygous transgenic kernels were evaluated under KSA conditions without inoculation (P ≤ 0.003–0.05). These two events were crossed with LH195, LH197, LH210, and PHW79 elite breeding lines and the resulting crosses supported less aflatoxin (P ≤ 0.02) than the crosses made with non-transgenic lines. In addition, significantly higher levels of aflM gene-specific small RNAs were detected in the transgenic leaf and kernel tissues, indicating that the enhanced aflatoxin resistance in the homozygous transgenic kernels is likely due to suppression of aflM expression through HIGS.
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Affiliation(s)
- Yenjit Raruang
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Olanike Omolehin
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Dongfang Hu
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Qijian Wei
- Food and Feed Safety Research Unit, United States Department of Agriculture - Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Zhu-Qiang Han
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Kanniah Rajasekaran
- Food and Feed Safety Research Unit, United States Department of Agriculture - Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Jeffrey W Cary
- Food and Feed Safety Research Unit, United States Department of Agriculture - Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Zhi-Yuan Chen
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
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Sun L, Chen Y, Hua X, Chen Y, Hong J, Wu X, Jiang Y, van Schaik W, Qu T, Yu Y. Tandem amplification of the vanM gene cluster drives vancomycin resistance in vancomycin-variable enterococci. J Antimicrob Chemother 2020; 75:283-291. [PMID: 31742612 DOI: 10.1093/jac/dkz461] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 09/21/2019] [Accepted: 10/10/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Vancomycin-variable enterococci (VVE) are a potential risk factor for vancomycin resistance gene dissemination and clinical treatment failure. vanM has emerged as a new prevalent resistance determinant among clinical enterococci in China. A total of 54 vancomycin-susceptible enterococci (VSE) isolates carrying incomplete vanM gene clusters were isolated in our previous study. OBJECTIVES To determine the potential of vanM-carrying VSE to develop vancomycin resistance and investigate the mechanism of alteration of the resistance phenotype. METHODS Fifty-four vanM-positive VSE strains were induced in vitro by culturing in increasing concentrations of vancomycin. Genetic changes between three parent VVE strains and their resistant variants were analysed using Illumina and long-read sequencing technologies, quantitative PCR and Southern blot hybridization. Changes in expression level were determined by quantitative RT-PCR. RESULTS Twenty-five of the 54 VSE strains carrying vanM became resistant upon vancomycin exposure. A significant increase in vanM copy number was observed ranging from 5.28 to 127.64 copies per cell in induced resistant VVE strains. The vanM transposon was identified as tandem repeats with IS1216E between them, and occurred in either the plasmid or the chromosome of resistant VVE cells. In addition, an increase in vanM expression was observed after resistance conversion in VVE. CONCLUSIONS This study identified tandem amplification of the vanM gene cluster as a new mechanism for vancomycin resistance in VVE strains, offering a competitive advantage for VVE under antibiotic pressure.
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Affiliation(s)
- Lingyan Sun
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Yan Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Yiyi Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Jinjing Hong
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Xueqing Wu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Willem van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Tingting Qu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, Zhejiang Province, China
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Gao Y, Gao Y, Huang B, Meng Z, Jia Y. Reference gene validation for quantification of gene expression during ovarian development of turbot (Scophthalmus maximus). Sci Rep 2020; 10:823. [PMID: 31964949 PMCID: PMC6972784 DOI: 10.1038/s41598-020-57633-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 01/03/2020] [Indexed: 12/21/2022] Open
Abstract
Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is a powerful and sensitive method used in gene expression analysis. Suitable reference genes, which are stable under all experimental circumstances and tissues significantly improve the accuracy of qRT-PCR data. In this study, the stability of six genes, namely, 18S ribosomal RNA (18s), beta-actin (actb), elongation factor 1-alpha (ef1α), glyceraldehyde-3-phosphate-dehydrogenase (gapdh), cathepsin D (ctsd), and beta-2-microglobulin (b2m) were evaluated as potential references for qRT-PCR analysis. The genes were examined in the hypothalamus-pituitary-ovary-liver (HPOL) axis throughout turbot ovarian development via using the geNorm, NormFinder and BestKeeper algorithms. Results showed that the most stable reference genes were ef1α, actb, and ctsd in the hypothalamus, pituitary, ovary and liver, respectively. The best-suited gene combinations for normalization were 18s, ef1α, and ctsd in the hypothalamus; actb, ctsd, and 18s in the pituitary; actb, and ctsd in the ovary; gapdh and ctsd in the liver. Moreover, the expression profile of estrogen receptor α (erα) manifested no significant difference normalization to the aforementioned best-suited gene during turbot ovarian development. However, no single gene or pair of genes is suitable as an internal control and account for the amplification differences among the four tissues during ovarian development. In summary, these results provide a basic data for the optimal reference gene selection and obtain highly accurate normalization of qRT-PCR data in HPOL axis-related gene expression analysis during turbot ovarian development.
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Affiliation(s)
- Yunhong Gao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Yuntao Gao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Bin Huang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
| | - Zhen Meng
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
| | - Yudong Jia
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China.
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Differential Expression of Nicotine Acetylcholine Receptors Associates with Human Breast Cancer and Mediates Antitumor Activity of αO-Conotoxin GeXIVA. Mar Drugs 2020; 18:md18010061. [PMID: 31963558 PMCID: PMC7024346 DOI: 10.3390/md18010061] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 12/14/2022] Open
Abstract
Nicotinic acetylcholine receptors (nAChRs) are membrane receptors and play a major role in tumorigenesis and cancer progression. Here, we have investigated the differential expression of nAChR subunits in human breast cancer cell lines and breast epithelial cell lines at mRNA and protein levels and the effects of the αO-conotoxin GeXIVA, antagonist of α9α10 nAChR, on human breast cancer cells. Reverse transcription polymerase chain reaction (PCR) demonstrated that all nAChR subunits, except α6, were expressed in the 20 tested cell lines. Real time quantitative PCR (QRT-PCR) suggested that the mRNA of α5, α7, α9 and β4 nAChR subunits were overexpressed in all the breast cancer cell lines compared with the normal epithelial cell line HS578BST. α9 nAChR was highly expressed in almost all the breast cancer cell lines in comparison to normal cells. The different expression is prominent (p < 0.001) as determined by flow cytometry and Western blotting, except for MDA-MB-453 and HCC1395 cell lines. αO-conotoxin GeXIVA that targeted α9α10 nAChR were able to significantly inhibit breast cancer cell proliferation in vitro and merits further investigation as potential agents for targeted therapy.
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Dautt-Castro M, Estrada-Rivera M, Olguin-Martínez I, Rocha-Medina MDC, Islas-Osuna MA, Casas-Flores S. TBRG-1 a Ras-like protein in Trichoderma virens involved in conidiation, development, secondary metabolism, mycoparasitism, and biocontrol unveils a new family of Ras-GTPases. Fungal Genet Biol 2019; 136:103292. [PMID: 31730908 DOI: 10.1016/j.fgb.2019.103292] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 10/07/2019] [Accepted: 10/31/2019] [Indexed: 01/02/2023]
Abstract
Ras-GTPases are nucleotide hydrolases involved in key cellular processes. In fungi, Ras-GTPases regulate conidiation, development, virulence, and interactions with other fungi or plants. Trichoderma spp. are filamentous saprophytic fungi, widely distributed along all latitudes, characterized by their rapid growth and metabolic diversity. Many species of this genus interact with other fungi, animals or plants. Furthermore, these fungi are used as biocontrol agents due to their ability to antagonize phytopathogenic fungi and oomycetes, through competence, antibiosis, and parasitism. However, the genetic and molecular regulation of these processes is scarcely described in these fungi. In this work, we investigated the role of the gene tbrg-1 product (GenBank accession number XP_013956100; JGI ID: Tv_70852) of T. virens during its interaction with other fungi and plants. Sequence analyses predicted that TBRG-1 bears the characteristic domains of Ras-GTPases; however, its size (1011 aa) is 3- to 4-times bigger compared with classical GTPases. Interestingly, phylogenetic analyses grouped the TBRG-1 protein with hypothetical proteins of similar sizes, sharing conserved regions; whereas other known Ras-GTPases were perfectly grouped with their respective families. These facts led us to classify TBRG-1 into a new family of Ras-GTPases, the Big Ras-GTPases (BRG). Therefore, the gene was named tbrg-1 (TrichodermaBigRas-GTPase-1). Quantification of conidia and scanning electron microscopy showed that the mutants-lacking tbrg-1 produced less conidia, as well as a delayed conidiophore development compared to the wild-type (wt). Moreover, a deregulation of conidiation-related genes (con-10, con-13, and stuA) was observed in tbrg-1-lacking strains, which indicates that TBRG-1 is necessary for proper conidiophore and conidia development. Furthermore, the lack of tbrg-1 affected positively the antagonistic capability of T. virens against the phytopathogens Rhizoctonia solani, Sclerotium rolfsii, and Fusarium oxysporum, which was consistent with the expression patterns of mycoparasitism-related genes, sp1 and cht1, that code for a protease and for a chitinase, respectively. Furthermore, the antibiosis effect of mycelium-free culture filtrates of Δtbrg-1 against R. solani was considerably enhanced. The expression of secondary metabolism-related genes, particularly gliP, showed an upregulation in Δtbrg-1, which paralleled an increase in gliotoxin production as compared to the wt. These results indicate that TBRG-1 plays a negative role in secondary metabolism and antagonism. Unexpectedly, the biocontrol activity of Δtbrg-1 was ineffective to protect the tomato seeds and seedlings against R. solani. On the contrary, Δtbrg-1 behaved like a plant pathogen, indicating that TBRG-1 is probably implicated in the recognition process for establishing a beneficial relationship with plants.
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Affiliation(s)
- Mitzuko Dautt-Castro
- IPICYT, División de Biología Molecular, Laboratorio de Genómica Funcional y Comparativa, San Luis Potosí, S.L.P., Mexico
| | - Magnolia Estrada-Rivera
- IPICYT, División de Biología Molecular, Laboratorio de Genómica Funcional y Comparativa, San Luis Potosí, S.L.P., Mexico
| | - Ignacio Olguin-Martínez
- IPICYT, División de Biología Molecular, Laboratorio de Genómica Funcional y Comparativa, San Luis Potosí, S.L.P., Mexico
| | - Ma Del Carmen Rocha-Medina
- IPICYT, Laboratorio Nacional de Biotecnología Agrícola, Médica y Ambiental, San Luis Potosí, S.L.P., Mexico
| | - María A Islas-Osuna
- Laboratorio de Genética y Biología Molecular de Plantas. Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora, Mexico
| | - Sergio Casas-Flores
- IPICYT, División de Biología Molecular, Laboratorio de Genómica Funcional y Comparativa, San Luis Potosí, S.L.P., Mexico.
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Charrier A, Vergne E, Joffrion C, Richer A, Dousset N, Chevreau E. An artificial miRNA as a new tool to silence and explore gene functions in apple. Transgenic Res 2019; 28:611-626. [PMID: 31538273 DOI: 10.1007/s11248-019-00170-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 09/06/2019] [Indexed: 12/29/2022]
Abstract
Artificial miRNA (amiRNA) is a powerful technology to silence genes of interest. It has a high efficiency and specificity that can be used to explore gene function through targeted gene regulation or to create new traits. To develop this gene regulation tool in apple, we designed two amiRNA constructs based on an apple endogenous miRNA backbone previously characterized (Md-miR156h), and we checked their efficiency on an easily scorable marker gene: the phytoene desaturase gene (MdPDS in apple). Two pairs of miRNA:miRNA* regions were designed (named h and w). The monocistronic Md-miR156h with these MdPDS targets was placed under the control of the CaMV 35S promoter to generate the two plasmids: pAmiRNA156h-PDSh and pAmiRNA156h-PDSw. Two Agrobacterium-mediated transformation experiments were performed on the cultivar 'Gala'. A total of 11 independent transgenic clones were obtained in the first experiment and 5 in the second. Most transgenic lines had a typical albino and dwarf phenotype. However, six clones had a wild type green phenotype. Molecular analyses indicated clear relationships between the degree of albino phenotype, the level of MdPDS gene expression and the amount of mature amiRNAs. This study demonstrated for the first time in apple the functionality of an artificial miRNA based on an endogenous miRNA backbone. It provides important opportunities for apple genetic functional studies as well as apple genetic improvement projects.
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Affiliation(s)
- Aurélie Charrier
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 Rue Georges Morel, 49071, Beaucouzé Cedex, France
| | - Emilie Vergne
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 Rue Georges Morel, 49071, Beaucouzé Cedex, France
| | - Clément Joffrion
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 Rue Georges Morel, 49071, Beaucouzé Cedex, France
| | - Andréa Richer
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 Rue Georges Morel, 49071, Beaucouzé Cedex, France
| | - Nicolas Dousset
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 Rue Georges Morel, 49071, Beaucouzé Cedex, France
| | - Elisabeth Chevreau
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 Rue Georges Morel, 49071, Beaucouzé Cedex, France.
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Liu XL, Ye S, Cheng CY, Li HW, Lu B, Yang WJ, Yang JS. Identification and characterization of a symbiotic agglutination-related C-type lectin from the hydrothermal vent shrimp Rimicaris exoculata. FISH & SHELLFISH IMMUNOLOGY 2019; 92:1-10. [PMID: 31141718 DOI: 10.1016/j.fsi.2019.05.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/16/2019] [Accepted: 05/25/2019] [Indexed: 06/09/2023]
Abstract
Rimicaris exoculata (Decapoda: Bresiliidae) is one of the dominant species of hydrothermal vent communities, which inside its gill chamber harbors ectosymbioses with taxonomic invariability while compositional flexibility. Several studies have revealed that the establishment of symbiosis can be initiated and selected by innate immunity-related pattern recognition receptors (PRRs), such as C-type lectins (CTLs). In this research, a CTL was identified in R. exoculata (termed RCTL), which showed high expression at both mRNA and protein levels in the scaphognathite, an organ where the ectosymbionts are attached outside its setae. Linear correlationships were observed between the relative quantities of two major symbionts and the expression of RCTL based on analyzing different shrimp individuals. The recombinant protein of RCTL could recognize and agglutinate the cultivable γ-proteobacterium of Escherichia coli in a Ca2+-dependent manner, obeying a dose-dependent and time-cumulative pattern. Unlike conventional crustacean CTLs, the involvement of RCTL could not affect the bacterial growth, which is a key issue for the successful establishment of symbiosis. These results implied that RCTL might play a critical role in symbiotic recognition and attachment to R. exoculata. It also provides insights to understand how R. exoculata adapted to such a chemosynthesis-based environment.
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Affiliation(s)
- Xiao-Li Liu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, PR China
| | - Sen Ye
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, PR China
| | - Cai-Yuan Cheng
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, PR China
| | - Hua-Wei Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, PR China
| | - Bo Lu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, 310012, PR China
| | - Wei-Jun Yang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, PR China
| | - Jin-Shu Yang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, PR China.
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Németh MZ, Pintye A, Horváth ÁN, Vági P, Kovács GM, Gorfer M, Kiss L. Green Fluorescent Protein Transformation Sheds More Light on a Widespread Mycoparasitic Interaction. PHYTOPATHOLOGY 2019; 109:1404-1416. [PMID: 30900938 DOI: 10.1094/phyto-01-19-0013-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Powdery mildews, ubiquitous obligate biotrophic plant pathogens, are often attacked in the field by mycoparasitic fungi belonging to the genus Ampelomyces. Some Ampelomyces strains are commercialized biocontrol agents of crop pathogenic powdery mildews. Using Agrobacterium tumefaciens-mediated transformation (ATMT), we produced stable Ampelomyces transformants that constitutively expressed green fluorescent protein (GFP) to (i) improve the visualization of the mildew-Ampelomyces interaction and (ii) decipher the environmental fate of Ampelomyces fungi before and after acting as a mycoparasite. Detection of Ampelomyces structures, and especially hyphae, was greatly enhanced when diverse powdery mildew, leaf, and soil samples containing GFP transformants were examined with fluorescence microscopy compared with brightfield and differential interference contrast optics. We showed for the first time, to our knowledge, that Ampelomyces strains can persist up to 21 days on mildew-free host plant surfaces, where they can attack powdery mildew structures as soon as these appear after this period. As saprobes in decomposing, powdery mildew-infected leaves on the ground and also in autoclaved soil, Ampelomyces strains developed new hyphae but did not sporulate. These results indicate that Ampelomyces strains occupy a niche in the phyllosphere where they act primarily as mycoparasites of powdery mildews. Our work has established a framework for a molecular genetic toolbox for the genus Ampelomyces using ATMT.
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Affiliation(s)
- Márk Z Németh
- 1Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1525 Budapest, Hungary
| | - Alexandra Pintye
- 1Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1525 Budapest, Hungary
| | - Áron N Horváth
- 1Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1525 Budapest, Hungary
| | - Pál Vági
- 1Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1525 Budapest, Hungary
- 2Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Gábor M Kovács
- 1Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1525 Budapest, Hungary
- 2Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Markus Gorfer
- 3Austrian Institute of Technology, BOKU University of Natural Resources and Life Sciences, A-3430 Tulln, Austria
| | - Levente Kiss
- 1Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1525 Budapest, Hungary
- 4Institute for Life Sciences and the Environment, Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland 4350, Australia
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Liu L, Schepers E, Lum A, Rice J, Yalpani N, Gerber R, Jiménez-Juárez N, Haile F, Pascual A, Barry J, Qi X, Kassa A, Heckert MJ, Xie W, Ding C, Oral J, Nguyen M, Le J, Procyk L, Diehn SH, Crane VC, Damude H, Pilcher C, Booth R, Liu L, Zhu G, Nowatzki TM, Nelson ME, Lu AL, Wu G. Identification and Evaluations of Novel Insecticidal Proteins from Plants of the Class Polypodiopsida for Crop Protection against Key Lepidopteran Pests. Toxins (Basel) 2019; 11:E383. [PMID: 31266212 PMCID: PMC6669613 DOI: 10.3390/toxins11070383] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/21/2019] [Accepted: 06/22/2019] [Indexed: 12/12/2022] Open
Abstract
Various lepidopteran insects are responsible for major crop losses worldwide. Although crop plant varieties developed to express Bacillus thuringiensis (Bt) proteins are effective at controlling damage from key lepidopteran pests, some insect populations have evolved to be insensitive to certain Bt proteins. Here, we report the discovery of a family of homologous proteins, two of which we have designated IPD083Aa and IPD083Cb, which are from Adiantum spp. Both proteins share no known peptide domains, sequence motifs, or signatures with other proteins. Transgenic soybean or corn plants expressing either IPD083Aa or IPD083Cb, respectively, show protection from feeding damage by several key pests under field conditions. The results from comparative studies with major Bt proteins currently deployed in transgenic crops indicate that the IPD083 proteins function by binding to different target sites. These results indicate that IPD083Aa and IPD083Cb can serve as alternatives to traditional Bt-based insect control traits with potential to counter insect resistance to Bt proteins.
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Affiliation(s)
- Lu Liu
- Corteva Agriscience, Hayward, CA 94545, USA
| | | | - Amy Lum
- Corteva Agriscience, Hayward, CA 94545, USA
| | - Janet Rice
- Corteva Agriscience, Johnston, IA 50131, USA
| | | | - Ryan Gerber
- Corteva Agriscience, Johnston, IA 50131, USA
| | | | - Fikru Haile
- Corteva Agriscience, Johnston, IA 50131, USA
| | | | | | - Xiuli Qi
- Corteva Agriscience, Johnston, IA 50131, USA
| | - Adane Kassa
- Corteva Agriscience, Johnston, IA 50131, USA
| | | | | | | | | | | | - James Le
- Corteva Agriscience, Hayward, CA 94545, USA
| | - Lisa Procyk
- Corteva Agriscience, Johnston, IA 50131, USA
| | | | | | | | | | - Russ Booth
- Corteva Agriscience, Johnston, IA 50131, USA
| | - Lu Liu
- Corteva Agriscience, Johnston, IA 50131, USA
| | - Genhai Zhu
- Corteva Agriscience, Hayward, CA 94545, USA
| | | | | | - Albert L Lu
- Corteva Agriscience, Johnston, IA 50131, USA
| | - Gusui Wu
- Corteva Agriscience, Hayward, CA 94545, USA
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Urea Addition Promotes the Metabolism and Utilization of Nitrogen in Cucumber. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9050262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nitrogen (N) forms include ammonium [NH4+-N], nitrate [NO3−-N], and urea [CO(NH2)2]. Urea is the most common nitrogen fertilizer in agriculture due to its inexpensive price and high N content. Although the reciprocal influence between NO3−-N and NH4+-N is well known, CO(NH2)2 interactions with these inorganic N forms have been poorly studied. We studied the effects of different nitrogen forms with equal nitrogen on dry matter, yield, enzyme activity, and gene expression levels in cucumber. NO3−-N treatment with equal CO(NH2)2 promoted nitrate reduction, urea utilization, and the GS/GOGAT cycle but reduced the nitrate content. UR-2, NR-2, NR-3, NiR, GOGAT-1-1, and GS-4 were upregulated in response to these changes. NH4+-N treatment with equal CO(NH2)2 promoted nitrogen metabolism and relieved the ammonia toxicity of pure NH4+-N treatment. UR-2, GOGAT-2-2, and GS-4 were upregulated, and GDH-3 was downregulated in response to these changes. Treatment with both NO3−-N with added equal CO(NH2)2 and NH4+-N with added equal CO(NH2)2 enhanced the activities of GOGAT, GS, and UR and the amino acid pathway of urea metabolism; manifested higher glutamate, protein, chlorophyll, and nitrogen contents; and improved dry matter weight. A greater proportion of dry matter was distributed to the fruit, generating significantly higher yields. Therefore, the addition of urea to ammonium or nitrate promoted N metabolism and N utilization in cucumber plants, especially treatments with 50% NO3−-N + 50% CO(NH2)2, as the recommended nitrogen form in this study.
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48
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Pischedda E, Scolari F, Valerio F, Carballar-Lejarazú R, Catapano PL, Waterhouse RM, Bonizzoni M. Insights Into an Unexplored Component of the Mosquito Repeatome: Distribution and Variability of Viral Sequences Integrated Into the Genome of the Arboviral Vector Aedes albopictus. Front Genet 2019; 10:93. [PMID: 30809249 PMCID: PMC6379468 DOI: 10.3389/fgene.2019.00093] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/29/2019] [Indexed: 01/01/2023] Open
Abstract
The Asian tiger mosquito Aedes albopictus is an invasive mosquito and a competent vector for public-health relevant arboviruses such as Chikungunya (Alphavirus), Dengue and Zika (Flavivirus) viruses. Unexpectedly, the sequencing of the genome of this mosquito revealed an unusually high number of integrated sequences with similarities to non-retroviral RNA viruses of the Flavivirus and Rhabdovirus genera. These Non-retroviral Integrated RNA Virus Sequences (NIRVS) are enriched in piRNA clusters and coding sequences and have been proposed to constitute novel mosquito immune factors. However, given the abundance of NIRVS and their variable viral origin, their relative biological roles remain unexplored. Here we used an analytical approach that intersects computational, evolutionary and molecular methods to study the genomic landscape of mosquito NIRVS. We demonstrate that NIRVS are differentially distributed across mosquito genomes, with a core set of seemingly the oldest integrations with similarity to Rhabdoviruses. Additionally, we compare the polymorphisms of NIRVS with respect to that of fast and slow-evolving genes within the Ae. albopictus genome. Overall, NIRVS appear to be less polymorphic than slow-evolving genes, with differences depending on whether they occur in intergenic regions or in piRNA clusters. Finally, two NIRVS that map within the coding sequences of genes annotated as Rhabdovirus RNA-dependent RNA polymerase and the nucleocapsid-encoding gene, respectively, are highly polymorphic and are expressed, suggesting exaptation possibly to enhance the mosquito's antiviral responses. These results greatly advance our understanding of the complexity of the mosquito repeatome and the biology of viral integrations in mosquito genomes.
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Affiliation(s)
- Elisa Pischedda
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Francesca Scolari
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Federica Valerio
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Rebeca Carballar-Lejarazú
- Department of Microbiology & Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | | | - Robert M. Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Liu XL, Ye S, Li HW, Lu B, Yu YQ, Fan YP, Yang WJ, Yang JS. An H-ferritin from the hydrothermal vent shrimp Rimicaris exoculata and its potential role in iron metabolism. Biometals 2019; 32:251-264. [PMID: 30756217 DOI: 10.1007/s10534-019-00174-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/19/2019] [Indexed: 01/17/2023]
Abstract
Rimicaris exoculata (Decapoda: Bresiliidae) is one of the dominant species among hydrothermal vent communities along the Mid-Atlantic Ridge. This shrimp can tolerate high concentrations of heavy metals such as iron, but the mechanisms used for detoxification and utilization of excess metals remain largely unknown. Ferritin is a major iron storage protein in most living organisms. The central heavy subunit of ferritin (H-ferritin) possesses ferroxidase activity and converts iron from Fe2+ to Fe3+, the non-toxic form used for storage. In the present study, the H-ferritin RexFrtH was identified in the hydrothermal vent shrimp R. exoculata, and found to be highly expressed in the gill, the main organ involved in bioaccumulation of metals, at both RNA and protein levels. Accumulation of RexFrtH decreased from efferent to afferent vessels, coinciding with the direction of water flow through the gills. Fe3+ was localized with RexFrtH, and in vitro iron-binding and ferroxidase assays using recombinant RexFrtH confirmed the high affinity for iron. Based on these results, we propose a model of iron metabolism in R. exoculata gills; ferrous iron from ambient hydrothermal water accumulates and is converted and stored in ferric form by RexFrtH as an iron reservoir when needed for metabolism, or excreted as an intermediate to prevent iron overload. The findings expand our understanding of the adaptation strategies used by shrimps inhabiting extreme hydrothermal vents to cope with extremely high heavy metal concentrations.
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Affiliation(s)
- Xiao-Li Liu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Sen Ye
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Hua-Wei Li
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Bo Lu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, Zhejiang, People's Republic of China
| | - Yan-Qin Yu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China.,Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, People's Republic of China
| | - Yu-Peng Fan
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Wei-Jun Yang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China.
| | - Jin-Shu Yang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China.
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Khan A, Shrestha A, Dey N. Biochemical and Molecular Characterization of Novel Pararetroviral Promoters in Plants. Methods Mol Biol 2019; 1991:223-236. [PMID: 31041776 DOI: 10.1007/978-1-4939-9458-8_20] [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] [Indexed: 06/09/2023]
Abstract
Special attention needs to be given to defining and studying the regulatory apparatus of different pararetroviral promoters under various physiological conditions because they have significant sequence heterogeneity and unique distributions of stress-responsive cis-elements. Transcriptional regulation studies of a pararetroviral promoter involve both gene expression analyses and investigation of its structural/regulatory framework. The expression of reporter genes such as β-Glucuronidase (GUS) or Luciferase (LUC) transcriptionally fused to a promoter usually determines the strength or function of a target promoter. In parallel, DNA-protein interaction studies are employed to assess the functional relevance of predicted transcription factor binding sites in target pararetroviral promoter sequences. In this chapter, we will describe protocols used to determine the transgene integration and expression in transgenic plant systems. Alongside, we will also discuss the fusion reporter assays that can determine the promoter activity and DNA-protein interaction studies that aid in the evaluation of its transcriptional regulation.
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Affiliation(s)
- Ahamed Khan
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Government of India, Bhubaneswar, Odisha, India
| | - Ankita Shrestha
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Government of India, Bhubaneswar, Odisha, India
| | - Nrisingha Dey
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Government of India, Bhubaneswar, Odisha, India.
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