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Xiao X, Luo X, Huang C, Feng X, Wu M, Lu M, Kuang J, Peng S, Guo Y, Zhang Z, Hu Z, Zhou X, Chen M, Liu Z. Transcriptome analysis reveals the peptide toxins diversity of Macrothele palpator venom. Int J Biol Macromol 2023; 253:126577. [PMID: 37648132 DOI: 10.1016/j.ijbiomac.2023.126577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/01/2023]
Abstract
Spider venom is a large pharmacological repertoire of different bioactive peptide toxins. However, obtaining crude venom from some spiders is challenging. Thus, studying individual toxins through venom purification is a daunting task. In this study, we constructed the cDNA library and transcriptomic sequencing from the Macrothele palpator venom glands. Subsequently, 718 high-quality expressed sequence tags (ESTs) were identified, and grouped into three categories, including 449 toxin-like (62.53 %), 136 cellular component (18.94 %) and 133 non-matched (18.52 %) based on the gene function annotation. Additionally, 112 non-redundant toxin-like peptides were classified into 13 families (families A-M) based on their sequence homology and cysteine framework. Bioinformatics analysis revealed a high sequence similarity between families A-J and the toxins from Macrothele gigas in the NR database. In contrast, families K-M had a generally low sequence homology with known spider peptide toxins and unpredictable biological functions. Taken together, this study adds many new members to the spider toxin superfamily and provides a basis for identifying various potential biological tools in M. palpator venom.
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Affiliation(s)
- Xin Xiao
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and small molecule drug R&D plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China
| | - Xiaoqing Luo
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and small molecule drug R&D plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China
| | - Cuiling Huang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Xujun Feng
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and small molecule drug R&D plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China
| | - Meijing Wu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and small molecule drug R&D plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China
| | - Minjuan Lu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and small molecule drug R&D plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China
| | - Jiating Kuang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Siyi Peng
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Yingmei Guo
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Zixuan Zhang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Zhaotun Hu
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, College of Biological and Food Engineering, Huaihua College, Huaihua, Hunan 418008, China
| | - Xi Zhou
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and small molecule drug R&D plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China.
| | - Minzhi Chen
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and small molecule drug R&D plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China.
| | - Zhonghua Liu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Peptide and small molecule drug R&D plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China.
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Yadav BNS, Sharma P, Maurya S, Yadav RK. Metagenomics and metatranscriptomics as potential driving forces for the exploration of diversity and functions of micro-eukaryotes in soil. 3 Biotech 2023; 13:423. [PMID: 38047037 PMCID: PMC10689336 DOI: 10.1007/s13205-023-03841-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
Micro-eukaryotes are ubiquitous and play vital roles in diverse ecological systems, yet their diversity and functions are scarcely known. This may be due to the limitations of formerly used conventional culture-based methods. Metagenomics and metatranscriptomics are enabling to unravel the genomic, metabolic, and phylogenetic diversity of micro-eukaryotes inhabiting in different ecosystems in a more comprehensive manner. The in-depth study of structural and functional characteristics of micro-eukaryote community residing in soil is crucial for the complete understanding of this major ecosystem. This review provides a deep insight into the methodologies employed under these approaches to study soil micro-eukaryotic organisms. Furthermore, the review describes available computational tools, pipelines, and database sources and their manipulation for the analysis of sequence data of micro-eukaryotic origin. The challenges and limitations of these approaches are also discussed in detail. In addition, this review summarizes the key findings of metagenomic and metatranscriptomic studies on soil micro-eukaryotes. It also highlights the exploitation of these methods to study the structural as well as functional profiles of soil micro-eukaryotic community and to screen functional eukaryotic protein coding genes for biotechnological applications along with the future perspectives in the field.
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Affiliation(s)
- Bhupendra Narayan Singh Yadav
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Priyanka Sharma
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Shristy Maurya
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Rajiv Kumar Yadav
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
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Zhu L, Li Y, Qiu L, Chen X, Guo B, Li H, Qi P. Screening of genes encoding proteins that interact with Nrf2: Probing a cDNA library from Mytilus coruscus using a yeast two-hybrid system. Fish Shellfish Immunol 2023; 142:109112. [PMID: 37751644 DOI: 10.1016/j.fsi.2023.109112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/08/2023] [Accepted: 09/22/2023] [Indexed: 09/28/2023]
Abstract
The Nuclear factor Erythroid 2-related factor 2 (Nrf2) is the most important endogenous antioxidant factor in organisms, and it has been demonstrated that it exerts extensive control over the immune response by interacting with crucial innate immunity components directly or indirectly. Although Nrf2 has been widely confirmed to be involved in stress resistance in mammals and some fish, its contribution to mollusks oxidative stress resistance has not frequently been documented. In this investigation, total RNA was taken from the digestive gland of M. coruscus, and a cDNA library was constructed and screened using the GATEWAY recombination technology. The Nrf2 cDNA sequence of M. coruscus was cloned into the pGBKT7 vector to prepare the bait plasmid. Using yeast two-hybrid system, after auxotrophic medium screening, sequencing, and bioinformatics analysis, 13 binding proteins that interacted with Nrf2 were finally identified. They were QM-like protein, 40S ribosomal protein S4 (RPS4), ribosomal protein S2 (RPS2), ribosomal protein L12 (RPL12), EF1-alpha mRNA for elongation factor 1 alpha (eEF1-alpha), ferritin, alpha-amylase, trypsin, vdg3, period clock protein, cyclophilin A isoform 1 (CYP A), serine protease CFSP2, histone variant H2A.Z (H2A.Z). For a better understanding the physiological function of Nrf2 in animals and as a potential target for future research on protein roles in Nrf2 interactions, it is crucial to clarify these protein interactions.
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Affiliation(s)
- Li Zhu
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China
| | - Yaru Li
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China
| | - Longmei Qiu
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China
| | - Xinglu Chen
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China
| | - Baoying Guo
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China
| | - Hongfei Li
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China; Donghai Laboratory, Zhoushan, Zhejiang, 316021, China.
| | - Pengzhi Qi
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China; Donghai Laboratory, Zhoushan, Zhejiang, 316021, China.
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Huang S, Zhang H, Chen W, Wang J, Wu Z, He M, Zhang J, Hu X, Xiang S. Screening of Tnfaip1-Interacting Proteins in Zebrafish Embryonic cDNA Libraries Using a Yeast Two-Hybrid System. Curr Issues Mol Biol 2023; 45:8215-8226. [PMID: 37886961 PMCID: PMC10605426 DOI: 10.3390/cimb45100518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/01/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023] Open
Abstract
TNFAIP1 regulates cellular biological functions, including DNA replication, DNA repair, and cell cycle, by binding to target proteins. Identification of Tnfaip1-interacting proteins contributes to the understanding of the molecular regulatory mechanisms of their biological functions. In this study, 48 hpf, 72 hpf, and 96 hpf wild-type zebrafish embryo mRNAs were used to construct yeast cDNA library. The library titer was 1.12 × 107 CFU/mL, the recombination rate was 100%, and the average length of the inserted fragments was greater than 1000 bp. A total of 43 potential interacting proteins of Tnfaip1 were identified using zebrafish Tnfaip1 as a bait protein. Utilizing GO functional annotation and KEGG signaling pathway analysis, we found that these interacting proteins are mainly involved in translation, protein catabolic process, ribosome assembly, cytoskeleton formation, amino acid metabolism, and PPAR signaling pathway. Further yeast spotting analyses identified four interacting proteins of Tnfaip1, namely, Ubxn7, Tubb4b, Rpl10, and Ybx1. The Tnfaip1-interacting proteins, screened from zebrafish embryo cDNA in this study, increased our understanding of the network of Tnfaip1-interacting proteins during the earliest embryo development and provided a molecular foundation for the future exploration of tnfaip1's biological functions.
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Affiliation(s)
- Shulan Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (S.H.); (H.Z.); (W.C.); (J.W.); (Z.W.); (M.H.); (J.Z.)
| | - Hongning Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (S.H.); (H.Z.); (W.C.); (J.W.); (Z.W.); (M.H.); (J.Z.)
| | - Wen Chen
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (S.H.); (H.Z.); (W.C.); (J.W.); (Z.W.); (M.H.); (J.Z.)
| | - Jiawei Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (S.H.); (H.Z.); (W.C.); (J.W.); (Z.W.); (M.H.); (J.Z.)
| | - Zhen Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (S.H.); (H.Z.); (W.C.); (J.W.); (Z.W.); (M.H.); (J.Z.)
| | - Meiqi He
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (S.H.); (H.Z.); (W.C.); (J.W.); (Z.W.); (M.H.); (J.Z.)
| | - Jian Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (S.H.); (H.Z.); (W.C.); (J.W.); (Z.W.); (M.H.); (J.Z.)
| | - Xiang Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (S.H.); (H.Z.); (W.C.); (J.W.); (Z.W.); (M.H.); (J.Z.)
| | - Shuanglin Xiang
- Engineering Research Center for Antibodies from Experimental Animals of Hunan Province, College of Life Sciences, Hunan Normal University, Changsha 410081, China
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Iqbal A, Yang Y. Utilizing Dichloromethane as an Extremely Proficient Substitute for Phenol/Chloroform in Extracting RNA with Exceptional Purity from Woody Tissues of Coconut. Methods Protoc 2023; 6:75. [PMID: 37736958 PMCID: PMC10514881 DOI: 10.3390/mps6050075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/23/2023] Open
Abstract
Procuring high-grade RNA from mature coconut tissues is a tricky and labor-intensive process due to the intricate scaffold of polysaccharides, polyphenols, lipids, and proteins that form firm complexes with nucleic acids. However, we have effectively developed a novel method for the first time, letting the retrieval of high-grade RNA from the roots, endosperm, and mesocarp of mature coconut trees take place. In this method, we exploited dichloromethane as a replacement to phenol/chloroform for RNA recovery from mature coconut tissues. The amount of high-grade RNA acquired from the roots of mature coconut trees was 120.7 µg/g, with an A260/280 ratio of 1.95. Similarly, the mature coconut mesocarp yielded 134.6 µg/g FW of quality RNA with A260/280 ratio of 1.98, whereas the mature coconut endosperm produced 120.4 µg/g FW of quality RNA with A260/280 ratio of 2.01. Furthermore, the RNA isolation using the dichloromethane method exhibited excellent performance in downstream experiments, particularly in RT-PCR for cDNA production and amplification. On the contrary, the RNA plant kit, TRIZOL, and Cetyl Trimethyl Ammonium Bromide (CTAB) methods were unsuccessful in isolating substantial quantities of RNA with exceptional purities from the mentioned coconut tissues. In view of these findings, we conclude that the newly developed method will be pivotal in effectively extracting RNA with high purity from mature coconut tissues.
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Affiliation(s)
- Amjad Iqbal
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Science, Wenchang 571339, China
- Department of Food Science & Technology, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Science, Wenchang 571339, China
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Wu X, Chen Y, Liu H, Kong X, Liang X, Zhang Y, Tang C, Liu Z. The Molecular Composition of Peptide Toxins in the Venom of Spider Lycosa coelestis as Revealed by cDNA Library and Transcriptomic Sequencing. Toxins (Basel) 2023; 15. [PMID: 36828457 DOI: 10.3390/toxins15020143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
In the so-called "struggle for existence" competition, the venomous animals developed a smart and effective strategy, envenomation, for predation and defense. Biochemical analysis revealed that animal venoms are chemical pools of proteinase, peptide toxins, and small organic molecules with various biological activities. Of them, peptide toxins are of great molecular diversity and possess the capacity to modulate the activity of ion channels, the second largest group of drug targets expressed on the cell membrane, which makes them a rich resource for developing peptide drug pioneers. The spider Lycosa coelestis (L. coelestis) commonly found in farmland in China is a dominant natural enemy of agricultural pests; however, its venom composition and activity were never explored. Herein, we conducted cDNA library and transcriptomic sequencing of the venom gland of L. coelestis, which identified 1131 high-quality expressed sequence tags (ESTs), grouped into three categories denoted as toxin-like ESTs (597, 52.79%), cellular component ESTs (357, 31.56%), and non-matched ESTs (177, 15.65%). These toxin-like ESTs encode 98 non-reductant toxins, which are artificially divided into 11 families based on their sequence homology and cysteine frameworks (2-14 cysteines forming 1-7 disulfide bonds to stabilize the toxin structure). Furthermore, RP-HPLC purification combined with off-line MALDI-TOF analysis have detected 147 different peptides physically existing in the venom of L. coelestis. Electrophysiology analysis confirmed that the venom preferably inhibits the voltage-gated calcium channels in rat dorsal root ganglion neurons. Altogether, the present study has added a great lot of new members to the spider toxin superfamily and built the foundation for characterizing novel active peptides in the L. coelestis venom.
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Sreeja S, Shylaja MR, Nazeem PA, Mathew D. Peroxisomal KAT2 (3-ketoacyl-CoA thiolase 2) gene has a key role in gingerol biosynthesis in ginger ( Zingiber officinale Rosc.). J Plant Biochem Biotechnol 2023; 32:1-16. [PMID: 36685987 PMCID: PMC9838548 DOI: 10.1007/s13562-022-00825-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
Ginger is an important spice crop with medicinal values and gingerols are the most abundant pungent polyphenols present in ginger, responsible for most of its pharmacological properties. The present study focuses on the molecular mechanism of gingerol biosynthesis in ginger using transcriptome analysis. Suppression Subtractive Hybridization (SSH) was done in leaf and rhizome tissues using high gingerol-producing ginger somaclone B3 as the tester and parent cultivar Maran as the driver and generated high-quality leaf and rhizome Expressed Sequence Tags (ESTs). The Blast2GO annotations of the ESTs revealed the involvement of leaf ESTs in secondary metabolite production, identifying the peroxisomal KAT2 gene (Leaf EST 9) for the high gingerol production in ginger. Rhizome ESTs mostly coded for DNA metabolic processes and differential genes for high gingerol production were not observed in rhizomes. In the qRT-PCR analysis, somaclone B3 had shown high chalcone synthase (CHS: rate-limiting gene in gingerol biosynthetic pathway) activity (0.54 fold) in the leaves of rhizome sprouts. The presence of a high gingerol gene in leaf ESTs and high expression of CHS in leaves presumed that the site of synthesis of gingerols in ginger is the leaves. A modified pathway for gingerol/polyketide backbone formation has been constructed explaining the involvement of KAT gene isoforms KAT2 and KAT5 in gingerol/flavonoid biosynthesis, specifically the KAT2 gene which is otherwise thought to be involved mainly in β-oxidation. The results of the present investigations have the potential of utilizing KAT/thiolase superfamily enzymes for protein/metabolic pathway engineering in ginger for large-scale production of gingerols. Supplementary Information The online version contains supplementary material available at 10.1007/s13562-022-00825-x.
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Affiliation(s)
- S. Sreeja
- Centre for Plant Biotechnology and Molecular Biology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Kerala India
| | - M. R. Shylaja
- Centre for Plant Biotechnology and Molecular Biology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Kerala India
| | - P. A. Nazeem
- Centre for Plant Biotechnology and Molecular Biology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Kerala India
| | - Deepu Mathew
- Centre for Plant Biotechnology and Molecular Biology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Kerala India
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8
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Santonico E. The Lambda Display Technology: A Useful Tool for the Identification of Ubiquitin-and Ubiquitin-Like-Binding Domains. Methods Mol Biol 2023; 2602:163-175. [PMID: 36446974 DOI: 10.1007/978-1-0716-2859-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ubiquitin-binding domains (UBDs) are modular units that mediate non-covalent recognition of ubiquitin modifications. They are found in ubiquitin (Ub)-binding proteins and recognize defined surface patches of a single Ub through typically weak interactions. Although more than 200 Ub-binding proteins have been identified to date, only 29 UBD types have been reported in the human proteome, suggesting that much remains to be learned about Ub recognition. Several methods, from bioinformatics to experimental, have successfully identified Ub-binding properties in several proteins. We here report the protocol to identify Ub-binding domains by panning a human brain cDNA library whose products are displayed on the surface of lambda capsid. In parallel, we carried out a panning experiment aimed at identifying domains interacting with the Ub-like NEDD8 (neural precursor cell-expressed developmentally downregulated), which is the Ub-like protein showing the closest sequence identity (58%) to Ub. This approach proved to be very effective for the discovery of the previously unidentified UBDs CUBAN and CoCUN, and it is in principle applicable to investigate the interaction network of any other Ub-like protein.
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Affiliation(s)
- Elena Santonico
- University of Rome Tor Vergata, Via della ricerca scientifica, Rome, Italy.
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9
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Elmore JM, Velásquez-Zapata V, Wise RP. Next-Generation Yeast Two-Hybrid Screening to Discover Protein-Protein Interactions. Methods Mol Biol 2023; 2690:205-222. [PMID: 37450150 DOI: 10.1007/978-1-0716-3327-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Yeast two-hybrid is a powerful approach to discover new protein-protein interactions. Traditional methods involve screening a target protein against a cDNA expression library and assaying individual positive colonies to identify interacting partners. Here we describe a simple approach to perform yeast two-hybrid screens of a cDNA expression library in batch liquid culture. Positive yeast cell populations are enriched under selection and then harvested en masse. Prey cDNAs are amplified and used as input for next-generation sequencing libraries for identification, quantification, and ranking.
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Affiliation(s)
- J Mitch Elmore
- USDA-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, USA.
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research, Ames, IA, USA.
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA, USA.
| | - Valeria Velásquez-Zapata
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA, USA
- Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA, USA
| | - Roger P Wise
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research, Ames, IA, USA
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA, USA
- Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA, USA
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Liu X, Zhang L, Zhang Y, Vakharia VN, Zhang X, Lv X, Sun W. Screening of genes encoding proteins that interact with ISG15: Probing a cDNA library from a snakehead fish cell line using a yeast two-hybrid system. Fish Shellfish Immunol 2022; 128:300-306. [PMID: 35921933 DOI: 10.1016/j.fsi.2022.07.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/20/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
Interferon-stimulated gene 15 (ISG15) regulates cellular life processes, including defense responses against infection by a variety of viral pathogens, by binding to target proteins. At present, various fish ISG15s have been identified, but the biological function of ISG15 in snakehead fish is still unclear. In this study, total RNA was extracted from snakehead fish cell line E11, ds cDNA was synthesized and purified using SMART technology, and the resulting cDNA library was screened by co-transforming yeast cells. The library titer was 4.28 × 109 CFU/mL. Using snakehead ISG15 as the bait protein, the recombinant bait vector pGBKT7-ISG15 was constructed and transformed into the yeast strain Y2HGold. The toxicity and self-activation activity of the bait vector were detected on the deficient medium, and the prey proteins interacting with ISG15 were screened. In total, 19 interacting proteins of ISG15 were identified, including mitotic checkpoint protein BUB3, hypothetical protein SnRVgp6, elongation factor 1-beta, 60S ribosomal protein L9, dual specificity protein phosphatase 5-like, eukaryotic translation initiation factor 3 subunit I and ferritin. A yeast spotting assay further probed the interaction between ISG15 and DUSP5. These results increase our understanding of the interaction network of snakehead ISG15 and will aid in exploring the underlying mechanisms of snakehead ISG15 functions in the future.
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Affiliation(s)
- Xiaodan Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
| | - Liwen Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Yanbing Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Vikram N Vakharia
- Institute of Marine and Environmental Technology, University of Maryland Baltimore Country, Baltimore, MD, 21202, USA
| | - Xiaojun Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Xiaoyang Lv
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Wei Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.
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Wang N, He F, Yu H, He L, Xiong G, Lu J, Yu C, Wang S. [Specific amplification of plasma exosome miRNA in cancer patients for construction of cDNA library]. Sheng Wu Gong Cheng Xue Bao 2022; 38:2213-2223. [PMID: 35786473 DOI: 10.13345/j.cjb.210758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plasma exosome microRNAs (miRNAs) are closely related with the occurrence, diagnosis, and treatment of cancers. However, the underlying molecular mechanisms remain unclear. We herein investigated the solution for tackling the unspecific amplification of plasma exosome microRNAs from cancer patients during the construction of its cDNA library. For the restriction enzyme digesting method, the primers were degraded by exonuclease T (EXOT) and phi29 DNA polymerase. For the magnetic bead separation method, the templates and primers were separated through the DNA binding beads. The separation effects of magnetic beads were detected by agarose gel electrophoresis and modified polyacrylamide gel electrophoresis. The levels of plasma exosome miRNAs from cancer patients and various primers were assayed by RT-qPCR. The results indicated that the unspecific amplification stemmed from USR5SR. EXOT and phi29 DNA polymerase could degrade USR5SR, but the templates were also degraded simultaneously. Regarding the magnetic bead separation method, the best effect was achieved via precipitation of primer fragments by 9% PEG and precipitation of templates by 15% PEG. In conclusion, the magnetic bead separation method efficiently circumvented the unspecific amplification during the construction of cDNA library, and therefore led to the successful construction of cDNA library from plasma exosome miRNA of cancer patients and 293T cells.
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Affiliation(s)
- Na Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Fei He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hongwei Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Luanying He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Guoliang Xiong
- Shenzhen Hospital of Traditional Chinese Medicine, Shenzhen 518000, Guangdong, China
| | - Jiandong Lu
- Shenzhen Hospital of Traditional Chinese Medicine, Shenzhen 518000, Guangdong, China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shihui Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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Sing TL, Conlon K, Lu SH, Madrazo N, Morse K, Barker JC, Hollerer I, Brar GA, Sudmant PH, Ünal E. Meiotic cDNA libraries reveal gene truncations and mitochondrial proteins important for competitive fitness in Saccharomyces cerevisiae. Genetics 2022; 221:iyac066. [PMID: 35471663 PMCID: PMC9157139 DOI: 10.1093/genetics/iyac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 04/13/2022] [Indexed: 01/16/2023] Open
Abstract
Gametogenesis is an evolutionarily conserved developmental program whereby a diploid progenitor cell undergoes meiosis and cellular remodeling to differentiate into haploid gametes, the precursors for sexual reproduction. Even in the simple eukaryotic organism Saccharomyces cerevisiae, the meiotic transcriptome is very rich and complex, thereby necessitating new tools for functional studies. Here, we report the construction of 5 stage-specific, inducible complementary DNA libraries from meiotic cells that represent over 84% of the genes found in the budding yeast genome. We employed computational strategies to detect endogenous meiotic transcript isoforms as well as library-specific gene truncations. Furthermore, we developed a robust screening pipeline to test the effect of each complementary DNA on competitive fitness. Our multiday proof-of-principle time course revealed 877 complementary DNAs that were detrimental for competitive fitness when overexpressed. The list included mitochondrial proteins that cause dose-dependent disruption of cellular respiration as well as library-specific gene truncations that expose a dominant negative effect on competitive growth. Together, these high-quality complementary DNA libraries provide an important tool for systematically identifying meiotic genes, transcript isoforms, and protein domains that are important for a specific biological function.
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Affiliation(s)
- Tina L Sing
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Katie Conlon
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Stephanie H Lu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Nicole Madrazo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Kaitlin Morse
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Juliet C Barker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Ina Hollerer
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Peter H Sudmant
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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Lu Y, Chen JX, Song P, Li H, Ai L, Cai YC, Chu YH, Chen SH. [Construction of a cDNA library for Sparganum mansoni and screening of diagnostic antigen cadidates]. Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi 2021; 33:380-386. [PMID: 34505445 DOI: 10.16250/j.32.1374.2021143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To construct a cDNA library of Sparganum mansoni and immunoscreen antigen candidates for immunodiagnosis of sparganosis mansoni. METHODS Total RNA was extracted from S. mansoni, and reversely transcribed into cDNA, which was ligated into the phage vector. These recombinant vectors were packaged in vitro to construct the SMART cDNA library of S. mansoni. Then, the cDNA library was immunoscreened with sera from patients with sparganosis mansoni to yield positive clones. The inserted fragments of positive clones were sequenced and subjected to homology analyses, and the structure and functions of the coding proteins were predicted. RESULTS The SMATR cDNA library of S. mansoni was successfully constructed. The titer of the cDNA library was 6.25 × 106 pfu/mL, with a recombinant efficiency of 100%, and the mean length of the inserted fragments in the library was larger than 1 100 bp. A total of 12 positive clones were obtained by immunoscreening, and were categorized into Sm-I (Sm60-1), Sm-II (Sm58-1), Sm-III (Sm20-1) and Sm-IV (Sm22-3), with 1 134, 1 063, 883 bp and 969 bp long inserted fragments. Their coding proteins were highly homologous with the Spirometra erinaceieuropaei antigenic polypeptide, cytoplasmic antigen, ribosomal protein S4-like protein and unnamed protein product, respectively. CONCLUSIONS A SMART cDNA library of S. mansoni has been successfully constructed and 4 categories of positive clones have been identified, which provides a basis for further studies on diagnostic antigens for sparganosis mansoni.
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Affiliation(s)
- Y Lu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - J X Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - P Song
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - H Li
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - L Ai
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - Y C Cai
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - Y H Chu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - S H Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
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Islam MS, Mohamed G, Polash SA, Hasan MA, Sultana R, Saiara N, Dong W. Antimicrobial Peptides from Plants: A cDNA-Library Based Isolation, Purification, Characterization Approach and Elucidating Their Modes of Action. Int J Mol Sci 2021; 22:8712. [PMID: 34445412 DOI: 10.3390/ijms22168712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 12/19/2022] Open
Abstract
Even in a natural ecosystem, plants are continuously threatened by various microbial diseases. To save themselves from these diverse infections, plants build a robust, multilayered immune system through their natural chemical compounds. Among the several crucial bioactive compounds possessed by plants’ immune systems, antimicrobial peptides (AMPs) rank in the first tier. These AMPs are environmentally friendly, anti-pathogenic, and do not bring harm to humans. Antimicrobial peptides can be isolated in several ways, but recombinant protein production has become increasingly popular in recent years, with the Escherichia coli expression system being the most widely used. However, the efficacy of this expression system is compromised due to the difficulty of removing endotoxin from its system. Therefore, this review suggests a high-throughput cDNA library-based plant-derived AMP isolation technique using the Bacillus subtilis expression system. This method can be performed for large-scale screening of plant sources to classify unique or homologous AMPs for the agronomic and applied field of plant studies. Furthermore, this review also focuses on the efficacy of plant AMPs, which are dependent on their numerous modes of action and exceptional structural stability to function against a wide range of invaders. To conclude, the findings from this study will be useful in investigating how novel AMPs are distributed among plants and provide detailed guidelines for an effective screening strategy of AMPs.
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Shi Y, Bethea JP, Hetzel-Ebben HL, Landim-Vieira M, Mayper RJ, Williams RL, Kessler LE, Ruiz AM, Gargiulo K, Rose JSM, Platt G, Pinto JR, Washburn BK, Chase PB. Mandibular muscle troponin of the Florida carpenter ant Camponotus floridanus: extending our insights into invertebrate Ca 2+ regulation. J Muscle Res Cell Motil 2021; 42:399-417. [PMID: 34255253 DOI: 10.1007/s10974-021-09606-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/07/2021] [Indexed: 12/18/2022]
Abstract
Ants use their mandibles for a variety of functions and behaviors. We investigated mandibular muscle structure and function from major workers of the Florida carpenter ant Camponotus floridanus: force-pCa relation and velocity of unloaded shortening of single, permeabilized fibres, primary sequences of troponin subunits (TnC, TnI and TnT) from a mandibular muscle cDNA library, and muscle fibre ultrastructure. From the mechanical measurements, we found Ca2+-sensitivity of isometric force was markedly shifted rightward compared with vertebrate striated muscle. From the troponin sequence results, we identified features that could explain the rightward shift of Ca2+-activation: the N-helix of TnC is effectively absent and three of the four EF-hands of TnC (sites I, II and III) do not adhere to canonical sequence rules for divalent cation binding; two alternatively spliced isoforms of TnI were identified with the alternatively spliced exon occurring in the region of the IT-arm α-helical coiled-coil, and the N-terminal extension of TnI may be involved in modulation of regulation, as in mammalian cardiac muscle; and TnT has a Glu-rich C-terminus. In addition, a structural homology model was built of C. floridanus troponin on the thin filament. From analysis of electron micrographs, we found thick filaments are almost as long as the 6.8 μm sarcomeres, have diameter of ~ 16 nm, and typical center-to-center spacing of ~ 46 nm. These results have implications for the mechanisms by which mandibular muscle fibres perform such a variety of functions, and how the structure of the troponin complex aids in these tasks.
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Affiliation(s)
- Yun Shi
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Julia P Bethea
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Hannah L Hetzel-Ebben
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Maicon Landim-Vieira
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, 32306, USA
| | - Ross J Mayper
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Regan L Williams
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Lauren E Kessler
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Amanda M Ruiz
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Kathryn Gargiulo
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Jennifer S M Rose
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Grayson Platt
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Jose R Pinto
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, 32306, USA
| | - Brian K Washburn
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - P Bryant Chase
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA. .,Department of Biological Science, Florida State University, Biology Unit One, Box 3064370, Tallahassee, FL, 32306-4370, USA.
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Liu D, Li L, Cao X, Wu J, Du G, Shang Y. Selection and identification of single-domain antibody against Peste des Petits Ruminants virus. J Vet Sci 2021; 22:e45. [PMID: 34170088 PMCID: PMC8318796 DOI: 10.4142/jvs.2021.22.e45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/08/2020] [Accepted: 02/10/2021] [Indexed: 12/11/2022] Open
Abstract
Background Peste des petits ruminants (PPR) is an infectious disease caused by the peste des petits ruminants virus (PPRV) that mainly produces respiratory symptoms in affected animals, resulting in great losses in the world's agriculture industry every year. Single-domain variable heavy chain (VHH) antibody fragments, also referred to as nanobodies, have high expression yields and other advantages including ease of purification and high solubility. Objectives The purpose of this study is to obtain a single-domain antibody with good reactivity and high specificity against PPRV. Methods A VHH cDNA library was established by immunizing camels with PPRV vaccine, and the capacity and diversity of the library were examined. Four PPRV VHHs were selected, and the biological activity and antigen-binding capacity of the four VHHs were identified by western blot, indirect immunofluorescence, and enzyme-linked immunosorbent assay (ELISA) analyses. ELISA was used to identify whether the four VHHs were specific for PPRV, and VHH neutralization tests were carried out. ELISA and western blot analyses were used to identify which PPRV protein was targeted by VHH2. Results The PPRV cDNA library was constructed successfully. The library capacity was greater than 2.0 × 106 cfu/mL, and the inserted fragment size was approximately 400 bp to 2000 bp. The average length of the cDNA library fragment was about 1000 bp, and the recombination rate was approximately 100%. Four single-domain antibody sequences were selected, and proteins expressed in the supernatant were obtained. The four VHHs were shown to have biological activity, close affinity to PPRV, and no cross-reaction with common sheep diseases. All four VHHs had neutralization activity, and VHH2 was specific to the PPRV M protein. Conclusions The results of this preliminary research of PPRV VHHs showed that four screened VHH antibodies could be useful in future applications. This study provided new materials for inclusion in PPRV research.
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Affiliation(s)
- Dan Liu
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Lingxia Li
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Xiaoan Cao
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Jinyan Wu
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Guoyu Du
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Youjun Shang
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
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Seike T, Narazaki Y, Kaneko Y, Shimizu H, Matsuda F. Random Transfer of Ogataea polymorpha Genes into Saccharomyces cerevisiae Reveals a Complex Background of Heat Tolerance. J Fungi (Basel) 2021; 7:302. [PMID: 33921057 DOI: 10.3390/jof7040302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 01/20/2023] Open
Abstract
Horizontal gene transfer, a process through which an organism acquires genes from other organisms, is a rare evolutionary event in yeasts. Artificial random gene transfer can emerge as a valuable tool in yeast bioengineering to investigate the background of complex phenotypes, such as heat tolerance. In this study, a cDNA library was constructed from the mRNA of a methylotrophic yeast, Ogataea polymorpha, and then introduced into Saccharomyces cerevisiae. Ogataea polymorpha was selected because it is one of the most heat-tolerant species among yeasts. Screening of S. cerevisiae populations expressing O. polymorpha genes at high temperatures identified 59 O. polymorpha genes that contribute to heat tolerance. Gene enrichment analysis indicated that certain S. cerevisiae functions, including protein synthesis, were highly temperature-sensitive. Additionally, the results confirmed that heat tolerance in yeast is a complex phenotype dependent on multiple quantitative loci. Random gene transfer would be a useful tool for future bioengineering studies on yeasts.
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Islas-Flores T, Galán-Vásquez E, Villanueva MA. Screening a Spliced Leader-Based Symbiodinium microadriaticum cDNA Library Using the Yeast-Two Hybrid System Reveals a Hemerythrin-Like Protein as a Putative SmicRACK1 Ligand. Microorganisms 2021; 9:microorganisms9040791. [PMID: 33918967 PMCID: PMC8070245 DOI: 10.3390/microorganisms9040791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/13/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022] Open
Abstract
The dinoflagellate Symbiodiniaceae family plays a central role in the health of the coral reef ecosystem via the symbiosis that establishes with its inhabiting cnidarians and supports the host metabolism. In the last few decades, coral reefs have been threatened by pollution and rising temperatures which have led to coral loss. These events have raised interest in studying Symbiodiniaceae and their hosts; however, progress in understanding their metabolism, signal transduction pathways, and physiology in general, has been slow because dinoflagellates present peculiar characteristics. We took advantage of one of these peculiarities; namely, the post-transcriptional addition of a Dino Spliced Leader (Dino-SL) to the 5' end of the nuclear mRNAs, and used it to generate cDNA libraries from Symbiodinium microadriaticum. We compared sequences from two Yeast-Two Hybrid System cDNA Libraries, one based on the Dino-SL sequence, and the other based on the SMART technology (Switching Mechanism at 5' end of RNA Transcript) which exploits the template switching function of the reverse transcriptase. Upon comparison of the performance of both libraries, we obtained a significantly higher yield, number and length of sequences, number of transcripts, and better 5' representation from the Dino-SL based library than from the SMART library. In addition, we confirmed that the cDNAs from the Dino-SL library were adequately expressed in the yeast cells used for the Yeast-Two Hybrid System which resulted in successful screening for putative SmicRACK1 ligands, which yielded a putative hemerythrin-like protein.
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Affiliation(s)
- Tania Islas-Flores
- Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, UNAM, Prolongación Avenida Niños Héroes S/N, Puerto Morelos, Quintana Roo 77580, México
- Correspondence: (T.I.-F.); (M.A.V.); Tel.: +52-998-871-0009 (T.I.-F. & M.A.V.)
| | - Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigación en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, UNAM, Circuito Escolar 3000, Ciudad Universitaria, Ciudad de México CP 04510, México;
| | - Marco A. Villanueva
- Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, UNAM, Prolongación Avenida Niños Héroes S/N, Puerto Morelos, Quintana Roo 77580, México
- Correspondence: (T.I.-F.); (M.A.V.); Tel.: +52-998-871-0009 (T.I.-F. & M.A.V.)
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Bacon K, Blain A, Bowen J, Burroughs M, McArthur N, Menegatti S, Rao BM. Quantitative Yeast-Yeast Two Hybrid for the Discovery and Binding Affinity Estimation of Protein-Protein Interactions. ACS Synth Biol 2021; 10:505-514. [PMID: 33587591 DOI: 10.1021/acssynbio.0c00472] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Quantifying the binding affinity of protein-protein interactions is important for elucidating connections within biochemical signaling pathways, as well as characterization of binding proteins isolated from combinatorial libraries. We describe a quantitative yeast-yeast two-hybrid (qYY2H) system that not only enables the discovery of specific protein-protein interactions but also efficient, quantitative estimation of their binding affinities (KD). In qYY2H, the bait and prey proteins are expressed as yeast cell surface fusions using yeast surface display. We developed a semiempirical framework for estimating the KD of monovalent bait-prey interactions, using measurements of bait-prey yeast-yeast binding, which is mediated by multivalent interactions between yeast-displayed bait and prey. Using qYY2H, we identified interaction partners of SMAD3 and the tandem WW domains of YAP from a cDNA library and characterized their binding affinities. Finally, we showed that qYY2H could also quantitatively evaluate binding interactions mediated by post-translational modifications on the bait protein.
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Affiliation(s)
- Kaitlyn Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Abigail Blain
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - John Bowen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Matthew Burroughs
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Nikki McArthur
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
- Golden LEAF Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Balaji M. Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
- Golden LEAF Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, North Carolina 27695, United States
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Ghildiyal R, Gabrani R. Deciphering the human cellular interactors of alphavirus unique domain of chikungunya virus. Virus Res 2021; 295:198288. [PMID: 33418023 DOI: 10.1016/j.virusres.2020.198288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 12/07/2020] [Accepted: 12/25/2020] [Indexed: 01/10/2023]
Abstract
The life-threatening re-emerged chikungunya virus (CHIKV) can cause an epidemic outbreak and still has no vaccine available so far. Alphavirus unique domain (AUD) of CHIKV nsP3 is a multifunctional domain that remains conserved among alphaviruses and is critical for CHIKV replication. The understanding of AUD-host protein-protein interactions and their association with the cellular processes concerning CHIKV infection are not well studied. In the current study, the protein-protein interactions of AUD and its human host were elucidated by screening of universal human cDNA library using yeast two-hybrid system. The chosen interactions were further validated by GST pull-down assay, and their network mapping was analyzed. The study revealed that the identified interactors are linked with the vesicle trafficking and transcription corepressor activities. Further, the interfacial residues of interactions between viral and host proteins were predicted, which will further provide the new platform to develop novel antivirals.
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Affiliation(s)
- Ritu Ghildiyal
- Center for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, Noida, UP, 201309, India.
| | - Reema Gabrani
- Center for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, Noida, UP, 201309, India.
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Hsiao CJ, Hsieh CY, Hsieh LS. Cloning and characterization of the Bambusa oldhamii BoMDH-encoded malate dehydrogenase. Protein Expr Purif 2020; 174:105665. [PMID: 32416131 DOI: 10.1016/j.pep.2020.105665] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/07/2020] [Accepted: 05/06/2020] [Indexed: 12/25/2022]
Abstract
Malate dehydrogenase (MDH), which is ubiquitously occurred in nature, catalyzes the interconversion of malate and oxaloacetate. Higher plants contain multiple forms of MDH that differ in coenzyme specificity, subcellular localization and physiological function. A putative Bambusa oldhamii BoMDH cDNA was screened with the specific probe from the bamboo cDNA library. Sequence alignment shows that there's a high homology between the deduced amino acid sequence of BoMDH and MDH protein in Oryza sativa glyoxysome (92%). A 57 kDa fusion protein was expressed by IPTG induction in Escherichia coli BL21 (DE3), and an obvious MDH activity was detected in the recombinant protein. The molecular mass of recombinant BoMDH was estimated to be 120 kDa, and the subunit form was 57 kDa by denatured SDS-PAGE, indicating that BoMDH presents as a homodimer. The optimum temperature and pH for BoMDH activity were 40 °C and 9.5, respectively. The Km values of BoMDH for malate and NAD+ were 5.2 mM and 0.52 mM. The kcat/Km values of BoMDH for malate and NAD+ were 163 min-1 mM-1 and 3060 min-1 mM-1.
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Affiliation(s)
- Che-Jen Hsiao
- Department of Ecology and Conservation Biology, Texas A&M University, 2126 TAMU College Station, TX, 77843, USA
| | - Chun-Yen Hsieh
- Department of Pathology and Laboratory Medicine, Shin Kong Wu Ho-Su Memorial Hospital, No. 95, Wen Chang Road, Shih Lin District, Taipei City 111, Taiwan, ROC
| | - Lu-Sheng Hsieh
- Department of Food Science, Tunghai University, No. 1727, Section 4, Taiwan Boulevard, Xitun District, Taichung, 40704, Taiwan, ROC.
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Shen H, Zhang X, Al Hafiz MA, Liang X, Yao Q, Guo M, Xu G, Zhong X, Zhou Q, Zhao H. The Proteins Interacting with Prmt5 in Medaka (Oryzias latipes) Identified by Yeast Two-Hybridization. Protein Pept Lett 2020; 27:971-978. [PMID: 32370700 DOI: 10.2174/0929866527666200505213431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/08/2020] [Accepted: 03/31/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Prmt5 plays major role in regulation of gene expression, RNA processing, cell growth and differentiation, signal transduction, germ cell development, etc., in mammals. Prmt5 is also related to cancer. Knowing the proteins interacting with Prmt5 is important to understand Prmt5's function in cells. Although there have been reports on proteins binding with Prmt5 in mammals, the partner proteins of Prmt5 in fish are still unclear. OBJECTIVES The objective was to obtain proteins that bind with Prmt5 in medaka, a model fish. METHODS Yeast two hybridization was adopted to achieve the objective. Medaka Prmt5 was used as a bait to fish the prey, binding proteins in a cDNA library of medaka. Co-immunoprecipitation and in silicon analysis were performed to study the interaction of medaka Mep50 and Prmt5. RESULTS Eight proteins were identified to bind with Prmt5 from 69 preliminary positive colonies. The binding proteins are methylosome protein 50 (Mep50), apolipoprotein A-I-like (Apo-AI), PR domain containing protein 1a with zinc fingers (Prdm1a), Prdm1b, T-cell immunoglobulin mucin family member 3 (Tim-3), phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthase (Paics), NADH dehydrogenase subunit 4 (ND4) and sciellin (Scl). Co-immunoprecipitation confirmed the interaction of medaka Prmt5 and Mep50. Predicted structures of medaka Prtm5 and Mep50 are similar to that of human PRMT5 and MEP50. CONCLUSION Medaka Mep50, Prdm1a, Prdm1b, Apo-AI, Tim-3, Paics, ND4, and Scl bind with Prmt5.
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Affiliation(s)
- Hao Shen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xiaosha Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Md Abdullah Al Hafiz
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xiaoting Liang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Qiting Yao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Maomao Guo
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Gongyu Xu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xueping Zhong
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Qingchun Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Haobin Zhao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
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Yamada Y, Miyamoto T, Higuchi S, Ono M, Kobara H, Asaka R, Ando H, Suzuki A, Shiozawa T. cDNA expression library screening revealed novel functional genes involved in clear cell carcinogenesis of the ovary in vitro. J OBSTET GYNAECOL 2020; 41:100-105. [PMID: 32157937 DOI: 10.1080/01443615.2020.1716310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In order to identify genes involved in the pathogenesis of clear cell carcinoma of the ovary (CCC), functional screening using a cDNA expression library was performed. We extracted mRNA from a CCC cell line (RMG-1), established a cDNA library using a retroviral vector, transfected that library into mouse NIH3T3 cells and sequenced the resultant foci. The tissue-type specific expression of isolated genes and their transforming activities were evaluated. Seven genes were isolated. Of these genes, the mRNA expression of SEC61B and DVL1 is significantly stronger in CCC than in other histological types (p < .05). Immunohistochemical staining reveals the stronger expression of SEC61B and C1ORF38 than normal ovarian tissues (p < .05). Focus formation is confirmed by the transfection of SEC61B, C1ORF38, and DVL1 into NIH3T3 cells. The present study identified novel genes including SEC61B, C1ORF38, and DVL1, involved in the pathogenesis of CCC. These genes may be additional therapeutic targets for CCC.Impact statementWhat is already known on this subject? Several important genetic abnormalities, including ARID1A and PIK3CA mutations, have been reported in ovarian clear cell carcinoma (CCC).What the results of this study add? SEC61B, C1ORF38, and DVL1 were newly detected as candidate genes involved in ovarian clear cell carcinogenesis.What the implications are of these findings for clinical practice and/or further research? Functional screening using a cDNA expression library may be a useful technique to identify functional genes for pathogenesis. The information obtained using this technique may provide new therapeutic targets of CCC.
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Affiliation(s)
- Yasushi Yamada
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| | - Tsutomu Miyamoto
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| | - Shotaro Higuchi
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| | - Motoki Ono
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| | - Hisanori Kobara
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| | - Ryoichi Asaka
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| | - Hirofumi Ando
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| | - Akihisa Suzuki
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| | - Tanri Shiozawa
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
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Yee KT, Rojnuckarin P. Complementary DNA library of Myanmar Russell's viper (Daboia russelii siamensis) venom gland. Comp Biochem Physiol C Toxicol Pharmacol 2020; 227:108634. [PMID: 31655298 DOI: 10.1016/j.cbpc.2019.108634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 11/22/2022]
Abstract
Geographical variations of snake venoms of the same species are well-known. Exploring the components of venom from each region will give insights in its distinctive toxicities. Venom gland cDNA library of Russell's viper (RV) from Myanmar (Daboia russelii siamensis) was constructed to create a catalog of expressed sequences tags (ESTs) and to compare with sequences from RV of other countries. The cDNA library of venom gland was generated by using CloneMiner™ II cDNA Library Construction Kit. Clones were subjected to Sanger sequencing and analyses by bioinformatics tools. From 251 isolated clones, 38 ESTs were assembled into 6 clusters and 21 singlets. Toxin sequences contributed to 57.9% of all transcripts and Kunitz-type serine protease inhibitors are most abundant (45.5% of toxin transcripts). The Myanmar RV phospholipase A2 (PLA2) showed 98% and 74% identity to D. r. russelii PLA2 from India (DrK-bI) and PLA2 of D. r. siamensis from Thailand as well as Taiwan, respectively. The cysteine-rich secretory protein (CRISP) homologs from Myanmar RV were first identified here showing homology to CRISP from Taiwan RV and European vipers with 98% and 90% identity, respectively. The RV 5' nucleotidase was also first cloned. In summary, Myanmar RV showed a unique gene expression pattern and sequences. Large scale analysis by next-generation sequencing is warranted.
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Affiliation(s)
- Khin Than Yee
- Biochemistry Research Division, Department of Medical Research, Yangon 11191, Myanmar
| | - Ponlapat Rojnuckarin
- Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Rama IV Rd, Patumwan, Bangkok 10330, Thailand.
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Bharati AP, Ghosh SK. Construction of strains to identify novel factors for regulation of centromeric cohesion protection (CCP) and sister kinetochore mono-orientation (SKM). BMC Mol Cell Biol 2019; 20:44. [PMID: 31640543 PMCID: PMC6806570 DOI: 10.1186/s12860-019-0231-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 10/02/2019] [Indexed: 11/11/2022] Open
Abstract
Background Meiosis-I is a unique type of chromosome segregation where each chromosome aligns and segregates from its homolog. The mechanism of meiosis I homolog separation in different eukaryotes depends on their centromere and kinetochore architecture which in turn relies mainly on two processes, first on a specialized four protein complex known as monopolin and second, the centromeric cohesion protection (CCP). However, in mammals the complex has not been identified. Furthermore, in budding yeast, there could be additional factors in this process which includes some meiosis specific and some non meiosis specific factors. Result We constructed two strains. In the first strain we expressed Mam1 and Cdc5 which leads to sister kinetochore monoorientation (SKM) and in the second case we expressed Rec8 and Spo13 which enhanced CCP even in mitosis. The expression of these proteins in mitotically dividing cells caused co-orientation of the chromosomes, which lead to the cell death followed by miss-segregation of chromosomes. Then we utilized these strains to screen the cDNA libraries from yeast and mammals to identify the novel factors which participate in CCP and SKM. Finally, SGY4119 strain expressing Spo13 and Rec8 was transformed with pRS316 gal cDNA library and transformants were screened for lethality on galactose. We screened ~ 105 transformants colonies. Out of these ~ 3000 colonies were able to survive on galactose plate which was narrow down to 6 on the basis of desired phenotype. Conclusion So far, meiosis specific kinetochore proteins have been identified only in two yeasts. Recently, in mammals a meiosis specific kinetochore protein (MEIKIN) has been identified with similar function. Till now a single protein in mammals and four proteins monopolin complex in budding yeast has been identified to coorient the centromere. Many more novel factors have to be identified yet. That is why we wished to device genetic screen using a functional genomics approach. Since the list of proteins already identified in yeast is not exhaustive as the circumstantial evidence suggests, we wish to use the same yeast strains to identify additional novel yeast proteins that may be involved in the execution of meiosis.
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Ciesek S, von Hahn T. Expression Cloning of Host Factors Required for the HCV Replication Cycle. Methods Mol Biol 2019; 1911:169-82. [PMID: 30593625 DOI: 10.1007/978-1-4939-8976-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Chronic infection with the hepatitis C virus (HCV) is a common cause of chronic liver disease, cirrhosis, and liver cancer. Like most viruses, HCV depends of a number of factors encoded by its host cell to execute its replication cycle and create. Expression cloning is one of several possible approaches that have been employed to identify novel host factors essential for the HCV replication cycle. It involves generation of a cDNA library from a cell type with a desired trait (such as ability to bind E2 or being susceptible to HCV infection), expression of that library in a different cell type missing the trait of interest, and selection for cell clones that have acquired that trait through expression of a specific cDNA. This chapter describes an expression cloning approach similar to the one that was used to identify the tight junction component claudin-1 as an essential HCV cell entry factor.
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Hu L, Zhao YE, Niu DL, Yang R, Zeng JH. The Construction of Full-Length cDNA Library for Otodectes cynotis. Acta Parasitol 2019; 64:251-6. [PMID: 30864098 DOI: 10.2478/s11686-019-00034-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/16/2019] [Indexed: 02/04/2023]
Abstract
BACKGROUND Otodectes cynotis (Hering, 1838) is the pathogen of otodectic mange distributed worldwide. The mite mainly infests carnivores and, sometimes, humans. However, due to the lack of cDNA library, research on its pathogenesis has been challenging. METHODS To solve this problem, the present study first sampled O. cynotis mites from an infested cat from Xi'an, China, for RNA extraction. Then, the full-length cDNA library was constructed using the SMART technique. Finally, positive clones > 500 bp and Hsc70-5 gene fragment specifically amplified from the cDNA library were sequenced and analyzed to verify the library's reliability. RESULTS Results showed that RNA extracted from 300 mites had good quality with a concentration of 149 ng/μl and OD260/OD280 of 1.99. The library satisfied the quality standard of a good library with a titer of 5.02 × 105 PFU/ml and a combination rate of 97.61%. In addition, clone 4 and Hsc70-5 showed 98.38% and 99.72% identity with Ef1-α and Hsc70-5 gene sequences of O. cynotis in GenBank, respectively. CONCLUSION The cDNA library of O. cynotis constructed here was successful and reliable, creating the basis for research on RNA sequencing and functional genes of O. cynotis.
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Vigneron N, Stroobant V, Ma W, Michaux A, Van den Eynde BJ. Identifying Antigens Recognized by Cytolytic T Lymphocytes on Tumors. Methods Mol Biol 2019; 1988:159-86. [PMID: 31147940 DOI: 10.1007/978-1-4939-9450-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Identification of antigenic peptides recognized by cytolytic T lymphocytes (CTL) is a prerequisite for the development of targeted cancer immunotherapy approaches. This chapter provides a global approach for the identification of peptides recognized by CTL. It implies the identification of the HLA molecule presenting the peptide as well as the design and screening of a cDNA library derived from the tumor cells. Methods used for the identification of spliced peptides on tumors are also described.
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Iqbal A, Yang Y, Qadri R, Wu Y, Li J, Shah F, Hamayun M, Hussain A. QRREM method for the isolation of high-quality RNA from the complex matrices of coconut. Biosci Rep 2019; 39:BSR20181163. [PMID: 30429235 DOI: 10.1042/BSR20181163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/21/2018] [Accepted: 11/05/2018] [Indexed: 11/17/2022] Open
Abstract
Complex plant tissues vary in hardness, i.e. some are succulent, while others are complex to break. Besides, plant metabolites, such as polysaccharides, proteins, polyphenols and lipids, can greatly interfere with the RNA extraction. So, in order to obtain a high-quality RNA from the complex tissues (like coconut endosperm, coconut apple and coconut leaf bud) rich in secondary metabolites, a robust method is demanded. Several methods (MRIP, CTAB and TRIZOL) have been used previously for the isolation of quality RNA from the coconut tissues, but without any success. The present study will provide with the details of a new method (Quick and Reliable RNA Extraction Method or QRREM), which have efficiently isolated the intact RNA form the complex tissues of coconut compared with CTAB, Trizol and RNA plant. The method has been validated for the isolation of high-quality intact RNA from the other available plant species (Areca/betel nut, mint and spring onion). The method has various advantages over the other methods in terms of time and cost effectiveness. Furthermore, the resulted RNA from various tissues of coconut performed well in the downstream experiments, i.e. reverse transcription and PCR for the production and amplification of cDNA.
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Dharmaraj K, Cui W, Rikkerink EHA, Templeton MD. Construction of a kiwifruit yeast two-hybrid cDNA library to identify host targets of the Pseudomonas syringae pv. actinidiae effector AvrPto5. BMC Res Notes 2019; 12:63. [PMID: 30691538 PMCID: PMC6350409 DOI: 10.1186/s13104-019-4102-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/19/2019] [Indexed: 11/10/2022] Open
Abstract
Objective Bacterial canker is a destructive disease of kiwifruit caused by the Gram-negative bacterium Pseudomonas syringae pv. actinidiae (Psa). To understand the disease-causing mechanism of Psa, a kiwifruit yeast two-hybrid cDNA library was constructed to identify putative host targets of the Psa Type Three Secreted Effector AvrPto5. Results In this study, we used the Mate & Plate™ yeast two-hybrid library method for constructing a kiwifruit cDNA library from messenger RNA of young leaves. The constructed library consisted of 2.15 × 106 independent clones with an average insert size of 1.52 kb. The screening of the kiwifruit yeast two-hybrid cDNA library with Psa AvrPto5 revealed the interaction of a V-type proton ATPase subunit-H, a proline rich-protein and heavy metal-associated isoprenylated plant protein 26. Among these, heavy metal-associated isoprenylated plant protein 26 showed a positive interaction with Psa AvrPto5 as both prey and bait. Electronic supplementary material The online version of this article (10.1186/s13104-019-4102-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karthikeyan Dharmaraj
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.,The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand.,Plant Health and Environment Laboratory, Ministry for Primary Industries, 231 Morrin Road, Auckland, 1072, New Zealand
| | - Wei Cui
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Erik H A Rikkerink
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Matthew D Templeton
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand. .,The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand.
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Hu Z, Chen B, Xiao Z, Zhou X, Liu Z. Transcriptomic Analysis of the Spider Venom Gland Reveals Venom Diversity and Species Consanguinity. Toxins (Basel) 2019; 11:toxins11020068. [PMID: 30682870 PMCID: PMC6409621 DOI: 10.3390/toxins11020068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 01/09/2019] [Accepted: 01/19/2019] [Indexed: 11/16/2022] Open
Abstract
Selenocosmia jiafu (S. jiafu) has been recently identified as a new species of spider in China. It lives in the same habitat as various other venomous spiders, including Chilobrachys jingzhao (C. jingzhao), Selenocosmia huwena (S. huwena), and Macrothele raveni (M. raveni). The venom from these different species of spiders exhibits some similarities and some differences in terms of their biochemical and electrophysiological properties. With the objective to illustrate the diversity in venom peptide toxins and to establish the evolutionary relationship between different spider species, we first performed transcriptomic analysis on a cDNA library from the venom gland of S. jiafu. We identified 146 novel toxin-like sequences, which were classified into eighteen different superfamilies. This transcriptome was then compared with that of C. jingzhao, which revealed that the putative toxins from both spider venoms may have originated from the same ancestor, although novel toxins evolved independently in the two species. A BLAST search and pharmacological analysis revealed that the two venoms have similar sodium channel modulation activity. This study provides insights into the venom of two closely related species of spider, which will prove useful towards understanding the structure and function of their toxins.
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Affiliation(s)
- Zhaotun Hu
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, College of Biological and Food Engineering, Huaihua University, Huaihua 418008, China.
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China.
| | - Bo Chen
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China.
| | - Zhen Xiao
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China.
| | - Xi Zhou
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China.
| | - Zhonghua Liu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China.
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Abstract
Deep sequencing technology has revolutionized transcriptome analyses of both prokaryotes and eukaryotes. RNA-sequencing (RNA-seq), which is based on massively parallel sequencing of cDNAs, has been used to annotate transcript boundaries and has revealed widespread antisense transcription as well as a wealth of novel noncoding transcripts in many bacterial pathogens. Moreover, RNA-seq is nowadays also widely used to comprehensively explore the interaction between RNA-binding proteins and their RNA targets on a genome-wide level in many human-pathogenic bacteria. In particular, immunoprecipitation of an RNA-binding protein (RBP) of interest followed by isolation and analysis of all bound RNAs (RNA immunoprecipitation (RIP)) allows rapid characterization of its RNA regulon. Here, we describe an experimental approach which employs co-immunoprecipitation (coIP) of the RNA-binding chaperone Hfq along with bound RNAs followed by deep-sequencing of co-purified RNAs (RIP-Seq) from a genetically modified strain of Neisseria meningitidis expressing a chromosomally encoded Hfq-3×FLAG protein. This approach allowed us to comprehensively identify both mRNAs and sRNAs as targets of Hfq and served as an excellent starting point for sRNA research in this human pathogenic bacterium.
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Affiliation(s)
- Nadja Heidrich
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Saskia Bauriedl
- Institute for Molecular Infection Biology (IMIB) and Institute for Hygiene and Microbiology (IHM), University of Würzburg, Würzburg, Germany
| | - Christoph Schoen
- Institute for Hygiene and Microbiology (IHM), University of Würzburg, Würzburg, Germany.
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Zhang M, Zhang H, Zheng JX, Mo H, Xia KF, Jian SG. Functional Identification of Salt-Stress-Related Genes Using the FOX Hunting System from Ipomoea pes-caprae. Int J Mol Sci 2018; 19:ijms19113446. [PMID: 30400210 PMCID: PMC6274920 DOI: 10.3390/ijms19113446] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 10/09/2018] [Accepted: 10/31/2018] [Indexed: 01/02/2023] Open
Abstract
Ipomoea pes-caprae is a seashore halophytic plant and is therefore a good model for studying the molecular mechanisms underlying salt and stress tolerance in plant research. Here, we performed Full-length cDNA Over-eXpressor (FOX) gene hunting with a functional screening of a cDNA library using a salt-sensitive yeast mutant strain to isolate the salt-stress-related genes of I. pes-caprae (IpSR genes). The library was screened for genes that complemented the salt defect of yeast mutant AXT3 and could grow in the presence of 75 mM NaCl. We obtained 38 candidate salt-stress-related full-length cDNA clones from the I. pes-caprae cDNA library. The genes are predicted to encode proteins involved in water deficit, reactive oxygen species (ROS) scavenging, cellular vesicle trafficking, metabolic enzymes, and signal transduction factors. When combined with the quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analyses, several potential functional salt-tolerance-related genes were emphasized. This approach provides a rapid assay system for the large-scale screening of I. pes-caprae genes involved in the salt stress response and supports the identification of genes responsible for the molecular mechanisms of salt tolerance.
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Affiliation(s)
- Mei Zhang
- Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Hui Zhang
- Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- University of the Chinese Academy of Sciences, Beijing 100039, China.
| | - Jie-Xuan Zheng
- Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- University of the Chinese Academy of Sciences, Beijing 100039, China.
| | - Hui Mo
- Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Kuai-Fei Xia
- Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Shu-Guang Jian
- Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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Wang Y, Li N, Chen T, Gong Y. Generation and characterization of expressed sequence tags (ESTs) from coralloid root cDNA library of Cycas debaoensis. Plant Divers 2018; 40:245-252. [PMID: 30740571 PMCID: PMC6224666 DOI: 10.1016/j.pld.2018.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 08/31/2018] [Accepted: 09/03/2018] [Indexed: 06/09/2023]
Abstract
A normalized full-length cDNA library was constructed from the coralloid roots of Cycas debaoensis by the DSN (duplex-specific nuclease) normalization method combined with the SMART (Switching Mechanism At 5' end of the RNA Transcript) technique. The titer of the original cDNA library was about 1.5 × 106 cfu·mL-1 and the average insertion size was about 1 kb with a high recombination rate (97%). The 5011 high-quality expressed sequence tags (ESTs) were obtained from 5393 randomly picked cDNA clones. Clustering and assembly of ESTs resulted in 2984 unique sequences, consisting of 618 contigs and 2366 singlets. EST sequence annotation revealed that 2333 and 1901 unigenes were functionally annotated in the NCBI non-redundant database and Swiss-Prot protein database, respectively. Functional analysis demonstrated that 1495 (50.1%) unigenes were associated with 4082 Gene Ontology (GO) terms. A total of 847 unigenes were grouped into 22 Cluster of Orthologous Groups (COG) functional categories. Based on the EST dataset, 22 ESTs that encoded putative receptor-like protein kinase (RLK) genes were screened. Furthermore, a total of 94 simple sequence repeats (SSRs) were discovered, of which 20 loci were successfully amplified in C. debaoensis. This study is the first EST analysis for the coralloid roots of C. debaoensis and provides a valuable genomic resource for novel gene discovery, gene expression and comparative genomics, conservation and management studies as well as applications in C. debaoensis and related cycad species.
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Affiliation(s)
- Yunhua Wang
- Shenzhen Key Laboratory of Southern Subtropical Plant Diversity, Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, Guangdong, China
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Ye L, Gui-Hua Z, Kun Y, Hong-Fa W, Ting X, Gong-Zhen L, Wei-Xia Z, Yong C. [Primary culture of cat intestinal epithelial cell and construction of its cDNA library]. Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi 2018; 29:464-467. [PMID: 29508581 DOI: 10.16250/j.32.1374.2016271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Objective To establish the primary cat intestinal epithelial cells (IECs) culture methods and construct the cDNA library for the following yeast two-hybrid experiment, so as to screen the virulence interaction factors among the final host. Methods The primary cat IECs were cultured by the tissue cultivation and combined digestion with collagenase XI and dispase I separately. Then the cat IECs cultured was identified with the morphological observation and cyto-keratin detection, by using goat anti-cyto-keratin monoclonal antibodies. The mRNA of cat IECs was isolated and used as the template to synthesize the first strand cDNA by SMART™ technology, and then the double-strand cDNAs were acquired by LD-PCR, which were subsequently cloned into the plasmid PGADT7-Rec to construct yeast two-hybrid cDNA library in the yeast strain Y187 by homologous recombination. Matchmaker™ Insert Check PCR was used to detect the size distribution of cDNA fragments after the capacity calculation of the cDNA library. Results The comparison of the two cultivation methods indicated that the combined digestion of collagenase XI and dispase I was more effective than the tissue cultivation. The cat IECs system of continuous culture was established and the cat IECs with high purity were harvested for constructing the yeast two-hybrid cDNA library. The library contained 1.1×106 independent clones. The titer was 2.8×109 cfu/ml. The size of inserted fragments was among 0.5-2.0 kb. Conclusion The yeast two-hybrid cDNA library of cat IECs meets the requirements of further screen research, and this study lays the foundation of screening the Toxoplasma gondii virulence interaction factors among the cDNA libraries of its final hosts.
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Affiliation(s)
- L Ye
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Shandong Institute of Parasitic Diseases, Jining 272033, China; First people's Hospital of Jining City, China
| | - Z Gui-Hua
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Shandong Institute of Parasitic Diseases, Jining 272033, China
| | - Y Kun
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Shandong Institute of Parasitic Diseases, Jining 272033, China
| | - W Hong-Fa
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Shandong Institute of Parasitic Diseases, Jining 272033, China
| | - X Ting
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Shandong Institute of Parasitic Diseases, Jining 272033, China
| | - L Gong-Zhen
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Shandong Institute of Parasitic Diseases, Jining 272033, China
| | - Z Wei-Xia
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Shandong Institute of Parasitic Diseases, Jining 272033, China
| | - C Yong
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Shandong Institute of Parasitic Diseases, Jining 272033, China
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Zhao GH, Liu Y, Cheng YT, Zhao QS, Qiu X, Xu C, Xiao T, Zhu S, Liu GZ, Yin K. Primary culture of cat intestinal epithelial cells in vitro and the cDNA library construction. Acta Parasitol 2018; 63:360-367. [PMID: 29654680 DOI: 10.1515/ap-2018-0041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 02/13/2018] [Indexed: 01/15/2023]
Abstract
Felids are the only definitive hosts of Toxoplasma gondii. To lay a foundation for screening the T. gondii-felids interaction factors, we have developed a reproducible primary culture method for cat intestinal epithelial cells (IECs). The primary IECs were isolated from a new born cat's small intestine jejunum region without food ingress, and respectively in vitro cultured by tissue cultivation and combined digestion method with collagenase XI and dispase I, then purified by trypsinization. After identification, the ds cDNA of cat IECs was synthesized for constructing pGADT7 homogenization three-frame plasmid, and transformed into the yeast Y187 for generating the cDNA library. Our results indicated that cultivation of primary cat IECs relays on combined digestion to form polarized and confluent monolayers within 3 days with typical features of normal epithelial cells. The purified cells cultured by digestion method were identified to be nature intestinal epithelial cells using immunohistochemical analysis and were able to maintain viability for at least 15 passages. The homogenizable ds cDNA, which is synthesized from the total RNA extracted from our cultured IECs, distributed among 0.5-2.0 kb, and generated satisfying three-frame cDNA library with the capacity of 1.2 × 106 and the titer of 5.2 × 107 pfu/mL. Our results established an optimal method for the culturing and passage of cat IECs model in vitro, and laid a cDNA library foundation for the subsequent interaction factors screening by yeast two-hybrid.
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Affiliation(s)
- Gui Hua Zhao
- Shandong Institute of Parasitical Disease, Shandong Academy of Medical Sciences, 11 Taibai Middle Road, Jining, 272033, Shandong, People's Republic of China
| | - Ye Liu
- Shandong Institute of Parasitical Disease, Shandong Academy of Medical Sciences, 11 Taibai Middle Road, Jining, 272033, Shandong, People's Republic of China
- The first people's Hospital of Jining City, 6 Health Road, Jining, 272011, Shandong, People's Republic of China
| | - Yun Tang Cheng
- Jining Center for Disease Control and Prevention, Jining 272000, Shandong, People's Republic of China
| | - Qing Song Zhao
- The first people's Hospital of Jining City, 6 Health Road, Jining, 272011, Shandong, People's Republic of China
| | - Xiao Qiu
- Shandong Institute of Parasitical Disease, Shandong Academy of Medical Sciences, 11 Taibai Middle Road, Jining, 272033, Shandong, People's Republic of China
- The first people's Hospital of Jining City, 6 Health Road, Jining, 272011, Shandong, People's Republic of China
| | - Chao Xu
- Shandong Institute of Parasitical Disease, Shandong Academy of Medical Sciences, 11 Taibai Middle Road, Jining, 272033, Shandong, People's Republic of China
| | - Ting Xiao
- Shandong Institute of Parasitical Disease, Shandong Academy of Medical Sciences, 11 Taibai Middle Road, Jining, 272033, Shandong, People's Republic of China
| | - Song Zhu
- Shandong Institute of Parasitical Disease, Shandong Academy of Medical Sciences, 11 Taibai Middle Road, Jining, 272033, Shandong, People's Republic of China
| | - Gong Zhen Liu
- Shandong Institute of Parasitical Disease, Shandong Academy of Medical Sciences, 11 Taibai Middle Road, Jining, 272033, Shandong, People's Republic of China
| | - Kun Yin
- Shandong Institute of Parasitical Disease, Shandong Academy of Medical Sciences, 11 Taibai Middle Road, Jining, 272033, Shandong, People's Republic of China
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Pothong K, Komalamisra C, Kalambaheti T, Watthanakulpanich D, Yoshino TP, Dekumyoy P. ELISA based on a recombinant Paragonimus heterotremus protein for serodiagnosis of human paragonimiasis in Thailand. Parasit Vectors 2018; 11:322. [PMID: 29843786 PMCID: PMC5975669 DOI: 10.1186/s13071-018-2878-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 04/29/2018] [Indexed: 11/29/2022] Open
Abstract
Background Paragonimus heterotremus is the main causative agent of paragonimiasis in Thailand. In Western blot diagnostic assays for paragonimiasis, the 35 kDa band present in crude P. heterotremus somatic extracts represents one of the known diagnostic bands. This study aimed to use a P. heterotremus cDNA library to create a recombinant version of this antigen for use in immunodiagnosis of paragonimiasis. Methods To accomplish this aim a cDNA expression library was constructed from adult worm mRNA and immuno-screened using antibodies from mice that had been immunized with the 35 kDa antigen. Screening resulted in the identification of an immunoreactive protein encoded by clone CE3, which contained an inserted sequence composed of 1292 base pairs. This clone was selected for use in the construction of a recombinant P. heterotremus protein because of its similarity to proactivator polypeptide. For recombinant protein expression, the CE3 gene sequence was inserted into the plasmid vector pRset and the resulting product had the expected molecular weight of 35 kDa. An IgG-ELISA based on the CE3 recombinant protein was evaluated by using sera from healthy individuals, from patients with paragonimiasis and other parasitic infections. This ELISA was performed by using human sera diluted at 1:2000, an optimized antigen concentration of 1 μg/ml, and anti-human IgG diluted at 1:4000. Results The cut-off optical density value was set as the mean + 2 standard deviations (0.54), which resulted in the test having a sensitivity of 88.89% and a specificity of 95.51%. The recombinant antigen could react with antibodies from P. heterotremus, P. pseudoheterotremus and P. westermani infections. Cross-reactivity occurred with a few cases of Blastocystis hominis infection (2/3), Bancroftian filariasis (1/10), opisthorchiasis (3/10), strongyloidiasis (4/10) and neurocysticercosis (1/11). Conclusions Given the high test sensitivity and specificity, reflected in the low level of heterologous infection cross-reactivity (11/215 serum samples), observed in the IgG-ELISA, this 35 kDa antigen may be useful for the detection of paragonimiasis. Electronic supplementary material The online version of this article (10.1186/s13071-018-2878-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kanokkarn Pothong
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Chalit Komalamisra
- Mahidol-Bangkok School of Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Thareerat Kalambaheti
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Dorn Watthanakulpanich
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Timothy P Yoshino
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Paron Dekumyoy
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.
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Su J, Lei H, Xiao T, Cui S. Ci-AMBP: a highly conserved member of the microglobulin superfamily of proteinase inhibitors in grass carp, Ctenopharyngodon idellus. Genes Genet Syst 2018; 92:251-256. [PMID: 29199250 DOI: 10.1266/ggs.16-00059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A full-length cDNA clone encoding grass carp (Ctenopharyngodon idellus) α1-microglobulin/bikunin precursor (Ci-AMBP) was isolated by subtracted differential hybridization screening from a liver cDNA library. The deduced amino acid sequence shared approximately 50% sequence identity with its mammalian counterparts, but more than 90% identity with another fish species. AMBPs are the precursors of the plasma glycoproteins α1-microglobulin (α1m) and bikunin. Both peptide structures and their chromosomal organization were well conserved in Ci-AMBP. The α1m and bikunin polypeptides are separated by the typical tetrapeptide R-A-R-R that provides an endoproteolytic cleavage site for maturation. The genetic organization of domains and functional motifs indicated that Ci-AMBP is a typical member of the lipocalin and Kunitz-type protease inhibitor superfamilies. Expression of the Ci-AMBP gene in different tissues/organs was evaluated using semi-quantitative RT-PCR and, in contrast to the restricted expression in other species, transcripts were detected in a wide range of tissues. The most abundant expression occurred in the secretory organs, which supports the roles of α1m and bikunin in the immune response to diseases and in the stress response.
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Affiliation(s)
- Jianming Su
- College of Veterinary Medicine, Hunan Agricultural University
| | - Hongyu Lei
- College of Veterinary Medicine, Hunan Agricultural University
| | - Tiaoyi Xiao
- College of Animal Science and Technology, Hunan Agricultural University
| | - Shuliang Cui
- College of Veterinary Medicine, Hunan Agricultural University.,Australian Phenomics Facility, John Curtin School of Medical Research, Australian National University
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Narazaki Y, Nomura Y, Morita K, Shimizu H, Matsuda F. Expression of Saccharomyces cerevisiae cDNAs to enhance the growth of non-ethanol-producing S. cerevisiae strains lacking pyruvate decarboxylases. J Biosci Bioeng 2018; 126:317-21. [PMID: 29636254 DOI: 10.1016/j.jbiosc.2018.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 03/05/2018] [Accepted: 03/12/2018] [Indexed: 11/24/2022]
Abstract
Metabolic engineering of Saccharomyces cerevisiae often requires a restriction on the ethanol biosynthesis pathway. The non-ethanol-producing strains, however, are slow growers. In this study, a cDNA library constructed from S. cerevisiae was used to improve the slow growth of non-ethanol-producing S. cerevisiae strains lacking all pyruvate decarboxylase enzymes (Pdc-, YSM021). Among the obtained 120 constructs expressing cDNAs, 34 transformants showed a stable phenotype with quicker growth. Sequence analysis showed that the open reading frames of PDC1, DUG1 (Cys-Gly metallo-di-peptidase in the glutathione degradation pathway), and TEF1 (translational elongation factor EF-1 alpha) genes were inserted into the plasmids of 32, 1, and 1 engineered strains, respectively. DUG1 function was confirmed by the construction of YSM021 pGK416-DUG1 strain because the specific growth rate of YSM021 pGK416-DUG1 (0.032 ± 0.0005 h-1) was significantly higher than that of the control strains (0.029 ± 0.0008 h-1). This suggested that cysteine supplied from glutathione was probably used for cell growth and for construction of Fe-S clusters. The results showed that the overexpression of cDNAs is a promising approach to engineer S. cerevisiae metabolism.
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Baradaran M, Jalali A, Naderi-Soorki M, Jokar M, Galehdari H. First Transcriptome Analysis of Iranian Scorpion, Mesobuthus Eupeus Venom Gland. Iran J Pharm Res 2018; 17:1488-1502. [PMID: 30568706 PMCID: PMC6269579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Scorpions are generally an important source of bioactive components, including toxins and other small peptides as attractive molecules for new drug development. Mesobuthus eupeus, from medically important and widely distributed Buthidae family, is the most abundant species in Iran. Researchers are interesting on the gland of this scorpion due to the complexity of its venom. Here, we have analyzed the transcriptome based on expressed sequence tag (EST) database from the venom tissue of Iranian M. eupeus by constructing a cDNA library and subsequent Sanger sequencing of obtained inserts. Sixty-three unique transcripts were identified, which were grouped in different categories, including Toxins (44 transcripts), Cell Proteins (9 transcripts), Antimicrobial Peptides (4 transcripts) and Unknown Peptides (3 transcripts). The analysis of the ESTs revealed several new components categorized among various toxin families with effect on ion channels. Sequence analysis of a new precursor provides evidence to validate the first CaTxs from M. eupeus. The results are exploration of the diversity of precursors expressed of Iranian M. eupeus venom gland. We further described comparative analysis of venom components of Iranian M. eupeus with other sibling species.
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Affiliation(s)
- Masoumeh Baradaran
- Toxicology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Amir Jalali
- Department of Toxicology, School of Pharmacy and Toxicology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Maryam Naderi-Soorki
- Genetics Department, School of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran. ,Corresponding author: E-mail: ;
| | - Mahmoud Jokar
- Cotton Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran.
| | - Hamid Galehdari
- Toxicology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Corresponding author: E-mail: ;
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Li X, Huang L, Lu J, Cheng Y, You Q, Wang L, Song X, Zhou X, Jiao Y. Large-Scale Investigation of Soybean Gene Functions by Overexpressing a Full-Length Soybean cDNA Library in Arabidopsis. Front Plant Sci 2018; 9:631. [PMID: 29868085 PMCID: PMC5954216 DOI: 10.3389/fpls.2018.00631] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/20/2018] [Indexed: 05/20/2023]
Abstract
Molecular breeding has become an important approach for crop improvement, and a prerequisite for molecular breeding is elucidation of the functions of genetic loci or genes. Soybean is one of the most important food and oil crops worldwide. However, due to the difficulty of genetic transformation in soybean, studies of its functional genomics lag far behind those of other crops such as rice, which severely impairs the progress of molecular improvement in soybean. Here, we describe an effective large-scale strategy to investigate the functions of soybean genes via overexpression of a full-length soybean cDNA library in Arabidopsis. The overexpression vector pJL12 was modified for use in the construction of a normalized full-length cDNA library. The constructed cDNA library showed good quality; repetitive clones represented approximately 4%, insertion fragments were approximately 2.2 kb, and the full-length rate was approximately 98%. This cDNA library was then overexpressed in Arabidopsis, and approximately 2000 transgenic lines were preliminarily obtained. Phenotypic analyses of the positive T1 transgenic plants showed that more than 5% of the T1 transgenic lines displayed abnormal developmental phenotypes, and approximately 1% of the transgenic lines exhibited potentially favorable traits. We randomly amplified 4 genes with obvious phenotypes (enlarged seeds, yellowish leaves, more branches, and dense siliques) and repeated the transgenic analyses in Arabidopsis. Subsequent phenotypic observation demonstrated that these phenotypes were indeed due to the overexpression of soybean genes. We believe our strategy represents an effective large-scale approach to investigate the functions of soybean genes and further reveal genes favorable for molecular improvement in soybean.
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Affiliation(s)
- Xiang Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Lei Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jianhua Lu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yihui Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Qingbo You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Lijun Wang
- The College of Life Science, Yangtze University, Jingzhou, China
| | - Xuejiao Song
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Xinan Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yongqing Jiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Yongqing Jiao,
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Heyl A. Shuttling of Entire Libraries from an Entry Vector to a Destination Vector of the Gateway System. Methods Mol Biol 2018; 1794:235-242. [PMID: 29855961 DOI: 10.1007/978-1-4939-7871-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Large-scale experiments are the basis of functional genomics, the investigating of several hundred or even thousand genes or proteins in parallel. A prerequisite for such experiments is the ability to clone several thousand genes simultaneously into a vector of choice to investigate different aspects of protein function, e.g., protein interactions, or subcellular localization. In the recent past several such cloning systems have been developed and successfully used. Of the commercially available systems, the Gateway™ system is the most widely used.This protocol describes how to shuttle a library from an Entry vector to a destination vector of the Gateway™ system. Emphasis is placed on the efficiency of the shuttling process to avoid loss of complexity and on reproducibility of the method.
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Affiliation(s)
- Alexander Heyl
- Biology Department, Adelphi University, Garden City, NY, USA.
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Kato H, Jochim RC, Gomez EA, Tsunekawa S, Valenzuela JG, Hashiguchi Y. Salivary gland transcripts of the kissing bug, Panstrongylus chinai, a vector of Chagas disease. Acta Trop 2017; 174:122-129. [PMID: 28690145 DOI: 10.1016/j.actatropica.2017.06.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 06/15/2017] [Accepted: 06/20/2017] [Indexed: 10/19/2022]
Abstract
The saliva of hematophagous arthropods injected during blood feeding contains potent pharmacologically active components to counteract the host hemostatic and inflammatory systems. In the present study, dominant salivary gland transcripts of Panstrongylus chinai, a vector of Chagas disease, were analyzed by sequencing randomly selected clones of the salivary gland cDNA library. This analysis showed that 56.5% of the isolated transcripts coded for putative secreted proteins, of which 73.7% coded for proteins belonging to the lipocalin family. The most abundant transcript of lipocalin family proteins was a homologue of pallidipin 2, an inhibitor of collagen-induced platelet aggregation of Triatoma pallidipennis. In addition, homologues of triafestin, an inhibitor of the kallikrein-kinin system of T. infestans, were identified as the dominant transcript. Other salivary transcripts encoding lipocalin family proteins had homology to triplatin (an inhibitor of platelet aggregation) and others with unknown function. Other than lipocalin family proteins, homologues of a Kazal-type serine protease inhibitor (putative anticoagulant), a hemolysin-like protein (unknown function), inositol polyphosphate 5-related protein (a regulator of membrane phosphoinositide), antigen 5-related protein (unknown function) and apyrase (platelet aggregation inhibitor) were identified.
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Vergani S, Korsunsky I, Mazzarello AN, Ferrer G, Chiorazzi N, Bagnara D. Novel Method for High-Throughput Full-Length IGHV-D-J Sequencing of the Immune Repertoire from Bulk B-Cells with Single-Cell Resolution. Front Immunol 2017; 8:1157. [PMID: 28959265 PMCID: PMC5603803 DOI: 10.3389/fimmu.2017.01157] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/01/2017] [Indexed: 11/13/2022] Open
Abstract
Efficient and accurate high-throughput DNA sequencing of the adaptive immune receptor repertoire (AIRR) is necessary to study immune diversity in healthy subjects and disease-related conditions. The high complexity and diversity of the AIRR coupled with the limited amount of starting material, which can compromise identification of the full biological diversity makes such sequencing particularly challenging. AIRR sequencing protocols often fail to fully capture the sampled AIRR diversity, especially for samples containing restricted numbers of B lymphocytes. Here, we describe a library preparation method for immunoglobulin sequencing that results in an exhaustive full-length repertoire where virtually every sampled B-cell is sequenced. This maximizes the likelihood of identifying and quantifying the entire IGHV-D-J repertoire of a sample, including the detection of rearrangements present in only one cell in the starting population. The methodology establishes the importance of circumventing genetic material dilution in the preamplification phases and incorporates the use of certain described concepts: (1) balancing the starting material amount and depth of sequencing, (2) avoiding IGHV gene-specific amplification, and (3) using Unique Molecular Identifier. Together, this methodology is highly efficient, in particular for detecting rare rearrangements in the sampled population and when only a limited amount of starting material is available.
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Affiliation(s)
- Stefano Vergani
- Karches Centre for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States.,Hofstra-Northwell Health School of Medicine, Hempstead, NY, United States
| | - Ilya Korsunsky
- Robert S. Boas Center for Genomics & Human Genetics, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Andrea Nicola Mazzarello
- Karches Centre for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Gerardo Ferrer
- Karches Centre for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Nicholas Chiorazzi
- Karches Centre for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Davide Bagnara
- Karches Centre for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States.,Department of Experimental Medicine, University of Genoa, Genoa, Italy
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Tao B, Shao BH, Qiao YX, Wang XQ, Chang SJ, Qiu LJ. Identification and functional analysis of a new glyphosate resistance gene from a fungus cDNA library. Pestic Biochem Physiol 2017; 140:65-68. [PMID: 28755696 DOI: 10.1016/j.pestbp.2017.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 04/01/2017] [Accepted: 05/26/2017] [Indexed: 06/07/2023]
Abstract
Glyphosate is a widely used broad spectrum herbicide; however, this limits its use once crops are planted. If glyphosate-resistant crops are grown, glyphosate can be used for weed control in crops. While several glyphosate resistance genes are used in commercial glyphosate tolerant crops, there is interest in identifying additional genes for glyphosate tolerance. This research constructed a high-quality cDNA library form the glyphosate-resistant fungus Aspergillus oryzae RIB40 to identify genes that may confer resistance to glyphosate. Using a medium containing glyphosate (120mM), we screened several clones from the library. Based on a nucleotide sequence analysis, we identified a gene of unknown function (GenBank accession number: XM_001826835.2) that encoded a hypothetical 344-amino acid protein. The gene was named MFS40. Its ORF was amplified to construct an expression vector, pGEX-4T-1-MFS40, to express the protein in Escherichia coli BL21. The gene conferred glyphosate tolerance to E. coli ER2799 cells.
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Affiliation(s)
- Bo Tao
- College of Agronomy, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China.
| | - Bai-Hui Shao
- College of Agronomy, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Yu-Xin Qiao
- College of Agronomy, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Xiao-Qin Wang
- College of Agronomy, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Shu-Jun Chang
- College of Agronomy, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Li-Juan Qiu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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Niu D, Wang R, Zhao Y, Yang R, Hu L, Lei Y, Dan W. cDNA library construction of two human Demodexspecies. Acta Parasitol 2017; 62:354-376. [PMID: 28426424 DOI: 10.1515/ap-2017-0043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/19/2017] [Indexed: 01/28/2023]
Abstract
The research of Demodex, a type of pathogen causing various dermatoses in animals and human beings, is lacking at RNA level. This study aims at extracting RNA and constructing cDNA library for Demodex. First, P. cuniculiand D. farinaewere mixed to establish homogenization method for RNA extraction. Second, D. folliculorumand D. breviswere collected and preserved in Trizol, which were mixed with D. farinaerespectively to extract RNA. Finally, cDNA library was constructed and its quality was assessed. The results indicated that for D. folliculorum& D. farinae, the recombination rate of cDNA library was 90.67% and the library titer was 7.50 × 104 pfu/ml. 17 of the 59 positive clones were predicted to be of D. folliculorum; For D. brevis& D. farinae, the recombination rate was 90.96% and the library titer was 7.85 x104 pfu/ml. 40 of the 59 positive clones were predicted to be of D. brevis. Further detection by specific primers demonstrated that mtDNA cox1, cox3and ATP6 detected from cDNA libraries had 96.52%-99.73% identities with the corresponding sequences in GenBank. In conclusion, the cDNA libraries constructed for Demodexmixed with D. farinaewere successful and could satisfy the requirements for functional genes detection.
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Affiliation(s)
- DongLing Niu
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061
| | - RuiLing Wang
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061
| | - YaE Zhao
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061
| | - Rui Yang
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061
| | - Li Hu
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061
| | - YuYang Lei
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061
| | - WeiChao Dan
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061
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Soorki MN, Jalali A, Galehdari H. Molecular Characterization and Biodiversity of a Putative Chlorotoxin from the Iranian Yellow Scorpion Odontobuthus doriae. Iran Biomed J 2017; 21:342-6. [PMID: 28415833 PMCID: PMC5548967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 07/18/2016] [Accepted: 07/26/2016] [Indexed: 02/28/2024]
Abstract
BAckground Chloride channels have already been over-expressed in the different types of cancer. Chlorotoxins, as the blocking agent of these channels, have been indicated to be an effective drug against tumors. In this study, we characterized a putative chlorotoxin from a cDNA library of the venom glands obtained from the Iranian scorpion Odontobuthus doriae. Methods A cDNA library was constructed from venom gland transcriptome of six scorpions. The cDNA encoding Odontobuthus doriae chlorotoxin was isolated from the library, and its putative peptide was characterized by some bioinformatics software such as protein blast, SignalP4.0, DISULFIND and Clustal Omega. Results The mature Odontobuthus doriae chlorotoxin peptide has a 35-amino-acid residue and four disulfide bounds. This putative chlorotoxin is a small, compact, and stable molecule. Moreover, based on the open reading frame sequence similarity, this peptide is similar to Buthus martensii Karsch chlorotoxin like toxin and Bm12-b neurotoxins from the Chinese scorpion Mesobuthus martensii. Conclusion The small size of this putative chlorotoxin and its stability make it as a suitable candidate for medical and pharmacological research, especially in the cancer research.
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Affiliation(s)
- Maryam Naderi Soorki
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Amir Jalali
- Department of Pharmacology and Toxicology, School of Pharmacy and Toxicology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hamid Galehdari
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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Abstract
Yeast two-hybrid screening is a powerful method to identify proteins that interact with a protein of interest. CCN2 consists of four domains, and identification of new proteins that bind to individual domains of CCN2 may reveal a variety of CCN2 functions. To identify CCN2-interactive proteins that regulate CCN2 activity, we carried out GAL4-based yeast two-hybrid screening with a cDNA library derived from a chondrocytic cell line, HCS-2/8, with CCN2 cDNA used as a bait. In this chapter, we describe our methods for screening for CCN2 binding partners by this system in detail. This protocol may be applied to other CCN proteins as well.
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Rex EB, Shukla N, Gu S, Bredt D, DiSepio D. A Genome-Wide Arrayed cDNA Screen to Identify Functional Modulators of α7 Nicotinic Acetylcholine Receptors. SLAS Discov 2016; 22:155-165. [PMID: 27789755 DOI: 10.1177/1087057116676086] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cellular signaling is in part regulated by the composition and subcellular localization of a series of protein interactions that collectively form a signaling complex. Using the α7 nicotinic acetylcholine receptor (α7nAChR) as a proof-of-concept target, we developed a platform to identify functional modulators (or auxiliary proteins) of α7nAChR signaling. The Broad cDNA library was transiently cotransfected with α7nAChR cDNA in HEK293T cells in a high-throughput fashion. Using this approach in combination with a functional assay, we identified positive modulators of α7nAChR activity. We identified known positive modulators/auxiliary proteins present in the cDNA library that regulate α7nAChR signaling, in addition to identifying novel modulators of α7nAChR signaling. These included NACHO, SPDYE11, TCF4, and ZC3H12A, all of which increased PNU-120596-mediated nicotine-dependent calcium flux. Importantly, these auxiliary proteins did not modulate GluR1(o)-mediated Ca flux. To elucidate a possible mechanism of action, we employed an α7nAChR-HA surface staining assay. NACHO enhanced α7nAChR surface expression; however, the mechanism responsible for the SPDYE11-, TCF4-, and ZC3H12A-dependent modulation of α7nAChR has yet to be defined. This report describes the development and validation of a high-throughput, genome-wide cDNA screening platform coupled to FLIPR functional assays in order to identify functional modulators of α7nAChR signaling.
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Affiliation(s)
- Elizabeth B Rex
- 1 Discovery Sciences, Janssen Research and Development LLC, La Jolla, CA, USA
| | - Nikhil Shukla
- 1 Discovery Sciences, Janssen Research and Development LLC, La Jolla, CA, USA
| | - Shenyan Gu
- 2 Neuroscience, Janssen Research and Development LLC, La Jolla, CA, USA
| | - David Bredt
- 2 Neuroscience, Janssen Research and Development LLC, La Jolla, CA, USA
| | - Daniel DiSepio
- 1 Discovery Sciences, Janssen Research and Development LLC, La Jolla, CA, USA
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Rigó G, Valkai I, Faragó D, Kiss E, Van Houdt S, Van de Steene N, Hannah MA, Szabados L. Gene mining in halophytes: functional identification of stress tolerance genes in Lepidium crassifolium. Plant Cell Environ 2016; 39:2074-84. [PMID: 27343166 DOI: 10.1111/pce.12768] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 05/08/2016] [Indexed: 05/27/2023]
Abstract
Extremophile plants are valuable sources of genes conferring tolerance traits, which can be explored to improve stress tolerance of crops. Lepidium crassifolium is a halophytic relative of the model plant Arabidopsis thaliana, and displays tolerance to salt, osmotic and oxidative stresses. We have employed the modified Conditional cDNA Overexpression System to transfer a cDNA library from L. crassifolium to the glycophyte A. thaliana. By screening for salt, osmotic and oxidative stress tolerance through in vitro growth assays and non-destructive chlorophyll fluorescence imaging, 20 Arabidopsis lines were identified with superior performance under restrictive conditions. Several cDNA inserts were cloned and confirmed to be responsible for the enhanced tolerance by analysing independent transgenic lines. Examples include full-length cDNAs encoding proteins with high homologies to GDSL-lipase/esterase or acyl CoA-binding protein or proteins without known function, which could confer tolerance to one or several stress conditions. Our results confirm that random gene transfer from stress tolerant to sensitive plant species is a valuable tool to discover novel genes with potential for biotechnological applications.
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Affiliation(s)
- Gábor Rigó
- Biological Research Centre, Institute of Plant Biology, 6726, Szeged, Hungary
| | - Ildikó Valkai
- Biological Research Centre, Institute of Plant Biology, 6726, Szeged, Hungary
| | - Dóra Faragó
- Biological Research Centre, Institute of Plant Biology, 6726, Szeged, Hungary
| | - Edina Kiss
- Biological Research Centre, Institute of Plant Biology, 6726, Szeged, Hungary
| | | | | | | | - László Szabados
- Biological Research Centre, Institute of Plant Biology, 6726, Szeged, Hungary
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