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Zhang P, Wang Y, Zhu G, Zhu H. Developing carotenoids-enhanced tomato fruit with multi-transgene stacking strategies. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108575. [PMID: 38554536 DOI: 10.1016/j.plaphy.2024.108575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/01/2024]
Abstract
As natural dominant pigments, carotenoids and their derivatives not only contribute to fruit color and flavor quality but are regarded as phytochemicals beneficial to human health because of various bioactivities. Tomato is one of the most important vegetables as well as a main dietary source of carotenoids. So, it's of great importance to generate carotenoid-biofortified tomatoes. The carotenoid biosynthesis pathway is a network co-regulated by multiple enzymes and regulatory genes. Here, we assembled four binary constructs containing different combinations of four endogenous carotenoids metabolic-related genes, including SlORHis, SlDXS, SlPSY, and SlBHY by using a high efficiency multi-transgene stacking system and a series of fruit-specific promotors. Transgenic lines overexpression SlORHis alone, three genes (SlORHis/SlDXS/SlPSY), two genes (SlORHis/SlBHY), and all these four genes (SlORHis/SlDXS/SlPSY/SlBHY) were enriched with carotenoids to varying degrees. Notably, overexpressing SlORHis alone showed comparable effects with simultaneous overexpression of the key regulatory enzyme coding genes SlDXS, SlPSY, and SlORHis in promoting carotenoid accumulation. Downstream carotenoid derivatives zeaxanthin and violaxanthin were detected only in lines containing SlBHY. In addition, the sugar content and total antioxidant capacity of these carotenoids-enhanced tomatoes was also increased. These data provided useful information for the future developing of biofortified tomatoes with different carotenoid profiles, and confirmed a promising system for generation of nutrients biofortified tomatoes by multiple engineering genes stacking strategy.
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Affiliation(s)
- Peiyu Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, PR China
| | - Yifan Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, PR China
| | - Guoning Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, PR China
| | - Hongliang Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, PR China; Sichuan Advanced Agricultural & Industrial Institute, China Agriculture University, Chengdu, 611430, Sichuan, PR China.
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2
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England SJ, Rusnock AK, Mujcic A, Kowalchuk A, de Jager S, Hilinski WC, Juárez-Morales JL, Smith ME, Grieb G, Banerjee S, Lewis KE. Molecular analyses of zebrafish V0v spinal interneurons and identification of transcriptional regulators downstream of Evx1 and Evx2 in these cells. Neural Dev 2023; 18:8. [PMID: 38017520 PMCID: PMC10683209 DOI: 10.1186/s13064-023-00176-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/12/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND V0v spinal interneurons are highly conserved, glutamatergic, commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However, we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. METHODS To identify candidate members of V0v gene regulatory networks, we FAC-sorted wild-type and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression-profiled them using microarrays and single cell RNA-seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 double mutants and wild-type siblings. RESULTS Our data reveal two molecularly distinct subtypes of zebrafish V0v spinal interneurons at 48 h and suggest that, by this stage of development, evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons, or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons, plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly, we show that Hmx2/3a, repress dI2 interneuron expression of skor1a and nefma, two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. CONCLUSIONS This study identifies two molecularly distinct subsets of zebrafish V0v spinal interneurons, as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of these cells. Our data further suggest that in the absence of both Evx1 and Evx2, V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then, later, start to express markers of distinct types of inhibitory spinal interneurons, or motoneurons. Taken together, our findings significantly increase our knowledge of V0v and spinal development and move us closer towards the essential goal of identifying the complete gene regulatory networks that specify this crucial cell type.
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Affiliation(s)
| | | | - Amra Mujcic
- Biology Department, Syracuse University, Syracuse, NY, USA
| | | | - Sarah de Jager
- Physiology, Development and Neuroscience Department, Cambridge University, Cambridge, UK
| | | | - José L Juárez-Morales
- Biology Department, Syracuse University, Syracuse, NY, USA
- Programa de IxM-CONAHCYT, Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), La Paz, Baja California Sur, México
| | | | - Ginny Grieb
- Biology Department, Syracuse University, Syracuse, NY, USA
| | - Santanu Banerjee
- Biological Sciences Department, SUNY-Cortland, Cortland, NY, USA
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Zeng D, Jing C, Tang L, He P, Zhang J. Pyramiding stacking of multigenes (PSM): a simple, flexible and efficient multigene stacking system based on Gibson assembly and gateway cloning. Front Bioeng Biotechnol 2023; 11:1263715. [PMID: 38026899 PMCID: PMC10668122 DOI: 10.3389/fbioe.2023.1263715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Genetic engineering of complex metabolic pathways and multiple traits often requires the introduction of multiple genes. The construction of plasmids carrying multiple DNA fragments plays a vital role in these processes. In this study, the Gibson assembly and Gateway cloning combined Pyramiding Stacking of Multigenes (PSM) system was developed to assemble multiple transgenes into a single T-DNA. Combining the advantages of Gibson assembly and Gateway cloning, the PSM system uses an inverted pyramid stacking route and allows fast, flexible and efficient stacking of multiple genes into a binary vector. The PSM system contains two modular designed entry vectors (each containing two different attL sites and two selectable markers) and one Gateway-compatible destination vector (containing four attR sites and two negative selection markers). The target genes are primarily assembled into the entry vectors via two parallel rounds of Gibson assembly reactions. Then, the cargos in the entry constructs are integrated into the destination vector via a single tube Gateway LR reaction. To demonstrate PSM's capabilities, four and nine gene expression cassettes were respectively assembled into the destination vector to generate two binary expression vectors. The transgenic analysis of these constructs in Arabidopsis demonstrated the reliability of the constructs generated by PSM. Due to its flexibility, simplicity and versatility, PSM has great potential for genetic engineering, synthetic biology and the improvement of multiple traits.
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Affiliation(s)
- Dongdong Zeng
- The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- Department of Clinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Cuiyuan Jing
- The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Lin Tang
- The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Peng He
- The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- Department of Clinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Jie Zhang
- The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- Department of Clinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
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4
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England SJ, Woodard AK, Mujcic A, Kowalchuk A, de Jager S, Hilinski WC, Juárez-Morales JL, Smith ME, Grieb G, Banerjee S, Lewis KE. Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in these Cells. RESEARCH SQUARE 2023:rs.3.rs-3290462. [PMID: 37693471 PMCID: PMC10491344 DOI: 10.21203/rs.3.rs-3290462/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Background V0v spinal interneurons are highly conserved, glutamatergic, commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However, we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods To identify candidate members of V0v gene regulatory networks, we FAC-sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression-profiled them using microarrays and single cell RNA-seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 double mutants and wild-type siblings. Results Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that, by this stage of development, evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons, or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons, plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly, we show that Hmx2/3a, repress dI2 interneuronal expression of skor1a and nefma, two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions This study identifies two molecularly distinct subsets of V0v spinal interneurons, as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of these cells. Our data further suggest that in the absence of both Evx1 and Evx2, V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then, later, start to express markers of distinct types of inhibitory spinal interneurons, or motoneurons. Taken together, our findings significantly increase our knowledge of V0v and spinal development and move us closer towards the essential goal of identifying the complete gene regulatory networks that specify this crucial cell type.
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5
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Chuang H, Sakaguchi M, Lucky AB, Yamagishi J, Katakai Y, Kawai S, Kaneko O. SICA-mediated cytoadhesion of Plasmodium knowlesi-infected red blood cells to human umbilical vein endothelial cells. Sci Rep 2022; 12:14942. [PMID: 36056126 PMCID: PMC9440145 DOI: 10.1038/s41598-022-19199-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/25/2022] [Indexed: 11/12/2022] Open
Abstract
Zoonotic malaria due to Plasmodium knowlesi infection in Southeast Asia is sometimes life-threatening. Post-mortem examination of human knowlesi malaria cases showed sequestration of P. knowlesi-infected red blood cells (iRBCs) in blood vessels, which has been proposed to be linked to disease severity. This sequestration is likely mediated by the cytoadhesion of parasite-iRBCs to vascular endothelial cells; however, the responsible parasite ligands remain undetermined. This study selected P. knowlesi lines with increased iRBC cytoadhesion activity by repeated panning against human umbilical vein endothelial cells (HUVECs). Transcriptome analysis revealed that the transcript level of one gene, encoding a Schizont Infected Cell Agglutination (SICA) protein, herein termed SICA-HUVEC, was more than 100-fold increased after the panning. Transcripts of other P. knowlesi proteins were also significantly increased, such as PIR proteins exported to the iRBC cytosol, suggesting their potential role in increasing cytoadhesion activity. Transgenic P. knowlesi parasites expressing Myc-fused SICA-HUVEC increased cytoadhesion activity following infection of monkey as well as human RBCs, confirming that SICA-HUVEC conveys activity to bind to HUVECs.
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Affiliation(s)
- Huai Chuang
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
- Leading Program, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Miako Sakaguchi
- Central Laboratory, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
| | - Amuza Byaruhanga Lucky
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
- Leading Program, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Junya Yamagishi
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yuko Katakai
- The Corporation for Production and Research of Laboratory Primates, Tsukuba, Ibaraki, Japan
| | - Satoru Kawai
- Department of Tropical Medicine and Parasitology, Dokkyo Medical University, Tochigi, Japan
| | - Osamu Kaneko
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
- Leading Program, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
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6
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Qin G, Wu S, Zhang L, Li Y, Liu C, Yu J, Deng L, Xiao G, Zhang Z. An Efficient Modular Gateway Recombinase-Based Gene Stacking System for Generating Multi-Trait Transgenic Plants. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040488. [PMID: 35214820 PMCID: PMC8879548 DOI: 10.3390/plants11040488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 05/14/2023]
Abstract
Transgenic technology can transfer favorable traits regardless of reproductive isolation and is an important method in plant synthetic biology and genetic improvement. Complex metabolic pathway modification and pyramiding breeding strategies often require the introduction of multiple genes at once, but the current vector assembly systems for constructing multigene expression cassettes are not completely satisfactory. In this study, a new in vitro gene stacking system, GuanNan Stacking (GNS), was developed. Through the introduction of Type IIS restriction enzyme-mediated Golden Gate cloning, GNS allows the modular, standardized assembly of target gene expression cassettes. Because of the introduction of Gateway recombination, GNS facilitates the cloning of superlarge transgene expression cassettes, allows multiple expression cassettes to be efficiently assembled in a binary vector simultaneously, and is compatible with the Cre enzyme-mediated marker deletion mechanism. The linked dual positive-negative marker selection strategy ensures the efficient acquisition of target recombinant plasmids without prokaryotic selection markers in the T-DNA region. The host-independent negative selection marker combined with the TAC backbone ensures the cloning and transfer of large T-DNAs (>100 kb). Using the GNS system, we constructed a binary vector containing five foreign gene expression cassettes and obtained transgenic rice carrying the target traits, proving that the method developed in this research is a powerful tool for plant metabolic engineering and compound trait transgenic breeding.
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Affiliation(s)
- Guannan Qin
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.Q.); (Y.L.); (C.L.); (J.Y.); (L.D.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.W.); (L.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Suting Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.W.); (L.Z.)
| | - Liying Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.W.); (L.Z.)
| | - Yanyao Li
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.Q.); (Y.L.); (C.L.); (J.Y.); (L.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunmei Liu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.Q.); (Y.L.); (C.L.); (J.Y.); (L.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianghui Yu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.Q.); (Y.L.); (C.L.); (J.Y.); (L.D.)
| | - Lihua Deng
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.Q.); (Y.L.); (C.L.); (J.Y.); (L.D.)
| | - Guoying Xiao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.W.); (L.Z.)
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- Correspondence: (G.X.); (Z.Z.)
| | - Zhiguo Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.W.); (L.Z.)
- Correspondence: (G.X.); (Z.Z.)
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7
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Juárez-Morales JL, Weierud F, England SJ, Demby C, Santos N, Grieb G, Mazan S, Lewis KE. Evolution of lbx spinal cord expression and function. Evol Dev 2021; 23:404-422. [PMID: 34411410 DOI: 10.1111/ede.12387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/04/2021] [Accepted: 06/21/2021] [Indexed: 11/29/2022]
Abstract
Ladybird homeobox (Lbx) transcription factors have crucial functions in muscle and nervous system development in many animals. Amniotes have two Lbx genes, but only Lbx1 is expressed in spinal cord. In contrast, teleosts have three lbx genes and we show here that zebrafish lbx1a, lbx1b, and lbx2 are expressed by distinct spinal cell types, and that lbx1a is expressed in dI4, dI5, and dI6 interneurons, as in amniotes. Our data examining lbx expression in Scyliorhinus canicula and Xenopus tropicalis suggest that the spinal interneuron expression of zebrafish lbx1a is ancestral, whereas lbx1b has acquired a new expression pattern in spinal cord progenitor cells. lbx2 spinal expression was probably acquired in the ray-finned lineage, as this gene is not expressed in the spinal cords of either amniotes or S. canicula. We also show that the spinal function of zebrafish lbx1a is conserved with mouse Lbx1. In zebrafish lbx1a mutants, there is a reduction in the number of inhibitory spinal interneurons and an increase in the number of excitatory spinal interneurons, similar to mouse Lbx1 mutants. Interestingly, the number of inhibitory spinal interneurons is also reduced in lbx1b mutants, although in this case the number of excitatory interneurons is not increased. lbx1a;lbx1b double mutants have a similar spinal interneuron phenotype to lbx1a single mutants. Taken together these data suggest that lbx1b and lbx1a may be required in succession for correct specification of dI4 and dI6 spinal interneurons, although only lbx1a is required for suppression of excitatory fates in these cells.
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Affiliation(s)
| | - Frida Weierud
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | | | - Celia Demby
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Nicole Santos
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Ginny Grieb
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Sylvie Mazan
- Biologie Intégrative des Organismes Marins, UMR 7232 CNRS, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
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8
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Shanaka KASN, Jung S, Janson ND, Jayasingha JRP, Madushani KP, Kim MJ, Lee J. Growth and Antioxidant-Related Effects of the Reestablished Ascorbic Acid Pathway in Zebrafish ( Danio rerio) by Genomic Integration of L-Gulonolactone Oxidase From Cloudy Catshark ( Scyliorhinus torazame). Front Physiol 2021; 12:685595. [PMID: 34290620 PMCID: PMC8287572 DOI: 10.3389/fphys.2021.685595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/28/2021] [Indexed: 11/22/2022] Open
Abstract
Loss of L-gulonolactone oxidase (GULO), which catalyzes the last step of the ascorbic acid (AA) biosynthesis pathway, results in a complete lack of AA in several Osteichthyes fish species, including zebrafish. In this study, sGULO, the active GULO gene from cloudy catshark (Scyliorhinus torazame) was cloned into zebrafish using the Gateway cloning method. The resulting Tg(b-actin:sGULO:mCherry) fish were analyzed for the effects of a reestablished AA pathway. Fluorescent microscopy and PCR were used to analyze the integration of the construct into the zebrafish genome. Catalytic activity of sGULO, AA production, growth-related characteristics, and gene expression were investigated to evaluate the effects of AA production in Tg fish. The mCherry fluorescent protein indicated the proper integration and expression of the sGULO construct in zebrafish. The sGULO gene was ubiquitously expressed in all the studied tissues and the enzyme activity indicated an increased AA production in Tg fish. The growth of Tg fish was also increased, and antioxidant system analysis suggests that reactive oxygen species production was reduced in Tg fish compared with wild type. Expression of the AA transporter slc23a1 was significantly downregulated in Tg homozygous fish. These results collectively indicate the effects of reestablished AA synthesis in zebrafish.
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Affiliation(s)
- K A S N Shanaka
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, South Korea.,Marine Science Institute, Jeju National University, Jeju, South Korea
| | - Sumi Jung
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, South Korea.,Marine Science Institute, Jeju National University, Jeju, South Korea
| | - N D Janson
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, South Korea.,Marine Science Institute, Jeju National University, Jeju, South Korea
| | - J R P Jayasingha
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, South Korea.,Marine Science Institute, Jeju National University, Jeju, South Korea
| | - K P Madushani
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, South Korea.,Marine Science Institute, Jeju National University, Jeju, South Korea
| | - Myoung-Jin Kim
- Marine Science Institute, Jeju National University, Jeju, South Korea
| | - Jehee Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, South Korea.,Marine Science Institute, Jeju National University, Jeju, South Korea
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9
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Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
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10
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Luo Y, Qiu Y, Na R, Meerja F, Lu QS, Yang C, Tian L. A Golden Gate and Gateway double-compatible vector system for high throughput functional analysis of genes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 271:117-126. [PMID: 29650149 DOI: 10.1016/j.plantsci.2018.03.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/20/2018] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
Abstract
A major research topic nowadays is to study and understand the functions of the increasing number of predicted genes that have been discovered through the complete genome sequencing of many plant species. With the aim of developing tools for rapid and convenient gene function analysis, we have developed a set of "pGate" vectors based on the principle of Golden gate and Gateway cloning approaches. These vectors combine the positive aspects of both Golden gate and Gateway cloning strategies. pGate vectors can not only be used as Golden gate recipient vectors to assemble multiple DNA fragments in a pre-defined order, but they can also work as an entry vector to transfer the assembled DNA fragment(s) to a large number of already-existing, functionally diverse, Gateway compatible destination vectors without adding additional nucleotides during cloning. We show the pGate vectors are effective and convenient in several major aspects of gene function analyses, including BiFC (Bimolecular fluorescence complementation) to analyze protein-protein interaction, amiRNA (artificial microRNA) candidate screening and as assembly of CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeats, CRISPR-associated protein-9 nuclease) system elements together for genome editing. The pGate system is a practical and flexible tool which can facilitate plant gene function research.
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Affiliation(s)
- Yanjie Luo
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V4T3, Canada
| | - Yang Qiu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V4T3, Canada; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ren Na
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Farida Meerja
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V4T3, Canada; Department of Biology, Western University, London, ON, N6A5B7, Canada
| | - Qing Shi Lu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V4T3, Canada
| | - Chunyan Yang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Lining Tian
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V4T3, Canada.
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Abstract
Serine integrases catalyze precise rearrangement of DNA through site-specific recombination of small sequences of DNA called attachment (att) sites. Unlike other site-specific recombinases, the recombination reaction driven by serine integrases is highly directional and can only be reversed in the presence of an accessory protein called a recombination directionality factor (RDF). The ability to control reaction directionality has led to the development of serine integrases as tools for controlled rearrangement and modification of DNA in synthetic biology, gene therapy, and biotechnology. This review discusses recent advances in serine integrase technologies focusing on their applications in genome engineering, DNA assembly, and logic and data storage devices.
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Affiliation(s)
- Christine A. Merrick
- School
of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum
Brown Road, Edinburgh EH9
3FF, U.K
| | - Jia Zhao
- Novo
Nordisk (China) Pharmaceuticals Co., Ltd., Lei Shing Hong Center, Guangshunnan Avenue, Beijing 100102, China
| | - Susan J. Rosser
- School
of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum
Brown Road, Edinburgh EH9
3FF, U.K
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12
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Lukan T, Machens F, Coll A, Baebler Š, Messerschmidt K, Gruden K. Plant X-tender: An extension of the AssemblX system for the assembly and expression of multigene constructs in plants. PLoS One 2018; 13:e0190526. [PMID: 29300787 PMCID: PMC5754074 DOI: 10.1371/journal.pone.0190526] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 12/15/2017] [Indexed: 11/24/2022] Open
Abstract
Cloning multiple DNA fragments for delivery of several genes of interest into the plant genome is one of the main technological challenges in plant synthetic biology. Despite several modular assembly methods developed in recent years, the plant biotechnology community has not widely adopted them yet, probably due to the lack of appropriate vectors and software tools. Here we present Plant X-tender, an extension of the highly efficient, scar-free and sequence-independent multigene assembly strategy AssemblX, based on overlap-depended cloning methods and rare-cutting restriction enzymes. Plant X-tender consists of a set of plant expression vectors and the protocols for most efficient cloning into the novel vector set needed for plant expression and thus introduces advantages of AssemblX into plant synthetic biology. The novel vector set covers different backbones and selection markers to allow full design flexibility. We have included ccdB counterselection, thereby allowing the transfer of multigene constructs into the novel vector set in a straightforward and highly efficient way. Vectors are available as empty backbones and are fully flexible regarding the orientation of expression cassettes and addition of linkers between them, if required. We optimised the assembly and subcloning protocol by testing different scar-less assembly approaches: the noncommercial SLiCE and TAR methods and the commercial Gibson assembly and NEBuilder HiFi DNA assembly kits. Plant X-tender was applicable even in combination with low efficient homemade chemically competent or electrocompetent Escherichia coli. We have further validated the developed procedure for plant protein expression by cloning two cassettes into the newly developed vectors and subsequently transferred them to Nicotiana benthamiana in a transient expression setup. Thereby we show that multigene constructs can be delivered into plant cells in a streamlined and highly efficient way. Our results will support faster introduction of synthetic biology into plant science.
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Affiliation(s)
- Tjaša Lukan
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
- International Postgraduate School, Ljubljana, Slovenia
- * E-mail:
| | - Fabian Machens
- University of Potsdam, Cell2Fab Research Unit, Potsdam, Germany
| | - Anna Coll
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
| | - Špela Baebler
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
| | | | - Kristina Gruden
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
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13
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Abstract
Previously, we described a method for a recombinase-directed stacking of new DNA to an existing transgenic locus. Here, we describe how we can similarly stack DNA molecules in vitro and that the in vitro derived gene stack can be incorporated into an Agrobacterium transformation vector by in vitro recombination. After transfer to the chromosome by Agroinfection, the transgenic locus harbors a new target site that can be used for the subsequent in vivo stacking of new DNA. Alternatively, the in vitro derived gene stack has the potential to be integrated directly into the plant genome in vivo at a preexisting chromosomal target. Being able to stack DNA in vitro as well as in vivo, and with compatibility between the two systems, brings new flexibility for using the recombinase-mediated approach for transgene stacking.
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14
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Zhang J, Wu M, Li W, Bai G. Regulation of chlorogenic acid biosynthesis by hydroxycinnamoyl CoA quinate hydroxycinnamoyl transferase in Lonicera japonica. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 121:74-79. [PMID: 29096175 DOI: 10.1016/j.plaphy.2017.10.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 10/12/2017] [Accepted: 10/18/2017] [Indexed: 06/07/2023]
Abstract
For many centuries, Lonicera japonica has been used as an effective herb for the treatment of inflammation and swelling because of the presence of bioactive components such as chlorogenic acid (CGA). To clarify the relationship between L. japonica hydroxycinnamoyl CoA quinate hydroxycinnamoyl transferase (HQT) gene expression and CGA content, an HQT eukaryotic expression system was constructed using Gateway cloning. L. japonica callus transformed with HQT was obtained using Agrobacterium tumefaciens-mediated transformation. We found a positive correlation between CGA content, determined by High-Performance Liquid Chromatography (HPLC), and the expression of HQT, analyzed by semi-quantitative RT-PCR. This study demonstrates that the HQT gene positively regulates CGA synthesis and lays the foundation for further study into enhancing efficacious components of medicinal plants.
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Affiliation(s)
- Jingru Zhang
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 102488, PR China
| | - Minlin Wu
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 102488, PR China
| | - Weidong Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Genben Bai
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 102488, PR China.
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15
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A Modular Approach to Building Complex Synthetic Circuits. Methods Mol Biol 2017. [PMID: 28801911 DOI: 10.1007/978-1-4939-7223-4_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Efficient assembly of genetic circuits is a critical element in synthetic biology for implementing complex gene expression systems. Here we present an assembly framework that integrates recent developments in DNA recombination technologies and unique nucleotide sequences for modular and reliable construction of complex genetic circuits. All relevant protocols are described in detail. Implementing these protocols relies on readily available reagents and basic molecular biology techniques without the need for specialized equipment.
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16
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Aboulela M, Tanaka Y, Nishimura K, Mano S, Nishimura M, Ishiguro S, Kimura T, Nakagawa T. Development of an R4 dual-site (R4DS) gateway cloning system enabling the efficient simultaneous cloning of two desired sets of promoters and open reading frames in a binary vector for plant research. PLoS One 2017; 12:e0177889. [PMID: 28520787 PMCID: PMC5433782 DOI: 10.1371/journal.pone.0177889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/04/2017] [Indexed: 02/06/2023] Open
Abstract
Vast numbers of proteins work cooperatively to exert their functions in various cells. In order to understand the functions and molecular mechanisms of these proteins in plants, analyses of transgenic plants that concomitantly express two protein-coding genes are often required. We developed a novel Gateway cloning technology-compatible binary vector system, the R4 dual-site (R4DS) Gateway cloning system, which enables the easy and efficient cloning of two desired sets of promoters and open reading frames (ORFs) into a binary vector using promoter and ORF entry clones. In this system, C-terminal fusions with 17 kinds of tags including visible reporters and epitope tags are available for each ORF, and selection by four kinds of resistance markers is possible. We verified that the R4DS Gateway cloning system functioned well in Arabidopsis thaliana by observing the expression and localization patterns of fluorescent proteins fused with organelle-targeting signals and driven by stomatal-lineage specific promoters. We also confirmed that the two cloning sites in the R4DS Gateway cloning system were equivalent and independently regulated. The results obtained indicate that the R4DS Gateway cloning system facilitates detailed comparisons of the expression patterns of two promoters as well as co-localization and interaction analyses of two proteins in specific cells in plants.
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Affiliation(s)
- Mostafa Aboulela
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Organization for Research, Shimane University, Matsue, Japan
- Bioresources Science, The United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan
- Department of Botany and Microbiology, Faculty of Science, Assiut University, Assiut, Egypt
| | - Yuji Tanaka
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Organization for Research, Shimane University, Matsue, Japan
| | - Kohji Nishimura
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Organization for Research, Shimane University, Matsue, Japan
- Bioresources Science, The United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan
| | - Shoji Mano
- Department of Evolutionary Biology and Biodiversity, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Sumie Ishiguro
- Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tetsuya Kimura
- Department of Life Sciences, Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Tsuyoshi Nakagawa
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Organization for Research, Shimane University, Matsue, Japan
- Bioresources Science, The United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan
- * E-mail:
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17
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Juárez-Morales JL, Martinez-De Luna RI, Zuber ME, Roberts A, Lewis KE. Zebrafish transgenic constructs label specific neurons in Xenopus laevis spinal cord and identify frog V0v spinal neurons. Dev Neurobiol 2017; 77:1007-1020. [PMID: 28188691 DOI: 10.1002/dneu.22490] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/26/2017] [Accepted: 02/08/2017] [Indexed: 12/19/2022]
Abstract
A correctly functioning spinal cord is crucial for locomotion and communication between body and brain but there are fundamental gaps in our knowledge of how spinal neuronal circuitry is established and functions. To understand the genetic program that regulates specification and functions of this circuitry, we need to connect neuronal molecular phenotypes with physiological analyses. Studies using Xenopus laevis tadpoles have increased our understanding of spinal cord neuronal physiology and function, particularly in locomotor circuitry. However, the X. laevis tetraploid genome and long generation time make it difficult to investigate how neurons are specified. The opacity of X. laevis embryos also makes it hard to connect functional classes of neurons and the genes that they express. We demonstrate here that Tol2 transgenic constructs using zebrafish enhancers that drive expression in specific zebrafish spinal neurons label equivalent neurons in X. laevis and that the incorporation of a Gal4:UAS amplification cassette enables cells to be observed in live X. laevis tadpoles. This technique should enable the molecular phenotypes, morphologies and physiologies of distinct X. laevis spinal neurons to be examined together in vivo. We have used an islet1 enhancer to label Rohon-Beard sensory neurons and evx enhancers to identify V0v neurons, for the first time, in X. laevis spinal cord. Our work demonstrates the homology of spinal cord circuitry in zebrafish and X. laevis, suggesting that future work could combine their relative strengths to elucidate a more complete picture of how vertebrate spinal cord neurons are specified, and function to generate behavior. © 2017 Wiley Periodicals, Inc. Develop Neurobiol 77: 1007-1020, 2017.
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Affiliation(s)
- José L Juárez-Morales
- Department of Biology, Syracuse University, 107 College Place, Syracuse, New York, 13244.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, United Kingdom
| | - Reyna I Martinez-De Luna
- The Center for Vision Research, Department of Ophthalmology, SUNY Upstate Medical University, Institute for Human Performance, 505 Irving Ave. Syracuse, New York, 13210
| | - Michael E Zuber
- The Center for Vision Research, Department of Ophthalmology, SUNY Upstate Medical University, Institute for Human Performance, 505 Irving Ave. Syracuse, New York, 13210
| | - Alan Roberts
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, BS8 1TQ, United Kingdom
| | - Katharine E Lewis
- Department of Biology, Syracuse University, 107 College Place, Syracuse, New York, 13244
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18
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Tomimatsu K, Kokura K, Nishida T, Yoshimura Y, Kazuki Y, Narita M, Oshimura M, Ohbayashi T. Multiple expression cassette exchange via TP901-1, R4, and Bxb1 integrase systems on a mouse artificial chromosome. FEBS Open Bio 2017; 7:306-317. [PMID: 28286726 PMCID: PMC5337897 DOI: 10.1002/2211-5463.12169] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/17/2016] [Accepted: 11/24/2016] [Indexed: 01/21/2023] Open
Abstract
The site-specific excision of a target DNA sequence for genetic knockout or lineage tracing is a powerful tool for investigating biological systems. Currently, site-specific recombinases (SSRs), such as Cre or Flp recombination target cassettes, have been successfully excised or inverted by a single SSR to regulate transgene expression. However, the use of a single SSR might restrict the complex control of gene expression. This study investigated the potential for expanding the multiple regulation of transgenes using three different integrase systems (TP901-1, R4, and Bxb1). We designed three excision cassettes that expressed luciferase, where the luciferase expression could be exchanged to a fluorescent protein by site-specific recombination. Individual cassettes that could be regulated independently by a different integrase were connected in tandem and inserted into a mouse artificial chromosome (MAC) vector in Chinese hamster ovary cells. The transient expression of an integrase caused the targeted luciferase activity to be lost and fluorescence was activated. Additionally, the integrase system enabled the specific excision of targeted DNA sequences without cross-reaction with the other recombination targets. These results suggest that the combined use of these integrase systems in a defined locus on a MAC vector permits the multiple regulation of transgene expression and might contribute to genomic or cell engineering.
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Affiliation(s)
- Kosuke Tomimatsu
- Research Center for Bioscience and TechnologyTottori UniversityYonagoJapan
- Japan Society for the Promotion of ScienceTokyoJapan
| | - Kenji Kokura
- Chromosome Engineering Research CenterTottori UniversityYonagoJapan
- Division of Human Genome ScienceDepartment of Molecular and Cellular BiologySchool of Life SciencesFaculty of MedicineTottori UniversityYonagoJapan
| | - Tadashi Nishida
- Research Center for Bioscience and TechnologyTottori UniversityYonagoJapan
| | - Yuki Yoshimura
- Department of Biomedical ScienceInstitute of Regenerative Medicine and BiofunctionGraduate School of Medical SciencesTottori UniversityYonagoJapan
- Central Institute for Experimental AnimalsKawasakiJapan
| | - Yasuhiro Kazuki
- Chromosome Engineering Research CenterTottori UniversityYonagoJapan
- Department of Biomedical ScienceInstitute of Regenerative Medicine and BiofunctionGraduate School of Medical SciencesTottori UniversityYonagoJapan
| | - Masashi Narita
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeUK
| | - Mitsuo Oshimura
- Chromosome Engineering Research CenterTottori UniversityYonagoJapan
- Department of Biomedical ScienceInstitute of Regenerative Medicine and BiofunctionGraduate School of Medical SciencesTottori UniversityYonagoJapan
| | - Tetsuya Ohbayashi
- Research Center for Bioscience and TechnologyTottori UniversityYonagoJapan
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19
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Mimura Y, Takagi M, Clever M, Imamoto N. ELYS regulates the localization of LBR by modulating its phosphorylation state. J Cell Sci 2016; 129:4200-4212. [PMID: 27802161 PMCID: PMC5117198 DOI: 10.1242/jcs.190678] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 09/27/2016] [Indexed: 01/12/2023] Open
Abstract
Lamin B receptor (LBR), an inner nuclear membrane (INM) protein, contributes to the functional integrity of the nucleus by tethering heterochromatin to the nuclear envelope. We have previously reported that the depletion of embryonic large molecule derived from yolk sac (ELYS; also known as AHCTF1), a component of the nuclear pore complex, from cells perturbs the localization of LBR to the INM, but little is known about the underlying molecular mechanism. In this study, we found that the depletion of ELYS promoted LBR phosphorylation at the residues known to be phosphorylated by cyclin-dependent kinase (CDK) and serine/arginine protein kinases 1 and 2 (SRPK1 and SRPK2, respectively). These phosphorylation events were most likely to be counter-balanced by protein phosphatase 1 (PP1), and the depletion of PP1 from cells consistently caused the mislocalization of LBR. These observations point to a new mechanism regulating the localization of LBR, which is governed by an ELYS-mediated phosphorylation network. This phosphorylation-dependent coordination between INM proteins and the nuclear pore complex might be important for the integrity of the nucleus.
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Affiliation(s)
- Yasuhiro Mimura
- Cellular Dynamics Laboratory, Riken, Saitama 351-0198, Japan
| | | | - Michaela Clever
- Cellular Dynamics Laboratory, Riken, Saitama 351-0198, Japan
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, Riken, Saitama 351-0198, Japan
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20
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21
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Juárez-Morales JL, Schulte CJ, Pezoa SA, Vallejo GK, Hilinski WC, England SJ, de Jager S, Lewis KE. Evx1 and Evx2 specify excitatory neurotransmitter fates and suppress inhibitory fates through a Pax2-independent mechanism. Neural Dev 2016; 11:5. [PMID: 26896392 PMCID: PMC4759709 DOI: 10.1186/s13064-016-0059-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/04/2016] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND For neurons to function correctly in neuronal circuitry they must utilize appropriate neurotransmitters. However, even though neurotransmitter specificity is one of the most important and defining properties of a neuron we still do not fully understand how neurotransmitter fates are specified during development. Most neuronal properties are determined by the transcription factors that neurons express as they start to differentiate. While we know a few transcription factors that specify the neurotransmitter fates of particular neurons, there are still many spinal neurons for which the transcription factors specifying this critical phenotype are unknown. Strikingly, all of the transcription factors that have been identified so far as specifying inhibitory fates in the spinal cord act through Pax2. Even Tlx1 and Tlx3, which specify the excitatory fates of dI3 and dI5 spinal neurons work at least in part by down-regulating Pax2. METHODS In this paper we use single and double mutant zebrafish embryos to identify the spinal cord functions of Evx1 and Evx2. RESULTS We demonstrate that Evx1 and Evx2 are expressed by spinal cord V0v cells and we show that these cells develop into excitatory (glutamatergic) Commissural Ascending (CoSA) interneurons. In the absence of both Evx1 and Evx2, V0v cells still form and develop a CoSA morphology. However, they lose their excitatory fate and instead express markers of a glycinergic fate. Interestingly, they do not express Pax2, suggesting that they are acquiring their inhibitory fate through a novel Pax2-independent mechanism. CONCLUSIONS Evx1 and Evx2 are required, partially redundantly, for spinal cord V0v cells to become excitatory (glutamatergic) interneurons. These results significantly increase our understanding of the mechanisms of neuronal specification and the genetic networks involved in these processes.
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Affiliation(s)
- José L Juárez-Morales
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Claus J Schulte
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Sofia A Pezoa
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Grace K Vallejo
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - William C Hilinski
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, 505 Irving Avenue, Syracuse, NY, 13210, USA
| | - Samantha J England
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Sarah de Jager
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Katharine E Lewis
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA.
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22
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Miura T, Nishizawa A, Nishizawa T, Asayama M, Shirai M. Actinophage R4 integrase-based site-specific chromosomal integration of non-replicative closed circular DNA. J Basic Microbiol 2016; 56:635-44. [PMID: 26870903 DOI: 10.1002/jobm.201500658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/27/2016] [Indexed: 11/07/2022]
Abstract
The actinophage R4 integrase (Sre)-based molecular genetic engineering system was developed for the chromosomal integration of multiple genes in Escherichia coli. A cloned DNA fragment containing two attP sites, green fluorescent protein (gfp) as a first transgene, and an antibiotic resistance gene as a selection marker was self-ligated to generate non-replicative closed circular DNA (nrccDNA) for integration. nrccDNA was introduced into attB-inserted E. coli cells harboring the plasmid expressing Sre by electroporation. The expressed Sre catalyzed site-specific integration between one of the two attP sites on nrccDNA and the attB site on the E. coli chromosome. The integration frequency was affected by the chromosomal location of the target site. A second nrccDNA containing two attB sites, lacZα encoding the alpha fragment of β-galactosidase as a transgene, and another antibiotic resistance gene was integrated into the residual attP site on the gfp-integrated E. coli chromosome via one of the two attB sites according to reiterating site-specific recombination. The integrants clearly exhibited β-galactosidase activity and green fluorescence, suggesting the simultaneous expression of multiple recombinant proteins in E. coli. The results of the present study showed that a step-by-step integration procedure using nrccDNA achieved the chromosomal integration of multiple genes.
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Affiliation(s)
- Takamasa Miura
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Department of Bioresource Science, Ibaraki University College of Agriculture, Ibaraki, Japan
| | - Akito Nishizawa
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Department of Bioresource Science, Ibaraki University College of Agriculture, Ibaraki, Japan
| | - Tomoyasu Nishizawa
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Department of Bioresource Science, Ibaraki University College of Agriculture, Ibaraki, Japan
| | - Munehiko Asayama
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Department of Bioresource Science, Ibaraki University College of Agriculture, Ibaraki, Japan
| | - Makoto Shirai
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Department of Bioresource Science, Ibaraki University College of Agriculture, Ibaraki, Japan
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23
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Merrick C, Wardrope C, Paget J, Colloms S, Rosser S. Rapid Optimization of Engineered Metabolic Pathways with Serine Integrase Recombinational Assembly (SIRA). Methods Enzymol 2016; 575:285-317. [DOI: 10.1016/bs.mie.2016.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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24
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de Bruyns A, Geiling B, Dankort D. Construction of Modular Lentiviral Vectors for Effective Gene Expression and Knockdown. Methods Mol Biol 2016; 1448:3-21. [PMID: 27317169 DOI: 10.1007/978-1-4939-3753-0_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Elucidating gene function is heavily reliant on the ability to modulate gene expression in biological model systems. Although transient expression systems can provide useful information about the biological outcome resulting from short-term gene overexpression or silencing, methods providing stable integration of desired expression constructs (cDNA or RNA interference) are often preferred for functional studies. To this end, lentiviral vectors offer the ability to deliver long-term and regulated gene expression to mammalian cells, including the expression of gene targeting small hairpin RNAs (shRNAmirs). Unfortunately, constructing vectors containing the desired combination of cDNAs, markers, and shRNAmirs can be cumbersome and time-consuming if using traditional sequence based restriction enzyme and ligation-dependent methods. Here we describe the use of a recombination based Gateway cloning strategy to rapidly and efficiently produce recombinant lentiviral vectors for the expression of one or more cDNAs with or without simultaneous shRNAmir expression. Additionally, we describe a luciferase-based approach to rapidly triage shRNAs for knockdown efficacy and specificity without the need to create stable shRNAmir expressing cells.
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Affiliation(s)
| | - Ben Geiling
- Department of Biology, McGill University, Montréal, QC, H3G 0B1, Canada
| | - David Dankort
- Department of Biology, McGill University, Montréal, QC, H3G 0B1, Canada.
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25
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Watanabe-Iida I, Konno K, Akashi K, Abe M, Natsume R, Watanabe M, Sakimura K. Determination of kainate receptor subunit ratios in mouse brain using novel chimeric protein standards. J Neurochem 2015; 136:295-305. [DOI: 10.1111/jnc.13384] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/04/2015] [Accepted: 10/01/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Izumi Watanabe-Iida
- Department of Cellular Neurobiology; Brain Research Institute; Niigata University; Niigata Japan
- CREST; Japan Science and Technology Agency; Chiyoda-ku Japan
| | - Kohtarou Konno
- CREST; Japan Science and Technology Agency; Chiyoda-ku Japan
- Department of Anatomy; Hokkaido University School of Medicine; Sapporo Japan
| | - Kaori Akashi
- Department of Cellular Neurobiology; Brain Research Institute; Niigata University; Niigata Japan
- CREST; Japan Science and Technology Agency; Chiyoda-ku Japan
| | - Manabu Abe
- Department of Cellular Neurobiology; Brain Research Institute; Niigata University; Niigata Japan
- CREST; Japan Science and Technology Agency; Chiyoda-ku Japan
| | - Rie Natsume
- Department of Cellular Neurobiology; Brain Research Institute; Niigata University; Niigata Japan
- CREST; Japan Science and Technology Agency; Chiyoda-ku Japan
| | - Masahiko Watanabe
- CREST; Japan Science and Technology Agency; Chiyoda-ku Japan
- Department of Anatomy; Hokkaido University School of Medicine; Sapporo Japan
| | - Kenji Sakimura
- Department of Cellular Neurobiology; Brain Research Institute; Niigata University; Niigata Japan
- CREST; Japan Science and Technology Agency; Chiyoda-ku Japan
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26
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Liu D, Zhou H, Wu J, Liu W, Li Y, Shi G, Yue X, Sun X, Zhao Y, Hu X, Wang T, Zhang X. Infection by Cx43 adenovirus increased chemotherapy sensitivity in human gastric cancer BGC-823 cells: not involving in induction of cell apoptosis. Gene 2015; 574:217-24. [PMID: 26318481 DOI: 10.1016/j.gene.2015.08.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 07/24/2015] [Accepted: 08/06/2015] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE There is a lower basal expression of Connexin43 (Cx43) in human gastric cancer BGC-823 cells. In the present study, BGC-823 cells were transfected with recombinant Cx43 adenovirus plasmid vector, and we explored the influences of Cx43 expression on cell proliferation, chemo-sensitivity, colony forming ability, invasion ability and apoptosis. Moreover, we also determined the expression of Pgp, Cx43, as well as apoptosis-related proteins (bcl-2, bax, caspase3 and caspase 9). METHODS MTT assay was performed to determine the proliferation of BGC-823 cells before and after Cx43 transfection. The influences of Cx43 infection on sensitivity of chemotherapy (including Doxorubicin, fluorouracil, oxaliplatin) were detected by MTT assay. Expression levels of Pgp, Cx43, as well as apoptosis-related proteins (bcl-2, bax, caspase-3 and caspase-9) in BGC-823 cells were determined by Western blotting analysis before and after the infection with Cx43 adenovirus. MDR expression was determined by RT-PCR before and after Cx43 infection. Invasive ability was detected by invasion chamber. Influence of Cx43 adenovirus infection on apoptosis of BGC-823 cells was determined by flow cytometry. RESULTS After infection by Cx43 adenovirus, colony forming rate and invasive ability of BGC-823 cells were decreased. Flow cytometry results revealed that cell apoptosis were insignificantly increased. The data of MTT assay revealed that infection with Cx43 adenovirus, cell proliferation ability decreased and sensitivity to chemotherapy drugs (including doxorubicin, fluorouracil, oxaliplatin) increased. Results of Western blotting analysis revealed that increasing expression levels of Cx43, decreasing expression levels of Pgp, and insignificant changes of bcl-2, bax, caspase3 and caspase 9 were detected. RT-PCR revealed the expression of MDR1 gene, the gene encoding Pgp, decreased significantly (p<0.05). CONCLUSION The human gastric cancer BGC-823 cells were infected with Cx43-IRES2-EGFP recombinant adenovirus vector. Colony formation, invasive ability and cell proliferation all decreased, whereas chemo-sensitivity increased in Cx43 infected BGC-823 cells. The increasing Cx43 expression was accompanied by decreasing Pgp expression and MDR1 m RNA levels. However, apoptosis-related proteins (bcl-2, bax, caspase3 and caspase 9) and cell apoptosis increased insignificantly. All results demonstrated that Cx43 may be negatively regulated the development, invasion and metastasis of gastric cancers, however, it had no obvious relationship with tumor cell apoptosis.
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Affiliation(s)
- Dan Liu
- The Seventh Department of the Internal Medicine, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China
| | - Hongfeng Zhou
- The Seventh Department of the Internal Medicine, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China
| | - Jin Wu
- The Seventh Department of the Internal Medicine, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China.
| | - Wentao Liu
- The Seventh Department of the Internal Medicine, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China
| | - Yongqing Li
- Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Guangyue Shi
- The Seventh Department of the Internal Medicine, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China
| | - Xiaolong Yue
- The Seventh Department of the Internal Medicine, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China
| | - Xiwen Sun
- Harbin Medical University cancer Institute, Harbin, 150081, China
| | - Yanbin Zhao
- The Seventh Department of the Internal Medicine, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China
| | - Xiaowei Hu
- The Seventh Department of the Internal Medicine, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China
| | - Tianjiao Wang
- The Seventh Department of the Internal Medicine, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China
| | - Xufeng Zhang
- The Seventh Department of the Internal Medicine, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150081, China
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Casini A, Storch M, Baldwin GS, Ellis T. Bricks and blueprints: methods and standards for DNA assembly. Nat Rev Mol Cell Biol 2015; 16:568-76. [DOI: 10.1038/nrm4014] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Wall VE, Garvey LA, Mehalko JL, Procter LV, Esposito D. Combinatorial assembly of clone libraries using site-specific recombination. Methods Mol Biol 2014; 1116:193-208. [PMID: 24395366 DOI: 10.1007/978-1-62703-764-8_14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Generation of DNA clones for use in proteomic and genomic research often requires a significant level of parallel production, as the number of downstream options for these experiments increases. Where a single fluorescently tagged construct may have sufficed before, there is now the need for multiple types of labels for different readouts and different assays. Protein expression, which once utilized a very small set of vectors because of low throughput expression and purification, has now rapidly matured into a high throughput system in which dozens of conditions can be tested in parallel to identify the best candidate clones. This has returned the bottleneck in many of these technologies to the generation of DNA clones, and standard cloning techniques often dramatically limit the throughput and success of such processes. In order to overcome this bottleneck, higher-throughput and more parallel cloning processes need to be developed which would allow rapid, inexpensive production of final clones. In addition, there is a strong need to utilize standardized elements to avoid unnecessarily remaking fragments of clones that could be used in multiple constructs. The advent of recombinational cloning helped to increase the parallel processing of DNA clones, but was still limited by the need to generate different vector backbones for each specific need. The solution to this problem emerged with the introduction of combinatorial approaches to clone construction, based on either homologous or site-specific recombination processes. In particular, the Gateway Multisite system provides all of the necessary components for a highly parallel, inexpensive, rapid, and diverse platform for clone construction in many areas of proteomic and genomic research. Here we describe our optimized system for combinatorial cloning, including improvements in cloning protocols and construct design that permit users to easily generate libraries of clones which can be combined in parallel to create an unlimited number of final constructs. The system is capable of utilizing the tens of thousands of commercially available Gateway clones already in existence, and allows easy adaptation of most DNA vectors to the system.
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Affiliation(s)
- Vanessa E Wall
- Protein Expression Laboratory, SAIC Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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Assessing cellular efficacy of bromodomain inhibitors using fluorescence recovery after photobleaching. Epigenetics Chromatin 2014; 7:14. [PMID: 25097667 PMCID: PMC4115480 DOI: 10.1186/1756-8935-7-14] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 06/23/2014] [Indexed: 12/19/2022] Open
Abstract
Background Acetylation of lysine residues in histone tails plays an important role in the regulation of gene transcription. Bromdomains are the readers of acetylated histone marks, and, consequently, bromodomain-containing proteins have a variety of chromatin-related functions. Moreover, they are increasingly being recognised as important mediators of a wide range of diseases. The first potent and selective bromodomain inhibitors are beginning to be described, but the diverse or unknown functions of bromodomain-containing proteins present challenges to systematically demonstrating cellular efficacy and selectivity for these inhibitors. Here we assess the viability of fluorescence recovery after photobleaching (FRAP) assays as a target agnostic method for the direct visualisation of an on-target effect of bromodomain inhibitors in living cells. Results Mutation of a conserved asparagine crucial for binding to acetylated lysines in the bromodomains of BRD3, BRD4 and TRIM24 all resulted in reduction of FRAP recovery times, indicating loss of or significantly reduced binding to acetylated chromatin, as did the addition of known inhibitors. Significant differences between wild type and bromodomain mutants for ATAD2, BAZ2A, BRD1, BRD7, GCN5L2, SMARCA2 and ZMYND11 required the addition of the histone deacetylase inhibitor suberoylanilide hydroxamic acid (SAHA) to amplify the binding contribution of the bromodomain. Under these conditions, known inhibitors decreased FRAP recovery times back to mutant control levels. Mutation of the bromodomain did not alter FRAP recovery times for full-length CREBBP, even in the presence of SAHA, indicating that other domains are primarily responsible for anchoring CREBBP to chromatin. However, FRAP assays with multimerised CREBBP bromodomains resulted in a good assay to assess the efficacy of bromodomain inhibitors to this target. The bromodomain and extraterminal protein inhibitor PFI-1 was inactive against other bromodomain targets, demonstrating the specificity of the method. Conclusions Viable FRAP assays were established for 11 representative bromodomain-containing proteins that broadly cover the bromodomain phylogenetic tree. Addition of SAHA can overcome weak binding to chromatin, and the use of tandem bromodomain constructs can eliminate masking effects of other chromatin binding domains. Together, these results demonstrate that FRAP assays offer a potentially pan-bromodomain method for generating cell-based assays, allowing the testing of compounds with respect to cell permeability, on-target efficacy and selectivity.
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30
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Robust multi-type plasmid modifications based on isothermal in vitro recombination. Gene 2014; 548:39-42. [PMID: 25010726 DOI: 10.1016/j.gene.2014.07.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 07/04/2014] [Indexed: 11/21/2022]
Abstract
A robust strategy for multi-type plasmid modifications is developed based on the isothermal in vitro recombination technology, by which any combination of the sequence modifications can be efficiently achieved in plasmids at any desired position in a seamless manner. As an example, we showed that a plasmid modification with insertion of a GFP gene, deletion of a 623-bp fragment, and substitution of an ampicillin resistance gene by a kanamycin resistance gene was accomplished simultaneously by this method. Therefore, the isothermal in vitro recombination-based multi-type plasmid modification strategy is a useful approach for broad application prospects in molecular biology studies.
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Li MV, Shukla D, Rhodes BH, Lall A, Shu J, Moriarity BS, Largaespada DA. HomeRun Vector Assembly System: a flexible and standardized cloning system for assembly of multi-modular DNA constructs. PLoS One 2014; 9:e100948. [PMID: 24959875 PMCID: PMC4069157 DOI: 10.1371/journal.pone.0100948] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 06/01/2014] [Indexed: 11/29/2022] Open
Abstract
Advances in molecular and synthetic biology call for efficient assembly of multi-modular DNA constructs. We hereby present a novel modular cloning method that obviates the need for restriction endonucleases and significantly improves the efficiency in the design and construction of complex DNA molecules by standardizing all DNA elements and cloning reactions. Our system, named HomeRun Vector Assembly System (HVAS), employs a three-tiered vector series that utilizes both multisite gateway cloning and homing endonucleases, with the former building individual functional modules and the latter linking modules into the final construct. As a proof-of-principle, we first built a two-module construct that supported doxycycline-induced expression of green fluorescent protein (GFP). Further, with a three-module construct we showed quantitatively that there was minimal promoter leakage between neighbouring modules. Finally, we developed a method, in vitro Cre recombinase-mediated cassette exchange (RMCE) cloning, to regenerate a gateway destination vector from a previous multisite gateway cloning reaction, allowing access to existing DNA element libraries in conventional gateway entry clones, and simple creation of constructs ready for in vivo RMCE. We believe these methods constitute a useful addition to the standard molecular cloning techniques that could potentially support industrial scale synthesis of DNA constructs.
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Affiliation(s)
- Ming V. Li
- Division of Endocrinology and Diabetes, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- * E-mail:
| | - Dip Shukla
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Brian H. Rhodes
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Anjali Lall
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Jingmin Shu
- Division of Endocrinology and Diabetes, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Center for Genome Engineering and Institute of Human Genetics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Branden S. Moriarity
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Center for Genome Engineering and Institute of Human Genetics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - David A. Largaespada
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Center for Genome Engineering and Institute of Human Genetics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
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32
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Development of R4 Gateway Binary Vectors (R4pGWB) Enabling High-Throughput Promoter Swapping for Plant Research. Biosci Biotechnol Biochem 2014; 72:624-9. [DOI: 10.1271/bbb.70678] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
High-throughput, automated or semiautomated methodologies implemented by companies and structural genomics initiatives have accelerated the process of acquiring structural information for proteins via x-ray crystallography. This has enabled the application of structure-based drug design technologies to a variety of new structures that have potential pharmacologic relevance. Although there remain major challenges to applying these approaches more broadly to all classes of drug discovery targets, clearly the continued development and implementation of these structure-based drug design methodologies by the scientific community at large will help to address and provide solutions to these hurdles. The result will be a growing number of protein structures of important pharmacologic targets that will help to streamline the process of identification and optimization of lead compounds for drug development. These lead agonist and antagonist pharmacophores should, in turn, help to alleviate one of the current critical bottlenecks in the drug discovery process; that is, defining the functional relevance of potential novel targets to disease modification. The prospect of generating an increasing number of potential drug candidates will serve to highlight perhaps the most significant future bottleneck for drug development, the cost and complexity of the drug approval process.
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Affiliation(s)
- Leslie W Tari
- ActiveSight, 4045 Sorrento Valley Blvd, San Diego, CA 92121, USA.
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34
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Doskočilová A, Luptovčiak I, Smékalová V, Samaj J. Fluorescent protein tagging of Arabidopsis MAPKs for in vivo localization studies. Methods Mol Biol 2014; 1171:131-45. [PMID: 24908125 DOI: 10.1007/978-1-4939-0922-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Mitogen-activated protein kinases (MAPK) are key regulatory elements in many processes. They are highly conserved throughout eukaryotes. In plants, MAPKs are involved in biotic and abiotic stress responses; they regulate cell division, cell growth, and also programmed cell death. In vivo visualization of MAPKs is crucial for understanding of their spatiotemporal organization. Cloning of MAPK-fluorescent protein fusions might present difficulties related to the preservation of protein-protein interactions essential for MAPK localization, interactions with upstream and downstream regulators, and finally substrate targeting. In this chapter we describe cloning of MAPKs in the flexible MultiSite Gateway(®) cloning system followed by easy and quick testing of binary vectors by transient assays in Arabidopsis thaliana and Nicotiana benthamiana.
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Affiliation(s)
- Anna Doskočilová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 11, 783 71, Olomouc, Czech Republic,
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35
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Lampropoulos A, Sutikovic Z, Wenzl C, Maegele I, Lohmann JU, Forner J. GreenGate---a novel, versatile, and efficient cloning system for plant transgenesis. PLoS One 2013; 8:e83043. [PMID: 24376629 PMCID: PMC3869738 DOI: 10.1371/journal.pone.0083043] [Citation(s) in RCA: 285] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 11/08/2013] [Indexed: 12/02/2022] Open
Abstract
Building expression constructs for transgenesis is one of the fundamental day-to-day tasks in modern biology. Traditionally it is based on a multitude of type II restriction endonucleases and T4 DNA ligase. Especially in case of long inserts and applications requiring high-throughput, this approach is limited by the number of available unique restriction sites and the need for designing individual cloning strategies for each project. Several alternative cloning systems have been developed in recent years to overcome these issues, including the type IIS enzyme based Golden Gate technique. Here we introduce our GreenGate system for rapidly assembling plant transformation constructs, which is based on the Golden Gate method. GreenGate cloning is simple and efficient since it uses only one type IIS restriction endonuclease, depends on only six types of insert modules (plant promoter, N-terminal tag, coding sequence, C-terminal tag, plant terminator and plant resistance cassette), but at the same time allows assembling several expression cassettes in one binary destination vector from a collection of pre-cloned building blocks. The system is cheap and reliable and when combined with a library of modules considerably speeds up cloning and transgene stacking for plant transformation.
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Affiliation(s)
- Athanasios Lampropoulos
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Zoran Sutikovic
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Christian Wenzl
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Ira Maegele
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Jan U. Lohmann
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Joachim Forner
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
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36
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Colloms SD, Merrick CA, Olorunniji FJ, Stark WM, Smith MCM, Osbourn A, Keasling JD, Rosser SJ. Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination. Nucleic Acids Res 2013; 42:e23. [PMID: 24225316 PMCID: PMC3936721 DOI: 10.1093/nar/gkt1101] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Synthetic biology requires effective methods to assemble DNA parts into devices and to modify these devices once made. Here we demonstrate a convenient rapid procedure for DNA fragment assembly using site-specific recombination by C31 integrase. Using six orthogonal attP/attB recombination site pairs with different overlap sequences, we can assemble up to five DNA fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. C31 integrase-mediated assembly is highly efficient, allowing production of large libraries suitable for combinatorial gene assembly strategies. The resultant assemblies contain arrays of DNA cassettes separated by recombination sites, which can be used to manipulate the assembly by further recombination. We illustrate the utility of these procedures to (i) assemble functional metabolic pathways containing three, four or five genes; (ii) optimize productivity of two model metabolic pathways by combinatorial assembly with randomization of gene order or ribosome binding site strength; and (iii) modify an assembled metabolic pathway by gene replacement or addition.
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Affiliation(s)
- Sean D Colloms
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Bower Building, University Avenue, Glasgow G12 8QQ, Scotland, UK, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK, Department of Metabolic Biology, The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK, Joint BioEnergy Institute, Emeryville, CA 94608, USA, Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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37
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Abstract
Basic research has provided a much better understanding of the genetic networks and regulatory hierarchies in plants. To meet the challenges of agriculture, we must be able to rapidly translate this knowledge into generating improved plants. Therefore, in this Review, we discuss advanced tools that are currently available for use in plant biotechnology to produce new products in plants and to generate plants with new functions. These tools include synthetic promoters, 'tunable' transcription factors, genome-editing tools and site-specific recombinases. We also review some tools with the potential to enable crop improvement, such as methods for the assembly and synthesis of large DNA molecules, plant transformation with linked multigenes and plant artificial chromosomes. These genetic technologies should be integrated to realize their potential for applications to pressing agricultural and environmental problems.
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38
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Guye P, Li Y, Wroblewska L, Duportet X, Weiss R. Rapid, modular and reliable construction of complex mammalian gene circuits. Nucleic Acids Res 2013; 41:e156. [PMID: 23847100 PMCID: PMC3763561 DOI: 10.1093/nar/gkt605] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Revised: 06/10/2013] [Accepted: 06/18/2013] [Indexed: 11/13/2022] Open
Abstract
We developed a framework for quick and reliable construction of complex gene circuits for genetically engineering mammalian cells. Our hierarchical framework is based on a novel nucleotide addressing system for defining the position of each part in an overall circuit. With this framework, we demonstrate construction of synthetic gene circuits of up to 64 kb in size comprising 11 transcription units and 33 basic parts. We show robust gene expression control of multiple transcription units by small molecule inducers in human cells with transient transfection and stable chromosomal integration of these circuits. This framework enables development of complex gene circuits for engineering mammalian cells with unprecedented speed, reliability and scalability and should have broad applicability in a variety of areas including mammalian cell fermentation, cell fate reprogramming and cell-based assays.
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Affiliation(s)
- Patrick Guye
- Department of Biological Engineering, Massachusetts Institute of Technology, 40 Ames Street, Cambridge, MA 02142, USA, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 40 Ames Street, Cambridge, MA 02142, USA and INRIA Paris-Rocquencourt, Le Chesnay, 78153, France
| | - Yinqing Li
- Department of Biological Engineering, Massachusetts Institute of Technology, 40 Ames Street, Cambridge, MA 02142, USA, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 40 Ames Street, Cambridge, MA 02142, USA and INRIA Paris-Rocquencourt, Le Chesnay, 78153, France
| | - Liliana Wroblewska
- Department of Biological Engineering, Massachusetts Institute of Technology, 40 Ames Street, Cambridge, MA 02142, USA, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 40 Ames Street, Cambridge, MA 02142, USA and INRIA Paris-Rocquencourt, Le Chesnay, 78153, France
| | - Xavier Duportet
- Department of Biological Engineering, Massachusetts Institute of Technology, 40 Ames Street, Cambridge, MA 02142, USA, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 40 Ames Street, Cambridge, MA 02142, USA and INRIA Paris-Rocquencourt, Le Chesnay, 78153, France
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, 40 Ames Street, Cambridge, MA 02142, USA, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 40 Ames Street, Cambridge, MA 02142, USA and INRIA Paris-Rocquencourt, Le Chesnay, 78153, France
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39
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Gateway vectors for efficient artificial gene assembly in vitro and expression in yeast Saccharomyces cerevisiae. PLoS One 2013; 8:e64419. [PMID: 23675537 PMCID: PMC3651225 DOI: 10.1371/journal.pone.0064419] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 04/15/2013] [Indexed: 11/19/2022] Open
Abstract
Construction of synthetic genetic networks requires the assembly of DNA fragments encoding functional biological parts in a defined order. Yet this may become a time-consuming procedure. To address this technical bottleneck, we have created a series of Gateway shuttle vectors and an integration vector, which facilitate the assembly of artificial genes and their expression in the budding yeast Saccharomyces cerevisiae. Our method enables the rapid construction of an artificial gene from a promoter and an open reading frame (ORF) cassette by one-step recombination reaction in vitro. Furthermore, the plasmid thus created can readily be introduced into yeast cells to test the assembled gene's functionality. As flexible regulatory components of a synthetic genetic network, we also created new versions of the tetracycline-regulated transactivators tTA and rtTA by fusing them to the auxin-inducible degron (AID). Using our gene assembly approach, we made yeast expression vectors of these engineered transactivators, AIDtTA and AIDrtTA and then tested their functions in yeast. We showed that these factors can be regulated by doxycycline and degraded rapidly after addition of auxin to the medium. Taken together, the method for combinatorial gene assembly described here is versatile and would be a valuable tool for yeast synthetic biology.
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40
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Dolt KS, Lawrence ML, Miller-Hodges E, Slight J, Thornburn A, Devenney PS, Hohenstein P. A universal vector for high-efficiency multi-fragment recombineering of BACs and knock-in constructs. PLoS One 2013; 8:e62054. [PMID: 23637962 PMCID: PMC3639282 DOI: 10.1371/journal.pone.0062054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/17/2013] [Indexed: 01/20/2023] Open
Abstract
There is an increasing need for more efficient generation of transgenic constructs. Here we present a universal multi-site Gateway vector for use in recombineering reactions. Using transgenic mouse models, we show its use for the generation of BAC transgenics and targeting vectors. The modular nature of the vector allows for rapid modification of constructs to generate different versions of the same construct. As such it will help streamline the generation of series of related transgenic models.
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Affiliation(s)
- Karamjit Singh Dolt
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Melanie L. Lawrence
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Eve Miller-Hodges
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Joan Slight
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Anna Thornburn
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Paul S. Devenney
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Peter Hohenstein
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- * E-mail:
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Müller WEG, Schröder HC, Muth S, Gietzen S, Korzhev M, Grebenjuk VA, Wiens M, Schloßmacher U, Wang X. The silicatein propeptide acts as inhibitor/modulator of self-organization during spicule axial filament formation. FEBS J 2013; 280:1693-708. [DOI: 10.1111/febs.12183] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/02/2013] [Accepted: 02/06/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Werner E. G. Müller
- ERC Advanced Grant Research Group at the Institute for Physiological Chemistry; University Medical Center of the Johannes Gutenberg University Mainz; Mainz; Germany
| | - Heinz C. Schröder
- ERC Advanced Grant Research Group at the Institute for Physiological Chemistry; University Medical Center of the Johannes Gutenberg University Mainz; Mainz; Germany
| | - Sandra Muth
- Institute for Physical Chemistry; Johannes Gutenberg University Mainz; Mainz; Germany
| | - Sabine Gietzen
- Institute for Physical Chemistry; Johannes Gutenberg University Mainz; Mainz; Germany
| | - Michael Korzhev
- ERC Advanced Grant Research Group at the Institute for Physiological Chemistry; University Medical Center of the Johannes Gutenberg University Mainz; Mainz; Germany
| | - Vlad A. Grebenjuk
- ERC Advanced Grant Research Group at the Institute for Physiological Chemistry; University Medical Center of the Johannes Gutenberg University Mainz; Mainz; Germany
| | - Matthias Wiens
- ERC Advanced Grant Research Group at the Institute for Physiological Chemistry; University Medical Center of the Johannes Gutenberg University Mainz; Mainz; Germany
| | - Ute Schloßmacher
- ERC Advanced Grant Research Group at the Institute for Physiological Chemistry; University Medical Center of the Johannes Gutenberg University Mainz; Mainz; Germany
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42
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Kimura T, Nakao A, Murata S, Kobayashi Y, Tanaka Y, Shibahara K, Kawazu T, Nakagawa T. Development of the gateway recycling cloning system for multiple linking of expression cassettes in a defined order, and direction on gateway compatible binary vectors. Biosci Biotechnol Biochem 2013; 77:430-4. [PMID: 23391940 DOI: 10.1271/bbb.120877] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We developed the Gateway recycling cloning system, which allows multiple linking of expression cassettes by multiple rounds of the Gateway LR reaction. Employing this system, the recycling donor vector pRED419 was subjected to the first LR reaction with an attR1-attR2 type destination vector. Then conversion vector pCON was subjected to an LR reaction to restore the attR1-attR2 site on the destination vector for the next cloning cycle. By repetition of these two simple steps, we linked four expression cassettes of a reporter gene in Gateway binary vector pGWB1, introduced the constructs into tobacco BY-2 cells, and observed the expression of transgenes.
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Affiliation(s)
- Tetsuya Kimura
- Department of Sustainable Resource Science, Graduate School of Bioresources, Mie University, Tsu, Japan
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43
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Buntru M, Gärtner S, Staib L, Kreuzaler F, Schlaich N. Delivery of multiple transgenes to plant cells by an improved version of MultiRound Gateway technology. Transgenic Res 2013; 22:153-67. [PMID: 22972476 DOI: 10.1007/s11248-012-9640-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 07/27/2012] [Indexed: 11/30/2022]
Abstract
At present, only few methods for the effective assembly of multigene constructs have been described. Here we present an improved version of the MultiRound Gateway technology, which facilitates plant multigene transformation. The system consists of two attL-flanked entry vectors, which contain an attR cassette, and a transformation-competent artificial chromosome based destination vector. By alternate use of the two entry vectors, multiple transgenes can be delivered sequentially into the Gateway-compatible destination vector. Multigene constructs that carried up to seven transgenes corresponding to more than 26 kb were assembled by seven rounds of LR recombination. The constructs were successfully transformed into tobacco plants and were stably inherited for at least two generations. Thus, our system represents a powerful, highly efficient tool for multigene plant transformation and may facilitate genetic engineering of agronomic traits or the assembly of genetic pathways for the production of biofuels, industrial or pharmaceutical compounds in plants.
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Affiliation(s)
- Matthias Buntru
- Institute for Biology I, RWTH Aachen University, Worringer Weg 1, 52056, Aachen, Germany.
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44
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Abstract
One major obstacle in realizing the potential behind human embryonic stem cells (hESC) is the availability of efficient and reliable engineering methods. Such methods require cloning technologies that can be applied to a variety of platforms and can serve multiple functions. In the last two decades cloning technologies have become more efficient, widening the bottleneck in creating engineered hESC lines. Using TOPO(®) TA cloning kits, genes can be efficiently amplified and inserted into target vectors with minimal manipulation and purification. For more complex cloning procedures we introduce the Multisite Gateway(®) system. This is a cloning platform based on integrase technology that allows for the generation of complex multicistronic gene configurations that can transverse a variety of platforms with ease. These technologies allow the end user to quickly and efficiently select clones, as well as combine multiple genetic elements of interest between platform technologies in a high-throughput manner, providing scientists with a toolbox to create tools to dissect stem cell biology.
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Affiliation(s)
- Andrew Fontes
- Primary and Stem Cell Systems, Life Technologies, Carlsbad, CA, USA
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45
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Ishimoto T, Mano H, Ozawa T, Mori H. Measuring CREB activation using bioluminescent probes that detect KID-KIX interaction in living cells. Bioconjug Chem 2012; 23:923-32. [PMID: 22506514 DOI: 10.1021/bc200491j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The cyclic adenosine monophosphate response element-binding protein (CREB) is a transcription factor that contributes to memory formation. The transcriptional activity of CREB is induced by its phosphorylation at Ser-133 and subsequent interaction with the CREB-binding protein (CBP)/p300. We designed and optimized firefly split luciferase probe proteins that detect the interaction of the kinase-inducible domain (KID) of CREB and the KIX domain of CBP/p300. The increase in the light intensity of the probe proteins results from the phosphorylation of the responsible serine corresponding to Ser-133 of CREB. Because these proteins have a high signal-to-noise ratio and are nontoxic, it has become possible for the first time to carry out long-term measurement of KID-KIX interaction in living cells. Furthermore, we examined the usefulness of the probe proteins for future high-throughput cell-based drug screening and found several herbal extracts that activated CREB.
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Affiliation(s)
- Tetsuya Ishimoto
- Department of Molecular Neuroscience, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama , Toyama, Japan
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46
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Abstract
Multisite Gateway technology is a DNA cloning method based on in vitro site-specific recombination that is becoming increasingly popular because it allows quick and highly efficient assembly of multiple DNA fragments into a vector backbone. In the conventional Gateway Multisite strategy, cloning of multiple DNA fragments requires recombination of multiple entry clones with a single destination vector. The -limitation of this approach is that as the number of entry clones increases, the efficiency of the assembly reactions decreases due to difficulty in successfully recognizing multiple pairs of matched att signals simultaneously. To address this problem, we have devised methods to generate modular expression clones, modular entry clones, and modular destination vectors. These allow many DNA fragments to be -assembled stepwise into complex expression clones. We describe here how to construct these intermediate clones and vectors, and how to use these modules to construct expression clones comprising ten or more DNA -segments. These principles can be applied to make multicomponent DNAs for many applications.
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Affiliation(s)
- Takefumi Sone
- Division of Gene Therapy, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
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47
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Estornell LH, Granell A, Orzaez D. Exploiting Multisite Gateway and pENFRUIT plasmid collection for fruit genetic engineering. Methods Mol Biol 2012; 847:351-368. [PMID: 22351021 DOI: 10.1007/978-1-61779-558-9_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
MultiSite Gateway cloning techniques based on homologous recombination facilitate the combinatorial assembly of basic genetic pieces (i.e., promoters, CDS, and terminators) into gene expression or gene silencing cassettes. pENFRUIT is a collection of MultiSite Triple Gateway Entry vectors dedicated to genetic engineering in fruits. It comprises a number of fruit-operating promoters as well as C-terminal tags adapted to the Gateway standard. In this way, flanking regulatory/labeling sequences can be easily Gateway-assembled with a given gene of interest for its ectopic expression or silencing in fruits. The resulting gene constructs can be analyzed in stable transgenic plants or in transient expression assays, the latter allowing fast testing of the increasing number of combinations arising from MultiSite methodology. A detailed description of the use of MultiSite cloning methodology for the assembly of pENFRUIT elements is presented.
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48
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Hopkins RF, Wall VE, Esposito D. Optimizing transient recombinant protein expression in mammalian cells. Methods Mol Biol 2012; 801:251-268. [PMID: 21987258 DOI: 10.1007/978-1-61779-352-3_16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Transient gene expression (TGE) in mammalian cells has become a routine process for expressing recombinant proteins in cell lines such as human embryonic kidney 293 and Chinese hamster ovary cells. The rapidly increasing need for recombinant proteins requires further improvements in TGE technology. While a great deal of focus has been directed toward optimizing the secretion of antibodies and other naturally secreted targets, much less work has been done on ways to improve cytoplasmic expression in mammalian cells. The benefits to protein production in mammalian cells, particularly for eukaryotic proteins, should be very significant - glycosylation and other posttranslational modifications will likely be native or near-native, solubility and protein folding would likely improve overexpression in heterologous hosts, and expression of proteins in their proper intracellular compartments is much more likely to occur. Improvements in this area have been slow, however, due to limited development of the cell culture processes needed for low-cost, higher-throughput expression in mammalian cells, and the relatively low diversity of DNA vectors for protein production in these systems. Here, we describe how the use of recombinational cloning, coupled with improvements in transfection protocols which increase speed and lower cost, can be combined to make mammalian cells much more amenable for routine recombinant protein expression.
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Affiliation(s)
- Ralph F Hopkins
- Protein Expression Laboratory, SAIC-Frederick, Inc., Frederick, MD, USA
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Obayashi H, Kawabe Y, Makitsubo H, Watanabe R, Kameyama Y, Huang S, Takenouchi Y, Ito A, Kamihira M. Accumulative gene integration into a pre-determined site using Cre/loxP. J Biosci Bioeng 2011; 113:381-8. [PMID: 22136795 DOI: 10.1016/j.jbiosc.2011.10.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 10/27/2011] [Accepted: 10/31/2011] [Indexed: 02/06/2023]
Abstract
Site-specific gene recombination systems, such as Cre/loxP, have been used for genetic modification of cells and organisms in both basic and applied research. We previously developed an accumulative gene integration system (AGIS), in which target gene cassettes could be repeatedly integrated into a pre-determined site on a plasmid or cellular genome by recombinase-mediated cassette exchange (RMCE), using Cre and mutated loxPs. In the present study, we designed a simplified AGIS. For gene integration into a target site, the previous system used two loxP sites in the acceptor DNA, whereas the new system uses a single loxP site. The gene integration reactions were repeated four times in vitro using Cre protein and specific plasmids. The expected integration reactions mediated by Cre occurred at the loxP sites, resulting in integration of four target genes. The system was also used for genomic integration of reporter genes using Chinese hamster ovary (CHO) cells. The reporter genes were efficiently introduced into the CHO genome in a Cre-dependent manner, and transgene expression was detected after the integration reaction. The expression levels of the reporter genes were enhanced, corresponding to the increase of transgene copy number. Recombinase-mediated AGIS provides a useful tool for the modification of cellular genomes.
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Affiliation(s)
- Hirokazu Obayashi
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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Takata Y, Kishine H, Sone T, Andoh T, Nozaki M, Poderycki M, Chesnut JD, Imamoto F. Generation of iPS cells using a BacMam multigene expression system. Cell Struct Funct 2011; 36:209-22. [PMID: 21979235 DOI: 10.1247/csf.11008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Generation of iPS cells from mouse embryonic fibroblasts (MEF) was achieved using a BacMam transduction system containing a polycistronic plasmid expression vector for coincident and optimized expression of four defined reprogramming transcription factors. The sequences for Oct4, Klf4, Sox2 and c-Myc, were cloned as a fusion gene (OKSM) in a single open reading frame (ORF) via self-cleaving 2A peptides and expressed under the control of the CAG promoter. The transduction efficiency of primary MEF cells with BacMam particles carrying CAG-directed Venus reporter gene is 64-98%. After three successive transductions (at intervals of 3 days) of MEF cells with BacMam particles carrying a OKSM or OSKM cassette, the iPS cell colonies are observed in 15-24 days. A single transduction of MEF cells is also effective in generating sufficiently reprogrammed iPS cell lines. The iPS cell lines from colonies picked were positively stained by Nanog, SSEA-1 immunofluorescence and alkaline phosphatase substrate markers. The advantage of using the EOS-S(4+)-EmGFP reporter to identify sufficiently reprogrammed iPS cell lines is discussed by representing experimental results obtained with electroporated plasmids, such as a mixture of 2 tandem OS and KM plasmids and a polycistronic OKSM expression plasmid.
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Affiliation(s)
- Yoko Takata
- Department of Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
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