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Prusty A, Mehra P, Sharma S, Malik N, Agarwal P, Parida SK, Kapoor S, Tyagi AK. OsMED14_2, a tail module subunit of Mediator complex, controls rice development and involves jasmonic acid. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112146. [PMID: 38848769 DOI: 10.1016/j.plantsci.2024.112146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/15/2024] [Accepted: 05/31/2024] [Indexed: 06/09/2024]
Abstract
The Mediator complex is essential for eukaryotic transcription, yet its role and the function of its individual subunits in plants, especially in rice, remain poorly understood. Here, we investigate the function of OsMED14_2, a subunit of the Mediator tail module, in rice development. Overexpression and knockout of OsMED14_2 resulted in notable changes in panicle morphology and grain size. Microscopic analysis revealed impact of overexpression on pollen maturation, reflected by reduced viability, irregular shapes, and aberrant intine development. OsMED14_2 was found to interact with proteins involved in pollen development, namely, OsMADS62, OsMADS63 and OsMADS68, and its overexpression negatively affected the expression of OsMADS68 and the expression of other genes involved in intine development, including OsCAP1, OsGCD1, OsRIP1, and OsCPK29. Additionally, we found that OsMED14_2 overexpression influences jasmonic acid (JA) homeostasis, affecting bioactive JA levels, and expression of OsJAZ genes. Our data suggest OsMED14_2 may act as a regulator of JA-responsive genes through its interactions with OsHDAC6 and OsJAZ repressors. These findings contribute to better understanding of the Mediator complex's role in plant traits regulation.
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Affiliation(s)
- Ankita Prusty
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus (UDSC), New Delhi 110021, India
| | - Poonam Mehra
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus (UDSC), New Delhi 110021, India; Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Shivam Sharma
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus (UDSC), New Delhi 110021, India
| | - Naveen Malik
- National Institute of Plant Genome Research, New Delhi 110067, India; Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research, New Delhi 110067, India
| | | | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus (UDSC), New Delhi 110021, India
| | - Akhilesh Kumar Tyagi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus (UDSC), New Delhi 110021, India.
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Lee K, Cho MH, Kim MJ, Bhoo SH. A Small Epitope Tagging on the C-Terminus of a Target Protein Requires Extra Amino Acids to Enhance the Immune Responses of the Corresponding Antibody. J Microbiol Biotechnol 2024; 34:1222-1228. [PMID: 38783697 PMCID: PMC11239440 DOI: 10.4014/jmb.2401.01036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/01/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Protein-specific antibodies are essential for various aspects of protein research, including detection, purification, and characterization. When specific antibodies are unavailable, protein tagging is a useful alternative. Small epitope tags, typically less than 10 amino acids, are widely used in protein research due to the simple modification through PCR and reduced impact on the target protein's function compared to larger tags. The 2B8 epitope tag (RDPLPFFPP), reported by us in a previous study, has high specificity and sensitivity to the corresponding antibody. However, when attached to the C-terminus of the target protein in immunoprecipitation experiments, we observed a decrease in detection signal with reduced immunity and low protein recovery. This phenomenon was not unique to 2B8 and was also observed with the commercially available Myc tag. Our study revealed that C-terminal tagging of small epitope tags requires the addition of more than one extra amino acid to enhance (restore) antibody immunities. Moreover, among the amino acids we tested, serine was the best for the 2B8 tag. Our findings demonstrated that the interaction between a small epitope and a corresponding paratope of an antibody requires an extra amino acid at the C-terminus of the epitope. This result is important for researchers planning studies on target proteins using small epitope tags.
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Affiliation(s)
- Kyungha Lee
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Man-Ho Cho
- Department of Genetics and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Mi-Ju Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Seong-Hee Bhoo
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin 17104, Republic of Korea
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3
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Kim J, Kratz AF, Chen S, Sheng J, Kim HK, Zhang L, Singh BK, Chavez A. High-throughput tagging of endogenous loci for rapid characterization of protein function. SCIENCE ADVANCES 2024; 10:eadg8771. [PMID: 38691600 PMCID: PMC11062585 DOI: 10.1126/sciadv.adg8771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/28/2024] [Indexed: 05/03/2024]
Abstract
To facilitate the interrogation of protein function at scale, we have developed high-throughput insertion of tags across the genome (HITAG). HITAG enables users to rapidly produce libraries of cells, each with a different protein of interest C-terminally tagged. HITAG is based on a modified strategy for performing Cas9-based targeted insertions, coupled with an improved approach for selecting properly tagged lines. Analysis of the resulting clones generated by HITAG reveals high tagging specificity, with most successful tagging events being indel free. Using HITAG, we fuse mCherry to a set of 167 stress granule-associated proteins and elucidate the features that drive a subset of proteins to strongly accumulate within these transient RNA-protein granules.
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Affiliation(s)
- Joonwon Kim
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexander F. Kratz
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shiye Chen
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jenny Sheng
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hark Kyun Kim
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Liudeng Zhang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Brijesh Kumar Singh
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
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4
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Hoffmann SA, Cai Y. Engineering stringent genetic biocontainment of yeast with a protein stability switch. Nat Commun 2024; 15:1060. [PMID: 38316765 PMCID: PMC10844650 DOI: 10.1038/s41467-024-44988-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
Synthetic biology holds immense promise to tackle key problems in resource use, environmental remediation, and human health care. However, comprehensive safety measures are lacking to employ engineered microorganisms in open-environment applications. Genetically encoded biocontainment systems may solve this issue. Here, we describe such a system based on conditional stability of essential proteins. We used a destabilizing domain degron stabilized by estradiol addition (ERdd). We ERdd-tagged 775 essential genes and screened for strains with estradiol dependent growth. Three genes, SPC110, DIS3 and RRP46, were found to be particularly suitable targets. Respective strains showed no growth defect in the presence of estradiol and strong growth inhibition in its absence. SPC110-ERdd offered the most stringent containment, with an escape frequency of <5×10-7. Removal of its C-terminal domain decreased the escape frequency further to <10-8. Being based on conditional protein stability, the presented approach is mechanistically orthogonal to previously reported genetic biocontainment systems.
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Affiliation(s)
- Stefan A Hoffmann
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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5
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Weklak D, Tisborn J, Mangold MH, Scheu R, Wodrich H, Hagedorn C, Jönsson F, Kreppel F. Insights from the Construction of Adenovirus-Based Vaccine Candidates against SARS-CoV-2: Expecting the Unexpected. Viruses 2023; 15:2155. [PMID: 38005833 PMCID: PMC10675337 DOI: 10.3390/v15112155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
To contain the spread of the SARS-CoV-2 pandemic, rapid development of vaccines was required in 2020. Rational design, international efforts, and a lot of hard work yielded the market approval of novel SARS-CoV-2 vaccines based on diverse platforms such as mRNA or adenovirus vectors. The great success of these technologies, in fact, contributed significantly to control the pandemic. Consequently, most scientific literature available in the public domain discloses the results of clinical trials and reveals data of efficaciousness. However, a description of processes and rationales that led to specific vaccine design is only partially available, in particular for adenovirus vectors, even though it could prove helpful for future developments. Here, we disclose our insights from the endeavors to design compatible functional adenoviral vector platform expression cassettes for the SARS-CoV-2 spike protein. We observed that contextualizing genes from an ssRNA virus into a DNA virus provides significant challenges. Besides affecting physical titers, expression cassette design of adenoviral vaccine candidates can affect viral propagation and spike protein expression. Splicing of mRNAs was affected, and fusogenicity of the spike protein in ACE2-overexpressing cells was enhanced when the ER retention signal was deleted.
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Affiliation(s)
- Denice Weklak
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Stockumer Str. 10, 58453 Witten, Germany; (D.W.); (J.T.); (M.H.M.); (R.S.); (C.H.)
| | - Julian Tisborn
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Stockumer Str. 10, 58453 Witten, Germany; (D.W.); (J.T.); (M.H.M.); (R.S.); (C.H.)
| | - Maurin Helen Mangold
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Stockumer Str. 10, 58453 Witten, Germany; (D.W.); (J.T.); (M.H.M.); (R.S.); (C.H.)
| | - Raphael Scheu
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Stockumer Str. 10, 58453 Witten, Germany; (D.W.); (J.T.); (M.H.M.); (R.S.); (C.H.)
| | - Harald Wodrich
- Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, Université de Bordeaux, 33076 Bordeaux, France;
| | - Claudia Hagedorn
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Stockumer Str. 10, 58453 Witten, Germany; (D.W.); (J.T.); (M.H.M.); (R.S.); (C.H.)
| | - Franziska Jönsson
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Stockumer Str. 10, 58453 Witten, Germany; (D.W.); (J.T.); (M.H.M.); (R.S.); (C.H.)
| | - Florian Kreppel
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Stockumer Str. 10, 58453 Witten, Germany; (D.W.); (J.T.); (M.H.M.); (R.S.); (C.H.)
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6
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Junod SL, Tingey M, Kelich JM, Goryaynov A, Herbine K, Yang W. Dynamics of nuclear export of pre-ribosomal subunits revealed by high-speed single-molecule microscopy in live cells. iScience 2023; 26:107445. [PMID: 37599825 PMCID: PMC10433129 DOI: 10.1016/j.isci.2023.107445] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 06/24/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
We present a study on the nuclear export efficiency and time of pre-ribosomal subunits in live mammalian cells, using high-speed single-molecule tracking and single-molecule fluorescence resonance energy transfer techniques. Our findings reveal that pre-ribosomal particles exhibit significantly higher nuclear export efficiency compared to other large cargos like mRNAs, with around two-thirds of interactions between the pre-60S or pre-40S and the nuclear pore complexes (NPCs) resulting in successful export to the cytoplasm. We also demonstrate that nuclear transport receptor (NTR) chromosomal maintenance 1 (CRM1) plays a crucial role in nuclear export efficiency, with pre-60S and pre-40S particle export efficiency decreasing by 11-17-fold when CRM1 is inhibited. Our results suggest that multiple copies of CRM1 work cooperatively to chaperone pre-ribosomal subunits through the NPC, thus increasing export efficiency and decreasing export time. Significantly, this cooperative NTR mechanism extends beyond pre-ribosomal subunits, as evidenced by the enhanced nucleocytoplasmic transport of proteins.
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Affiliation(s)
- Samuel L. Junod
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Mark Tingey
- Department of Biology, Temple University, Philadelphia, PA, USA
| | | | | | - Karl Herbine
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA, USA
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7
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Zhang Y, Zhao L, Wang Q, Zhang Z, Ren X, Yang X, Zeng S, Lv L, Zhao L, Su S, Chen X, Fu B. A novel epitope tag from rabies virus has versatile in vitro applications. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12546-9. [PMID: 37166480 DOI: 10.1007/s00253-023-12546-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/12/2023]
Abstract
Fusion tag technology is an important tool for rapid separation, purification, and characterization of proteins. Combined with monoclonal antibodies, tag epitope systems can be rapidly adapted to many assay systems. A monoclonal antibody that reacts with the matrix protein of the rabies virus CVS-11 strain was reported. The epitope (termed M) targeted by this antibody contains only six amino acids. We examine whether this specific sequence epitope can be applied as a protein tag. We show ectopic expression of M-tagged proteins has little impact on cell viability or major signaling pathways. The M tag system can be used for western blotting, immunoprecipitation, immunofluorescence staining, and flow cytometry assays. The results indicate the specificity, sensitivity, and versatility of this novel epitope tag system are comparable to the widely used FLAG tag system, providing researchers with an additional tool for molecular analysis. KEY POINTS: • A short peptide (Pro Pro Tyr Asp Asp Asp) can be applied as a new tag. • The new epitope-tagging fusion system has no effect on the main cellular signaling pathway. • The epitope-tagging fusion system can be widely used for western blotting, immunoprecipitation, immunofluorescence, flow cytometry, etc.
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Affiliation(s)
- Yuelan Zhang
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Lin Zhao
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Qinyang Wang
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Zhuyou Zhang
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Xiaoyan Ren
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Xue Yang
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Shaowei Zeng
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Linyue Lv
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Ling Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural Universitygrid, 35155.37, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Shuo Su
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoqi Chen
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| | - Bishi Fu
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China.
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8
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Pargett M, Ram AR, Murthy V, Davies AE. Live-Cell Sender-Receiver Co-cultures for Quantitative Measurement of Paracrine Signaling Dynamics, Gene Expression, and Drug Response. Methods Mol Biol 2023; 2634:285-314. [PMID: 37074584 DOI: 10.1007/978-1-0716-3008-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Paracrine signaling is a fundamental process regulating tissue development, repair, and pathogenesis of diseases such as cancer. Herein we describe a method for quantitatively measuring paracrine signaling dynamics, and resultant gene expression changes, in living cells using genetically encoded signaling reporters and fluorescently tagged gene loci. We discuss considerations for selecting paracrine "sender-receiver" cell pairs, appropriate reporters, the use of this system to ask diverse experimental questions and screen drugs blocking intracellular communication, data collection, and the use of computational approaches to model and interpret these experiments.
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Affiliation(s)
- Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
| | - Abhineet R Ram
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
| | - Vaibhav Murthy
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
- Knight Cancer Institute, Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR, USA
| | - Alexander E Davies
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.
- Knight Cancer Institute, Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR, USA.
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Madina MH, Santhanam P, Asselin Y, Jaswal R, Bélanger RR. Progress and Challenges in Elucidating the Functional Role of Effectors in the Soybean- Phytophthora sojae Interaction. J Fungi (Basel) 2022; 9:12. [PMID: 36675833 PMCID: PMC9866111 DOI: 10.3390/jof9010012] [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: 11/25/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Phytophthora sojae, the agent responsible for stem and root rot, is one of the most damaging plant pathogens of soybean. To establish a compatible-interaction, P. sojae secretes a wide array of effector proteins into the host cell. These effectors have been shown to act either in the apoplastic area or the cytoplasm of the cell to manipulate the host cellular processes in favor of the development of the pathogen. Deciphering effector-plant interactions is important for understanding the role of P. sojae effectors in disease progression and developing approaches to prevent infection. Here, we review the subcellular localization, the host proteins, and the processes associated with P. sojae effectors. We also discuss the emerging topic of effectors in the context of effector-resistance genes interaction, as well as model systems and recent developments in resources and techniques that may provide a better understanding of the soybean-P. sojae interaction.
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10
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Shi W, Riemann M, Rieger SM, Nick P. Cold-Induced Nuclear Import of CBF4 Regulates Freezing Tolerance. Int J Mol Sci 2022; 23:ijms231911417. [PMID: 36232718 PMCID: PMC9570231 DOI: 10.3390/ijms231911417] [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: 08/24/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/22/2022] Open
Abstract
C-repeat binding factors (CBFs) are crucial transcriptional activators in plant responses to low temperature. CBF4 differs in its slower, but more persistent regulation and its role in cold acclimation. Cold acclimation has accentuated relevance for tolerance to late spring frosts as they have become progressively more common, as a consequence of blurred seasonality in the context of global climate change. In the current study, we explore the functions of CBF4 from grapevine, VvCBF4. Overexpression of VvCBF4 fused to GFP in tobacco BY-2 cells confers cold tolerance. Furthermore, this protein shuttles from the cytoplasm to the nucleus in response to cold stress, associated with an accumulation of transcripts for other CBFs and the cold responsive gene, ERD10d. This response differs for chilling as compared to freezing and is regulated differently by upstream signalling involving oxidative burst, proteasome activity and jasmonate synthesis. The difference between chilling and freezing is also seen in the regulation of the CBF4 transcript in leaves from different grapevines differing in their cold tolerance. Therefore, we propose the quality of cold stress is transduced by different upstream signals regulating nuclear import and, thus, the transcriptional activation of grapevine CBF4.
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11
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Boy RL, Hong A, Aoki JI, Floeter-Winter LM, Laranjeira-Silva MF. Reporter gene systems: a powerful tool for Leishmania studies. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100165. [DOI: 10.1016/j.crmicr.2022.100165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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12
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Yasmin IA, Mohana Sundaram S, Banerjee A, Varier L, Dharmarajan A, Warrier S. Netrin-like domain of sFRP4, a Wnt antagonist inhibits stemness, metastatic and invasive properties by specifically blocking MMP-2 in cancer stem cells from human glioma cell line U87MG. Exp Cell Res 2021; 409:112912. [PMID: 34762897 DOI: 10.1016/j.yexcr.2021.112912] [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: 09/06/2021] [Revised: 11/05/2021] [Accepted: 11/07/2021] [Indexed: 11/26/2022]
Abstract
Rapid proliferation, high stemness potential, high invasiveness and apoptotic evasion are the distinctive hallmarks of glioma malignancy. The dysregulation of the Wnt/β-catenin pathway is the key factor regulating glioma malignancy. Wnt antagonist, secreted frizzled-related protein 4 (sFRP4), which has a prominent pro-apoptotic role in glioma stem cells, has two functional domains, the netrin-like domain (NLD), and cysteine-rich domain (CRD) both of which contribute to apoptotic properties of the whole protein. However, there are no reports elucidating the specific effects of individual domains of sFRP4 in inhibiting the invasive properties of glioma. This study explores the efficacy of the domains of sFRP4 in inhibiting the key hallmarks of glioblastoma such as invasion, metastasis, and stemness. We overexpressed sFRP4 and its domains in the glioblastoma cell line, U87MG cells and observed that both CRD and NLD domains played prominent roles in attenuating cancer stem cell properties. Significantly, we could demonstrate for the first time that both NLD and CRD domains negatively impacted the key driver of metastasis and migration, the matrix metalloproteinase-2 (MMP-2). Mechanistically, compared to CRD, NLD domain suppressed MMP-2 mediated invasion more effectively in glioma cells as observed in matrigel invasion assay and a function-blocking antibody assay. Fluorescent matrix degradation assay further revealed that NLD reduces matrix degradation. NLD also significantly disrupted fibronectin assembly and decreased cell adhesion in another glioma cell line LN229. In conclusion, the NLD peptide of sFRP4 could be a potent short peptide therapeutic candidate for targeting MMP-2-mediated invasion in the highly malignant glioblastoma multiforme.
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Affiliation(s)
- Ishmat Ara Yasmin
- Division of Cancer Stem Cells and Cardiovascular Regeneration, Manipal Institute of Regenerative Medicine, Manipal Academy of Higher Education (MAHE), Bangalore, 560 065, India
| | - S Mohana Sundaram
- Division of Cancer Stem Cells and Cardiovascular Regeneration, Manipal Institute of Regenerative Medicine, Manipal Academy of Higher Education (MAHE), Bangalore, 560 065, India
| | - Anasuya Banerjee
- Division of Cancer Stem Cells and Cardiovascular Regeneration, Manipal Institute of Regenerative Medicine, Manipal Academy of Higher Education (MAHE), Bangalore, 560 065, India
| | | | - Arun Dharmarajan
- Department of Biomedical Sciences, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Institute of Higher Education and Research, Chennai, 600 116, India
| | - Sudha Warrier
- Division of Cancer Stem Cells and Cardiovascular Regeneration, Manipal Institute of Regenerative Medicine, Manipal Academy of Higher Education (MAHE), Bangalore, 560 065, India; Cuor Stem Cellutions Pvt Ltd, Manipal Institute of Regenerative Medicine, Manipal Academy of Higher Education (MAHE), Bangalore, 560 065, India.
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13
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Van Genechten W, Van Dijck P, Demuyser L. Fluorescent toys 'n' tools lighting the way in fungal research. FEMS Microbiol Rev 2021; 45:fuab013. [PMID: 33595628 PMCID: PMC8498796 DOI: 10.1093/femsre/fuab013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/14/2021] [Indexed: 12/13/2022] Open
Abstract
Although largely overlooked compared to bacterial infections, fungal infections pose a significant threat to the health of humans and other organisms. Many pathogenic fungi, especially Candida species, are extremely versatile and flexible in adapting to various host niches and stressful situations. This leads to high pathogenicity and increasing resistance to existing drugs. Due to the high level of conservation between fungi and mammalian cells, it is hard to find fungus-specific drug targets for novel therapy development. In this respect, it is vital to understand how these fungi function on a molecular, cellular as well as organismal level. Fluorescence imaging allows for detailed analysis of molecular mechanisms, cellular structures and interactions on different levels. In this manuscript, we provide researchers with an elaborate and contemporary overview of fluorescence techniques that can be used to study fungal pathogens. We focus on the available fluorescent labelling techniques and guide our readers through the different relevant applications of fluorescent imaging, from subcellular events to multispecies interactions and diagnostics. As well as cautioning researchers for potential challenges and obstacles, we offer hands-on tips and tricks for efficient experimentation and share our expert-view on future developments and possible improvements.
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Affiliation(s)
- Wouter Van Genechten
- VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001 Leuven-heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Belgium
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200g, 3001 Leuven-Heverlee, Belgium
| | - Patrick Van Dijck
- VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001 Leuven-heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Belgium
| | - Liesbeth Demuyser
- VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001 Leuven-heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Belgium
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14
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Govindarajan A, Gnanasambandam V. Toward Intracellular Bioconjugation Using Transition-Metal-Free Techniques. Bioconjug Chem 2021; 32:1431-1454. [PMID: 34197073 DOI: 10.1021/acs.bioconjchem.1c00173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Bioconjugation is the chemical strategy of covalent modification of biomolecules, using either an external reagent or other biomolecules. Since its inception in the twentieth century, the technique has grown by leaps and bounds, and has a variety of applications in chemical biology. However, it is yet to reach its full potential in the study of biochemical processes in live cells, mainly because the bioconjugation strategies conflict with cellular processes. This has mostly been overcome by using transition metal catalysts, but the presence of metal centers limit them to in vitro use, or to the cell surface. These hurdles can potentially be circumvented by using metal-free strategies. However, the very modifications that are necessary to make such metal-free reactions proceed effectively may impact their biocompatibility. This is because biological processes are easily perturbed and greatly depend on the prevailing inter- and intracellular environment. With this taken into consideration, this review analyzes the applicability of the transition-metal-free strategies reported in this decade to the study of biochemical processes in vivo.
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Affiliation(s)
- Aaditya Govindarajan
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry - 605014, India
| | - Vasuki Gnanasambandam
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry - 605014, India
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15
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Engel AJ, Kithil M, Langhans M, Rauh O, Cartolano M, Van Etten JL, Moroni A, Thiel G. Codon Bias Can Determine Sorting of a Potassium Channel Protein. Cells 2021; 10:cells10051128. [PMID: 34066987 PMCID: PMC8151079 DOI: 10.3390/cells10051128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 11/27/2022] Open
Abstract
Due to the redundancy of the genetic code most amino acids are encoded by multiple synonymous codons. It has been proposed that a biased frequency of synonymous codons can affect the function of proteins by modulating distinct steps in transcription, translation and folding. Here, we use two similar prototype K+ channels as model systems to examine whether codon choice has an impact on protein sorting. By monitoring transient expression of GFP-tagged channels in mammalian cells, we find that one of the two channels is sorted in a codon and cell cycle-dependent manner either to mitochondria or the secretory pathway. The data establish that a gene with either rare or frequent codons serves, together with a cell-state-dependent decoding mechanism, as a secondary code for sorting intracellular membrane proteins.
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Affiliation(s)
- Anja J. Engel
- Membrane Biophysics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany; (A.J.E.); (M.K.); (M.L.); (O.R.); (M.C.)
| | - Marina Kithil
- Membrane Biophysics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany; (A.J.E.); (M.K.); (M.L.); (O.R.); (M.C.)
| | - Markus Langhans
- Membrane Biophysics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany; (A.J.E.); (M.K.); (M.L.); (O.R.); (M.C.)
| | - Oliver Rauh
- Membrane Biophysics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany; (A.J.E.); (M.K.); (M.L.); (O.R.); (M.C.)
| | - Matea Cartolano
- Membrane Biophysics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany; (A.J.E.); (M.K.); (M.L.); (O.R.); (M.C.)
| | - James L. Van Etten
- Nebraska Center for Virology, Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA;
| | - Anna Moroni
- Department of Biosciences, University of Milan, 20133 Milan, Italy;
| | - Gerhard Thiel
- Membrane Biophysics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany; (A.J.E.); (M.K.); (M.L.); (O.R.); (M.C.)
- Correspondence: ; Tel.: +49-61511621940
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16
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Human Somatostatin SST 4 Receptor Transgenic Mice: Construction and Brain Expression Pattern Characterization. Int J Mol Sci 2021; 22:ijms22073758. [PMID: 33916620 PMCID: PMC8038480 DOI: 10.3390/ijms22073758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 12/13/2022] Open
Abstract
Somatostatin receptor subtype 4 (SST4) has been shown to mediate analgesic, antidepressant and anti-inflammatory functions without endocrine actions; therefore, it is proposed to be a novel target for drug development. To overcome the species differences of SST4 receptor expression and function between humans and mice, we generated an SST4 humanized mouse line to serve as a translational animal model for preclinical research. A transposon vector containing the hSSTR4 and reporter gene construct driven by the hSSTR4 regulatory elements were created. The vector was randomly inserted in Sstr4-deficient mice. hSSTR4 expression was detected by bioluminescent in vivo imaging of the luciferase reporter predominantly in the brain. RT-qPCR confirmed the expression of the human gene in the brain and various peripheral tissues consistent with the in vivo imaging. RNAscope in situ hybridization revealed the presence of hSSTR4 transcripts in glutamatergic excitatory neurons in the CA1 and CA2 regions of the hippocampus; in the GABAergic interneurons in the granular layer of the olfactory bulb and in both types of neurons in the primary somatosensory cortex, piriform cortex, prelimbic cortex and amygdala. This novel SST4 humanized mouse line might enable us to investigate the differences of human and mouse SST4 receptor expression and function and assess the effects of SST4 receptor agonist drug candidates.
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Yeong MY, Cheow PS, Abdullah S, Song AAL, Lei-Rossmann J, Tan TK, Yusoff K, Chia SL. Development of a T7 RNA polymerase expressing cell line using lentivirus vectors for the recovery of recombinant Newcastle disease virus. J Virol Methods 2021; 291:114099. [PMID: 33592218 DOI: 10.1016/j.jviromet.2021.114099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/02/2021] [Accepted: 02/08/2021] [Indexed: 11/28/2022]
Abstract
The development of a T7 RNA polymerase (T7 RNAP) expressing cell line i.e. BSR T7/5 cells marks an improvement of reverse genetics for the recovery of recombinant Newcastle disease virus (rNDV). BSR T7/5 is developed by transient transfection of plasmid encoding T7 RNAP gene for rNDV rescue. However, the gene expression decreases gradually over multiple passages and eventually hinders the rescue of rNDV. To address this issue, lentiviral vector was used to develop T7 RNAP-expressing HEK293-TA (HEK293-TA-Lv-T7) and SW620 (SW620-Lv-T7) cell lines, evidenced by the expression of T7 RNAP after subsequent 20 passages. rNDV was rescued successfully using HEK293-TA-Lv-T7 clones (R1D3, R1D8, R5B9) and SW620-Lv-T7 clones (R1C11, R3C5) by reverse transfection, yielding comparable virus rescue efficiency and virus titres to that of BSR T7/5. This study provides new tools for rNDV rescue and insights into cell line development and virology by reverse genetics.
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Affiliation(s)
- Ming Yue Yeong
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia.
| | - Pheik-Sheen Cheow
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia.
| | - Syahril Abdullah
- UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia.
| | - Adelene Ai-Lian Song
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia.
| | - Janet Lei-Rossmann
- Anticancer Viruses and Cancer Vaccines Research Group, Department of Oncology, University of Oxford, OX3 7DQ, Oxford, United Kingdom.
| | - Tiong-Kit Tan
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, Oxford, United Kingdom.
| | - Khatijah Yusoff
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia; UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia; Malaysia Genome Institute, Ministry of Science, Technology and Innovation, Jalan Bangi, 43000 Kajang, Selangor Darul Ehsan, Malaysia.
| | - Suet-Lin Chia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia; UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia.
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18
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Schulke D, Sass JO. Frequent sequence variants of human glycine N-acyltransferase (GLYAT) and inborn errors of metabolism. Biochimie 2021; 183:30-34. [PMID: 33567294 DOI: 10.1016/j.biochi.2021.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 01/30/2021] [Accepted: 02/02/2021] [Indexed: 11/30/2022]
Abstract
Glycine conjugation is an important phase II reaction and represents a central detoxification pathway which is essential for the recycling of free coenzyme A. Only few sequence variants have been reported in the human GLYAT gene and only two studies have overexpressed the human protein in bacterial systems and partially characterized it. This has prompted us to study the wild-type enzyme and two sequence variants not only in the E. coli strain Origami 2(DE3), but also to overexpress GLYAT in HEK293 cells, a human-derived cell line. Following purification of the recombinant proteins from E. coli the wild-type GLYAT protein and sequence variants, p.(Gln61Leu) yielded decreased specific activity than the wild-type enzyme, while specific activity of p.(Asn156Ser) activity of the latter variant was somewhat increased. KM values were similar for the three forms of GLYAT overexpressed in bacteria and for the wild-type enzyme overexpressed in HEK293 cells. Localization studies demonstrated intramitochondrial localization of human wild-type GLYAT, conjugated with eGFP, in the HEK293 cells. As p.(Gln61Leu) does not only impair GLYAT activity in vitro, but is of high prevalence in a Caucasian Afrikaner cohort in South Africa, potential pharmacogenetic implications, warrant further studies of GLYAT.
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Affiliation(s)
- Daniel Schulke
- Research Group Inborn Errors of Metabolism, Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, Rheinbach, Germany
| | - Jörn Oliver Sass
- Research Group Inborn Errors of Metabolism, Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, Rheinbach, Germany; Institute for Functional Gene Analytics (IFGA), Bonn-Rhein-Sieg University of Applied Sciences, Rheinbach, Germany.
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19
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Genome-Wide Identification and Expression Profiling of the PDI Gene Family Reveals Their Probable Involvement in Abiotic Stress Tolerance in Tomato ( Solanum Lycopersicum L.). Genes (Basel) 2020; 12:genes12010023. [PMID: 33375673 PMCID: PMC7824348 DOI: 10.3390/genes12010023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/04/2020] [Accepted: 12/23/2020] [Indexed: 12/18/2022] Open
Abstract
Protein disulfide isomerases (PDI) and PDI-like proteins catalyze the formation and isomerization of protein disulfide bonds in the endoplasmic reticulum and prevent the buildup of misfolded proteins under abiotic stress conditions. In the present study, we conducted the first comprehensive genome-wide exploration of the PDI gene family in tomato (Solanum lycopersicum L.). We identified 19 tomato PDI genes that were unevenly distributed on 8 of the 12 tomato chromosomes, with segmental duplications detected for 3 paralogous gene pairs. Expression profiling of the PDI genes revealed that most of them were differentially expressed across different organs and developmental stages of the fruit. Furthermore, most of the PDI genes were highly induced by heat, salt, and abscisic acid (ABA) treatments, while relatively few of the genes were induced by cold and nutrient and water deficit (NWD) stresses. The predominant expression of SlPDI1-1, SlPDI1-3, SlPDI1-4, SlPDI2-1, SlPDI4-1, and SlPDI5-1 in response to abiotic stress and ABA treatment suggested they play regulatory roles in abiotic stress tolerance in tomato in an ABA-dependent manner. Our results provide new insight into the structure and function of PDI genes and will be helpful for the selection of candidate genes involved in fruit development and abiotic stress tolerance in tomato.
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20
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Lee Y, Kwak JM, Lee JS. Endogenous p21-Dependent Transgene Control for CHO Cell Engineering. ACS Synth Biol 2020; 9:1572-1580. [PMID: 32539343 DOI: 10.1021/acssynbio.9b00526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Numerous engineering efforts have been made in Chinese hamster ovary (CHO) cells for high level production of therapeutic proteins. However, the dynamic regulation of transgene expression is limited in current systems. Here, we investigated the effective regulation of transgene expression in CHO cells via targeted integration-based endogenous gene tagging with engineering target genes. Targeted integration of EGFP-human Bcl-2 into the p21 locus effectively reduced the apoptosis, compared with random populations in which Bcl-2 expression was driven by cytomegalovirus (CMV) promoter. Endogenous p21 and EGFP-human Bcl-2 displayed similar expression dynamics in batch cultures, and the antiapoptotic effect altered the expression pattern of endogenous p21 showing the mutual influences between expression of p21 and Bcl-2. We further demonstrated the inducible transgene expression by adding low concentrations of hydroxyurea. The present engineering strategy will provide a valuable CHO cell engineering tool that can be used to control dynamic transgene expression in accordance with cellular states.
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Affiliation(s)
- Youngsik Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Jin Myeong Kwak
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 16499, Republic of Korea
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 16499, Republic of Korea
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21
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Jin X, Hapsari ND, Lee S, Jo K. DNA binding fluorescent proteins as single-molecule probes. Analyst 2020; 145:4079-4095. [DOI: 10.1039/d0an00218f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA binding fluorescent proteins are useful probes for a broad range of biological applications.
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Affiliation(s)
- Xuelin Jin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
- Chemistry Education Program
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
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22
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Fracasso G, Körner Y, Gonzales DTT, Dora Tang TY. In vitro gene expression and detergent-free reconstitution of active proteorhodopsin in lipid vesicles. Exp Biol Med (Maywood) 2019; 244:314-322. [PMID: 30630374 DOI: 10.1177/1535370218820290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
IMPACT STATEMENT Our results offer the potential for straightforward, additive-free, and molecularly simple routes to building complex bioreactors based on in vitro transcription-translation systems and lipid vesicles.
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Affiliation(s)
- Giorgio Fracasso
- Max-Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Yvonne Körner
- Max-Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | | | - T-Y Dora Tang
- Max-Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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23
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Nightingale DJH, Oliver SG, Lilley KS. Mapping the Saccharomyces cerevisiae Spatial Proteome with High Resolution Using hyperLOPIT. Methods Mol Biol 2019; 2049:165-190. [PMID: 31602611 DOI: 10.1007/978-1-4939-9736-7_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The subcellular localization of proteins is a posttranslational modification of paramount importance. The ability to study subcellular and organelle proteomes improves our understanding of cellular homeostasis and cellular dynamics. In this chapter, we describe a protocol for the unbiased and high-throughput study of protein subcellular localization in the yeast Saccharomyces cerevisiae: hyperplexed localization of organelle proteins by isotope tagging (hyperLOPIT), which involves biochemical fractionation of Saccharomyces cerevisiae and high resolution mass spectrometry-based protein quantitation using TMT 10-plex isobaric tags. This protocol enables the determination of the subcellular localizations of thousands of proteins in parallel in a single experiment and thereby deep sampling and high-resolution mapping of the spatial proteome.
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Affiliation(s)
- Daniel J H Nightingale
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Stephen G Oliver
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK.
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24
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Liu D, Lu J, Li H, Wang J, Pei Y. Characterization of the O-acetylserine(thiol)lyase gene family in Solanum lycopersicum L. PLANT MOLECULAR BIOLOGY 2019; 99:123-134. [PMID: 30535734 DOI: 10.1007/s11103-018-0807-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/03/2018] [Indexed: 05/04/2023]
Abstract
This research demonstrated the conservation and diversification of the functions of the O-acetylserine-(thiol) lyase gene family genes in Solanum lycopersicum L. Cysteine is the first sulfur-containing organic molecule generated by plants and is the precursor of many important biomolecules and defense compounds. Cysteine and its derivatives are also essential in various redox signaling-related processes. O-acetylserine(thiol)lyase (OASTL) proteins catalyze the last step of cysteine biosynthesis. Previously, researches focused mainly on OASTL proteins which were the most abundant or possessed the authentic OASTL activity, whereas few studies have ever given a comprehensive view of the functions of all the OASTL members in one specific species. Here, we characterized 8 genes belonging to the OASTL gene family from tomato genome (SlOAS2 to SlOAS9), including the sequence analyses, subcellular localization, enzymatic activity assays, expression patterns, as well as the interaction property with SATs. Apart from SlOAS3, all the other genes encoded OASTL-like proteins. Tomato OASTLs were differentially expressed during the development of tomato plants, and their encoded proteins had diverse compartmental distributions and functions. SlOAS5 and SlOAS6 catalyzed the biogenesis of cysteine in chloroplasts and in the cytosol, respectively, and this was in consistent with their interaction abilities with SlSATs. SlOAS4 catalyzed the generation of hydrogen sulfide, similar to its Arabidopsis ortholog, DES1. SlOAS2 also functioned as an L-cysteine desulfhydrase, but its expression pattern was very different from that of SlOAS4. Additionally, SlOAS8 might be a β-cyanoalanine synthase in mitochondria, and the S-sulfocysteine synthase activity appeared lost in tomato plants. SlOAS7 exhibited a transactivational ability in yeast; while the subcellular localization of SlOAS9 was in the peroxisome and correlated with the process of leaf senescence, indicating that these two genes might have novel roles.
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Affiliation(s)
- Danmei Liu
- College of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Juanjuan Lu
- College of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Hui Li
- College of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Juanjuan Wang
- Scientific Instrument Center, Shanxi University, Taiyuan, 030006, China
| | - Yanxi Pei
- College of Life Science, Shanxi University, Taiyuan, 030006, China.
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25
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Nguyen VN, Lee SB, Suh MC, An G, Jung KH. OsABCG9 Is an Important ABC Transporter of Cuticular Wax Deposition in Rice. FRONTIERS IN PLANT SCIENCE 2018; 9:960. [PMID: 30131812 PMCID: PMC6091143 DOI: 10.3389/fpls.2018.00960] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/14/2018] [Indexed: 05/18/2023]
Abstract
The importance of the cuticular layer in regulating a plant's water status and providing protection from environmental challenges has been recognized for a long time. The cuticular layer in plants restricts non-stomatal water loss and protects plants against damage from pathogen infection and UV radiation. Much genetic and biochemical research has been done about cutin and wax transportation in Arabidopsis thaliana, but little is known about it in rice. Here, we report that a rice ATP-binding cassette (ABC) transporter, OsABCG9, is essential for normal development during vegetative growth and could play a critical role in the transportation of epicuticular wax in rice. Rice phenotypes with mutated OsABCG9 exhibited growth retardation and sensitivity to low humidity. The total amount of cuticular wax on the leaves of the osabcg9-1 mutant diminished by 53% compared with the wild type, and wax crystals disappeared completely in osabcg9-2 mutant leaves. However, OsABCG9 does not seem to be involved in cutin transportation, even though its ortholog in Arabidopsis, AtABCG11, transports both wax and cutin. Furthermore, the osabcg9-1 mutant had increased leaf chlorophyll leaching and more severe drought susceptibility. This study provides new insights about differences between rice and A. thaliana in wax and cutin transportation associated with the ABCG family during evolution.
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Affiliation(s)
- Van N.T. Nguyen
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Seoul, South Korea
| | - Saet Buyl Lee
- Department of Bioenergy Science and Technology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Mi Chung Suh
- Department of Bioenergy Science and Technology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Gynheung An
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Seoul, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Seoul, South Korea
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26
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Norris JL, Hughes RM. protaTETHER - a method for the incorporation of variable linkers in protein fusions reveals impacts of linker flexibility in a PKAc-GFP fusion protein. FEBS Open Bio 2018; 8:1029-1042. [PMID: 29928581 PMCID: PMC5986021 DOI: 10.1002/2211-5463.12414] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/12/2018] [Accepted: 03/01/2018] [Indexed: 11/11/2022] Open
Abstract
Protein fusions are of fundamental importance in the study of cellular biology and the elucidation of cell signaling pathways, and the importance of linkers for the proper function of protein fusions is well documented in the literature. However, there are few convenient methods available to experimentalists for the systematic implementation of linkers in protein fusions. In this work, we describe a universal approach to the creation and insertion of focused linker libraries into protein fusions. This process, deemed protaTETHER, utilizes reiterative oligomer design, PCR-mediated linker library generation, and restriction enzyme-free cloning methods in a straightforward, three-step cloning process. We utilize a fusion between the catalytic subunit of cAMP-dependent protein kinase A (PKAc) and green fluorescent protein (GFP) for the development of the protaTETHER method, implementing small linker libraries that vary by length, sequence, and predicted secondary structural elements. We analyze the impact of linker length and sequence on the expression, activity, and subcellular localization of the PKAc-GFP fusions, and use these results to select a PKAc-GFP fusion construct with robust expression and enzymatic activity. Based upon the results of both biochemical experiments and molecular modeling, we determine that linker flexibility is more important than linker length for optimal kinase activity and expression.
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Li T, Liu N, Ou X, Zhao X, Qi F, Huang J, Liu D. Visualizing cellulase adsorption and quantitatively determining cellulose accessibility with an updated fungal cellulose-binding module-based fluorescent probe protein. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:105. [PMID: 29657580 PMCID: PMC5890345 DOI: 10.1186/s13068-018-1105-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/02/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Cellulose accessibility to cellulases (CAC) is a direct factor determining the enzymatic digestibility of lignocellulosic cellulose. Improving CAC by pretreatment is a prerequisite step for the efficient release of fermentable sugars from biomass cell wall. However, conventional methods to study the porosimetry of solid materials showed some limitations to be used for investigating CAC. In this work, an updated novel fusion protein comprising a fungal cellulose-binding module (CBM) from Cel7A cellobiohydrolase I (CBH I) of Trichoderma reesei QM6 and a di-green fluorescent protein (GFP2) was constructed for quantitative determination of CAC. RESULTS The obtained probe protein had similar molecular size (e.g., weight) with that of Cel7A and could give detectable signal for quantitative analysis. Several construction strategies were compared with regard to the site of His-tag and order of CBM and GFP2 modules in the protein sequence, in order to achieve good expression quantity and usability of the probe protein. His6-CBM-GFP2 has been identified as the best probe protein for investigating the effects of structural features of cellulosic substrates on cellulose accessibility. Substrate samples with different contents of xylan, lignin, and degree of substitution of cellulose -OH by formyl group were obtained, respectively, by mild H2SO4 pre-hydrolysis, NaClO2 selective delignification, and treatment of filter paper cellulose with concentrated formic acid. The determined CAC was in a wide range of 0.6-20.4 m2/g depending on the contents of hemicelluloses, lignin, and formyl group as well as cellulose degree of crystallization. CONCLUSIONS The obtained fusion probe protein could be used as a versatile tool to quantitatively investigate the impacts of biomass structural features on CAC and hydrolyzability of cellulose substrates, as well as nonproductive adsorption of cellulase enzymes on lignin.
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Affiliation(s)
- Tian Li
- Key Laboratory for Industrial Biocatalysis, Ministry of Education of China, Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Nan Liu
- Key Laboratory for Industrial Biocatalysis, Ministry of Education of China, Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian China
| | - Xianjin Ou
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xuebing Zhao
- Key Laboratory for Industrial Biocatalysis, Ministry of Education of China, Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Feng Qi
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian China
| | - Jianzhong Huang
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian China
| | - Dehua Liu
- Key Laboratory for Industrial Biocatalysis, Ministry of Education of China, Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
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Abstract
SUPPRESSOR OF PHYB-4#5DOMINANT (sob5-D) was previously identified as a suppressor of the phyB-4 long-hypocotyl phenotype in Arabidopsis thaliana. Overexpression of SOB5 conferred dwarf phenotypes similar to those observed in plants containing elevated levels of cytokinin (CK) nucleotides and nucleosides. Two SOB-FIVE- LIKE (SOFL) proteins, AtSOFL1 and AtSOFL2, which are more similar at the protein level to each other than they are to SOB5, conferred similar phenotypes to the sob5-D mutant when overexpressed. We used protein sequences of founding SOFL gene family members to perform database searches and identified a total of 289 SOFL homologs in genomes of 89 angiosperm species. Phylogenetic analysis results implied that the SOFL gene family emerged during the expansion of angiosperms and later evolved into four distinct clades. Among the newly identified gene family members are four previously unreported Arabidopsis SOFLs. Multiple sequence alignment of the 289 SOFL protein sequences revealed two highly conserved domains; SOFL-A and SOFL-B. We used overexpression and site-directed mutagenesis studies to demonstrate that SOFL domains are necessary for SOB5 and AtSOFL1’s overexpression phenotypes. Examination of the subcellular localization patterns of founding Arabidopsis thaliana SOFLs suggested they may be localized in the cytoplasm and/or the nucleus. Overall, we report that SOFLs are a plant-specific gene family characterized by two conserved domains that are important for function.
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Khatun K, Nath UK, Robin AHK, Park JI, Lee DJ, Kim MB, Kim CK, Lim KB, Nou IS, Chung MY. Genome-wide analysis and expression profiling of zinc finger homeodomain (ZHD) family genes reveal likely roles in organ development and stress responses in tomato. BMC Genomics 2017; 18:695. [PMID: 28874115 PMCID: PMC5585987 DOI: 10.1186/s12864-017-4082-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/21/2017] [Indexed: 01/23/2023] Open
Abstract
Background Zinc finger homeodomain proteins (ZHD) constitute a plant-specific transcription factor family with a conserved DNA binding homeodomain and a zinc finger motif. Members of the ZHD protein family play important roles in plant growth, development, and stress responses. Genome-wide characterization of ZHD genes has been carried out in several model plants, including Arabidopsis thaliana and Oryza sativa, but not yet in tomato (Solanum lycopersicum). Results In this study, we performed the first comprehensive genome-wide characterization and expression profiling of the ZHD gene family in tomato (Solanum lycopersicum). We identified 22 SlZHD genes and classified them into six subfamilies based on phylogeny. The SlZHD genes were generally conserved in each subfamily, with minor variations in gene structure and motif distribution. The 22 SlZHD genes were distributed on six of the 12 tomato chromosomes, with segmental duplication detected in four genes. Analysis of Ka/Ks ratios revealed that the duplicated genes are under negative or purifying selection. Comprehensive expression analysis revealed that the SlZHD genes are widely expressed in various tissues, with most genes preferentially expressed in flower buds compared to other tissues. Moreover, many of the genes are responsive to abiotic stress and phytohormone treatment. Conclusion Systematic analysis revealed structural diversity among tomato ZHD proteins, which indicates the possibility for diverse roles of SlZHD genes in different developmental stages as well as in response to abiotic stresses. Our expression analysis of SlZHD genes in various tissues/organs and under various abiotic stress and phytohormone treatments sheds light on their functional divergence. Our findings represent a valuable resource for further analysis to explore the biological functions of tomato ZHD genes. Electronic supplementary material The online version of this article (10.1186/s12864-017-4082-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Khadiza Khatun
- Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea
| | - Arif Hasan Khan Robin
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea
| | - Do-Jin Lee
- Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea.,Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea
| | - Min-Bae Kim
- Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea.,Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea
| | - Chang Kil Kim
- Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, South Korea
| | - Ki-Byung Lim
- Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, South Korea
| | - Ill Sup Nou
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea
| | - Mi-Young Chung
- Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea. .,Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea.
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30
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Significant inhibition of Tembusu virus envelope and NS5 gene using an adenovirus-mediated short hairpin RNA delivery system. INFECTION GENETICS AND EVOLUTION 2017; 54:387-396. [PMID: 28780191 DOI: 10.1016/j.meegid.2017.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/28/2017] [Accepted: 08/01/2017] [Indexed: 12/17/2022]
Abstract
Tembusu virus (TMUV) is a mosquito-borne flavivirus, which was first isolated in the tropics during the 1970s. Recently, a disease characterized by ovarian haemorrhage and neurological symptoms was observed in ducks in China, which threatens poultry production. However, there is no suitable vaccination strategy or effective antiviral drugs to combat TMUV infections. Consequently, there is an urgent need to develop a new anti-TMUV therapy. In this study, we report an efficient short hairpin RNA (shRNA) delivery strategy for the inhibition of TMUV production using an adenovirus vector system. Using specifically designed shRNAs based on the E and NS5 protein genes of TMUV, the vector-expressed viral genes, TMUV RNA replication and infectious virus production were downregulated at different levels in Vero cells, where the shRNA (NS52) was highly effective in inhibiting TMUV. Using the human adenovirus type 5 shRNA delivery system, the recombinant adenovirus (rAd-NS52) inhibited TMUV multiplication with high efficiency. Furthermore, the significant dose-dependent inhibition of viral RNA copies induced by rAd-NS52 was found in TMUV-infected cells, which could last for at least 96h post infection. Our results indicated that the adenovirus-mediated delivery of shRNAs could play an active role in future TMUV antiviral therapeutics.
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Kostrouchová M, Kostrouch D, Chughtai AA, Kaššák F, Novotný JP, Kostrouchová V, Benda A, Krause MW, Saudek V, Kostrouchová M, Kostrouch Z. The nematode homologue of Mediator complex subunit 28, F28F8.5, is a critical regulator of C. elegans development. PeerJ 2017; 5:e3390. [PMID: 28603670 PMCID: PMC5464003 DOI: 10.7717/peerj.3390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 05/08/2017] [Indexed: 11/20/2022] Open
Abstract
The evolutionarily conserved Mediator complex is a critical player in regulating transcription. Comprised of approximately two dozen proteins, the Mediator integrates diverse regulatory signals through direct protein-protein interactions that, in turn, modulate the influence of Mediator on RNA Polymerase II activity. One Mediator subunit, MED28, is known to interact with cytoplasmic structural proteins, providing a potential direct link between cytoplasmic dynamics and the control of gene transcription. Although identified in many animals and plants, MED28 is not present in yeast; no bona fide MED28 has been described previously in Caenorhabditis elegans. Here, we identify bioinformatically F28F8.5, an uncharacterized predicted protein, as the nematode homologue of MED28. As in other Metazoa, F28F8.5 has dual nuclear and cytoplasmic localization and plays critical roles in the regulation of development. F28F8.5 is a vital gene and its null mutants have severely malformed gonads and do not reproduce. F28F8.5 interacts on the protein level with the Mediator subunits MDT-6 and MDT-30. Our results indicate that F28F8.5 is an orthologue of MED28 and suggest that the potential to link cytoplasmic and nuclear events is conserved between MED28 vertebrate and nematode orthologues.
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Affiliation(s)
- Markéta Kostrouchová
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Department of Pathology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - David Kostrouch
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ahmed A Chughtai
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Filip Kaššák
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan P Novotný
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Aleš Benda
- Imaging Methods Core Facility, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michael W Krause
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Vladimír Saudek
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Marta Kostrouchová
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Zdeněk Kostrouch
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
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32
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Scaglione A, Montemiglio LC, Parisi G, Asteriti IA, Bruni R, Cerutti G, Testi C, Savino C, Mancia F, Lavia P, Vallone B. Subcellular localization of the five members of the human steroid 5α-reductase family. BIOCHIMIE OPEN 2017; 4:99-106. [PMID: 29082129 PMCID: PMC5656259 DOI: 10.1016/j.biopen.2017.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In humans the steroid 5α-reductase (SRD5A) family comprises five integral membrane enzymes that carry out reduction of a double bond in lipidic substrates: Δ4-3-keto steroids, polyprenol and trans-enoyl CoA. The best-characterized reaction is the conversion of testosterone into the more potent dihydrotestosterone carried out by SRD5A1-2. Some controversy exists on their possible nuclear or endoplasmic reticulum localization. We report the cloning and transient expression in HeLa cells of the five members of the human steroid 5α-reductase family as both N- and C-terminus green fluorescent protein tagged protein constructs. Following the intrinsic fluorescence of the tag, we have determined that the subcellular localization of these enzymes is in the endoplasmic reticulum, upon expression in HeLa cells. The presence of the tag at either end of the polypeptide chain can affect protein expression and, in the case of trans enoyl-CoA reductase, it induces the formation of protein aggregates. All members of human testosterone 5α-reductase family were expressed in HeLa cells. Subcellular localization of SRD5A proteins in the endoplasmic reticulum is reported. The effect of GFP tagging at N- or C-term on SRD5A proteins expression was assessed. The TECRL gene is expressed for the first time and its product localizes in the ER.
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Affiliation(s)
- Antonella Scaglione
- Dept. of Biochemical Sciences, Sapienza University of Rome, P.le A.Moro 5, 00185, Rome, Italy
| | - Linda Celeste Montemiglio
- Dept. of Biochemical Sciences, Sapienza University of Rome, P.le A.Moro 5, 00185, Rome, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti Dept. of Biochemical Sciences, Sapienza University of Rome
| | - Giacomo Parisi
- Dept. of Biochemical Sciences, Sapienza University of Rome, P.le A.Moro 5, 00185, Rome, Italy
| | | | - Renato Bruni
- New York Consortium on Membrane Protein Structure, New York, NY 10027, USA
| | - Gabriele Cerutti
- Dept. of Biochemical Sciences, Sapienza University of Rome, P.le A.Moro 5, 00185, Rome, Italy
| | - Claudia Testi
- Center for Life Nano Science@Sapienza, IIT, V.le Regina Elena 291, Rome I-00185, Italy
| | | | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | | | - Beatrice Vallone
- Dept. of Biochemical Sciences, Sapienza University of Rome, P.le A.Moro 5, 00185, Rome, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti Dept. of Biochemical Sciences, Sapienza University of Rome.,Schaefer Research Scholar at Columbia University and Fellow of the Italian Academy for Advanced Studies in America at Columbia University
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Chen N, Yu ZH, Xiao XG. Cytosolic and Nuclear Co-localization of Betalain Biosynthetic Enzymes in Tobacco Suggests that Betalains Are Synthesized in the Cytoplasm and/or Nucleus of Betalainic Plant Cells. FRONTIERS IN PLANT SCIENCE 2017; 8:831. [PMID: 28572813 PMCID: PMC5435750 DOI: 10.3389/fpls.2017.00831] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 05/03/2017] [Indexed: 05/02/2023]
Abstract
Betalains replace anthocyanins as color pigments in most families of Caryophyllales. Unlike anthocyanins, betalains are derived from tyrosine via three enzymatic steps: hydroxylation of L-tyrosine to L-3,4-dihydroxyphenylalanine (L-DOPA; step 1), and conversion of L-DOPA to betalamic acid (step 2), and to cyclo-DOPA (cDOPA; step 3). The principal enzymes responsible for these reactions have been elucidated at the molecular level, but their subcellular localizations have not been explored; hence, the intracellular compartments wherein betalains are biosynthesized remain unknown. Here, we report on the subcellular localization of these principal enzymes. Bioinformatic predictors and N- and C-terminal GFP tagging in transgenic tobacco, showed that Beta vulgaris CYP76AD1 which mediates both steps 1 and 3, DODA1 that catalyzes step 2, and CYP76AD6 which also mediates step 1, were similarly localized to the cytoplasm and nucleus (although the P450s were also weakly present in the endoplasmic reticulum). These two compartments were also the principal locations of Mirabilis jalapa cDOPA5GT. The cytoplasmic and nuclear co-localization of these key enzymes in tobacco suggests that betalains are biosynthesized in the cytoplasm and/or nucleus of betalain-containing plant cells. Elucidation of the subcellular compartmentation of betalain biosynthesis will facilitate the bioengineering of the betalain biosynthetic pathway in non-betalain-containing plants.
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34
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Debard S, Bader G, De Craene JO, Enkler L, Bär S, Laporte D, Hammann P, Myslinski E, Senger B, Friant S, Becker HD. Nonconventional localizations of cytosolic aminoacyl-tRNA synthetases in yeast and human cells. Methods 2017; 113:91-104. [DOI: 10.1016/j.ymeth.2016.09.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 09/27/2016] [Accepted: 09/30/2016] [Indexed: 11/26/2022] Open
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35
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Chen N, Teng XL, Xiao XG. Subcellular Localization of a Plant Catalase-Phenol Oxidase, AcCATPO, from Amaranthus and Identification of a Non-canonical Peroxisome Targeting Signal. FRONTIERS IN PLANT SCIENCE 2017; 8:1345. [PMID: 28824680 PMCID: PMC5539789 DOI: 10.3389/fpls.2017.01345] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/18/2017] [Indexed: 05/03/2023]
Abstract
AcCATPO is a plant catalase-phenol oxidase recently identified from red amaranth. Its physiological function remains unexplored. As the starting step of functional analysis, here we report its subcellular localization and a non-canonical targeting signal. Commonly used bioinformatics programs predicted a peroxisomal localization for AcCATPO, but failed in identification of canonical peroxisomal targeting signals (PTS). The C-terminal GFP tagging led the fusion protein AcCATPO-GFP to the cytosol and the nucleus, but N-terminal tagging directed the GFP-AcCATPO to peroxisomes and nuclei, in transgenic tobacco. Deleting the tripeptide (PTM) at the extreme C-terminus almost ruled out the peroxisomal localization of GFP-AcCATPOΔ3, and removing the C-terminal decapeptide completely excluded peroxisomes as the residence of GFP-AcCATPOΔ10. Furthermore, this decapeptide as a targeting signal could import GFP-10aa to the peroxisome exclusively. Taken together, these results demonstrate that AcCATPO is localized to the peroxisome and the nucleus, and its peroxisomal localization is attributed to a non-canonical PTS1, the C-terminal decapeptide which contains an internal SRL motif and a conserved tripeptide P-S/T-I/M at the extreme of C-terminus. This work may further the study as to the physiological function of AcCATPO, especially clarify its involvement in betalain biosynthesis, and provide a clue to elucidate more non-canonic PTS.
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36
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Waaijers S, Muñoz J, Berends C, Ramalho JJ, Goerdayal SS, Low TY, Zoumaro-Djayoon AD, Hoffmann M, Koorman T, Tas RP, Harterink M, Seelk S, Kerver J, Hoogenraad CC, Bossinger O, Tursun B, van den Heuvel S, Heck AJR, Boxem M. A tissue-specific protein purification approach in Caenorhabditis elegans identifies novel interaction partners of DLG-1/Discs large. BMC Biol 2016; 14:66. [PMID: 27506200 PMCID: PMC4977824 DOI: 10.1186/s12915-016-0286-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/19/2016] [Indexed: 01/06/2023] Open
Abstract
Background Affinity purification followed by mass spectrometry (AP/MS) is a widely used approach to identify protein interactions and complexes. In multicellular organisms, the accurate identification of protein complexes by AP/MS is complicated by the potential heterogeneity of complexes in different tissues. Here, we present an in vivo biotinylation-based approach for the tissue-specific purification of protein complexes from Caenorhabditis elegans. Tissue-specific biotinylation is achieved by the expression in select tissues of the bacterial biotin ligase BirA, which biotinylates proteins tagged with the Avi peptide. Results We generated N- and C-terminal tags combining GFP with the Avi peptide sequence, as well as four BirA driver lines expressing BirA ubiquitously and specifically in the seam and hyp7 epidermal cells, intestine, or neurons. We validated the ability of our approach to identify bona fide protein interactions by identifying the known LGL-1 interaction partners PAR-6 and PKC-3. Purification of the Discs large protein DLG-1 identified several candidate interaction partners, including the AAA-type ATPase ATAD-3 and the uncharacterized protein MAPH-1.1. We have identified the domains that mediate the DLG-1/ATAD-3 interaction, and show that this interaction contributes to C. elegans development. MAPH-1.1 co-purified specifically with DLG-1 purified from neurons, and shared limited homology with the microtubule-associated protein MAP1A, a known neuronal interaction partner of mammalian DLG4/PSD95. A CRISPR/Cas9-engineered GFP::MAPH-1.1 fusion was broadly expressed and co-localized with microtubules. Conclusions The method we present here is able to purify protein complexes from specific tissues. We uncovered a series of DLG-1 interactors, and conclude that ATAD-3 is a biologically relevant interaction partner of DLG-1. Finally, we conclude that MAPH-1.1 is a microtubule-associated protein of the MAP1 family and a candidate neuron-specific interaction partner of DLG-1. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0286-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Selma Waaijers
- Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Present address: Department of Physiology, Radboud University Medical Center, Geert Grooteplein 26, 6525 GA, Nijmegen, The Netherlands
| | - Javier Muñoz
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Present address: Proteomics Unit, Spanish National Cancer Research Centre (CNIO), ProteoRed-ISCIII, 28029, Madrid, Spain
| | - Christian Berends
- Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - João J Ramalho
- Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Soenita S Goerdayal
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Teck Y Low
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Adja D Zoumaro-Djayoon
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Michael Hoffmann
- Institut für Wissenschaftliche Medizin, D-40591, Düsseldorf, Germany
| | - Thijs Koorman
- Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Present address: Center for Cancer Research and Department of Pathology, Massachusetts General Hospital and Harvard Medical School Department of Pathology, 149 13th Street, 02129, Charlestown, MA, USA
| | - Roderick P Tas
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Martin Harterink
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Stefanie Seelk
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 10, Berlin, 13125, Germany
| | - Jana Kerver
- Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Casper C Hoogenraad
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Olaf Bossinger
- Molecular Cell Biology, Anatomy I, University of Cologne, D-50937, Cologne, Germany
| | - Baris Tursun
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 10, Berlin, 13125, Germany.
| | - Sander van den Heuvel
- Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Mike Boxem
- Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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Vandemoortele G, Staes A, Gonnelli G, Samyn N, De Sutter D, Vandermarliere E, Timmerman E, Gevaert K, Martens L, Eyckerman S. An extra dimension in protein tagging by quantifying universal proteotypic peptides using targeted proteomics. Sci Rep 2016; 6:27220. [PMID: 27264994 PMCID: PMC4893672 DOI: 10.1038/srep27220] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 05/11/2016] [Indexed: 11/16/2022] Open
Abstract
The use of protein tagging to facilitate detailed characterization of target proteins has not only revolutionized cell biology, but also enabled biochemical analysis through efficient recovery of the protein complexes wherein the tagged proteins reside. The endogenous use of these tags for detailed protein characterization is widespread in lower organisms that allow for efficient homologous recombination. With the recent advances in genome engineering, tagging of endogenous proteins is now within reach for most experimental systems, including mammalian cell lines cultures. In this work, we describe the selection of peptides with ideal mass spectrometry characteristics for use in quantification of tagged proteins using targeted proteomics. We mined the proteome of the hyperthermophile Pyrococcus furiosus to obtain two peptides that are unique in the proteomes of all known model organisms (proteotypic) and allow sensitive quantification of target proteins in a complex background. By combining these 'Proteotypic peptides for Quantification by SRM' (PQS peptides) with epitope tags, we demonstrate their use in co-immunoprecipitation experiments upon transfection of protein pairs, or after introduction of these tags in the endogenous proteins through genome engineering. Endogenous protein tagging for absolute quantification provides a powerful extra dimension to protein analysis, allowing the detailed characterization of endogenous proteins.
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Affiliation(s)
- Giel Vandemoortele
- VIB Medical Biotechnology Center, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - An Staes
- VIB Medical Biotechnology Center, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Giulia Gonnelli
- VIB Medical Biotechnology Center, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Noortje Samyn
- VIB Medical Biotechnology Center, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Delphine De Sutter
- VIB Medical Biotechnology Center, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Elien Vandermarliere
- VIB Medical Biotechnology Center, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Evy Timmerman
- VIB Medical Biotechnology Center, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Kris Gevaert
- VIB Medical Biotechnology Center, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Lennart Martens
- VIB Medical Biotechnology Center, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Sven Eyckerman
- VIB Medical Biotechnology Center, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
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Guichet PO, Guelfi S, Ripoll C, Teigell M, Sabourin JC, Bauchet L, Rigau V, Rothhut B, Hugnot JP. Asymmetric Distribution of GFAP in Glioma Multipotent Cells. PLoS One 2016; 11:e0151274. [PMID: 26953813 PMCID: PMC4783030 DOI: 10.1371/journal.pone.0151274] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 02/25/2016] [Indexed: 11/22/2022] Open
Abstract
Asymmetric division (AD) is a fundamental mechanism whereby unequal inheritance of various cellular compounds during mitosis generates unequal fate in the two daughter cells. Unequal repartitions of transcription factors, receptors as well as mRNA have been abundantly described in AD. In contrast, the involvement of intermediate filaments in this process is still largely unknown. AD occurs in stem cells during development but was also recently observed in cancer stem cells. Here, we demonstrate the asymmetric distribution of the main astrocytic intermediate filament, namely the glial fibrillary acid protein (GFAP), in mitotic glioma multipotent cells isolated from glioblastoma (GBM), the most frequent type of brain tumor. Unequal mitotic repartition of GFAP was also observed in mice non-tumoral neural stem cells indicating that this process occurs across species and is not restricted to cancerous cells. Immunofluorescence and videomicroscopy were used to capture these rare and transient events. Considering the role of intermediate filaments in cytoplasm organization and cell signaling, we propose that asymmetric distribution of GFAP could possibly participate in the regulation of normal and cancerous neural stem cell fate.
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Affiliation(s)
- Pierre-Olivier Guichet
- INSERM U1051, Institut des Neurosciences de Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34091 Montpellier Cedex 05, France
| | - Sophie Guelfi
- INSERM U1051, Institut des Neurosciences de Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34091 Montpellier Cedex 05, France
| | - Chantal Ripoll
- INSERM U1051, Institut des Neurosciences de Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34091 Montpellier Cedex 05, France
| | - Marisa Teigell
- INSERM U1051, Institut des Neurosciences de Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34091 Montpellier Cedex 05, France
| | - Jean-Charles Sabourin
- INSERM U1051, Institut des Neurosciences de Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34091 Montpellier Cedex 05, France
| | - Luc Bauchet
- CHU Montpellier, Hopital Gui de Chaulliac, 80, avenue Augustin Fliche, 34295 Montpellier, France
| | - Valérie Rigau
- CHU Montpellier, Hopital Gui de Chaulliac, 80, avenue Augustin Fliche, 34295 Montpellier, France
| | - Bernard Rothhut
- INSERM U1051, Institut des Neurosciences de Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34091 Montpellier Cedex 05, France
| | - Jean-Philippe Hugnot
- INSERM U1051, Institut des Neurosciences de Montpellier, Hôpital St Eloi, 80 avenue Augustin Fliche, 34091 Montpellier Cedex 05, France
- Université Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
- * E-mail: ;
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Zhai H, Ning W, Wu H, Zhang X, Lü S, Xia Z. DNA-binding protein phosphatase AtDBP1 acts as a promoter of flowering in Arabidopsis. PLANTA 2016; 243:623-33. [PMID: 26586176 DOI: 10.1007/s00425-015-2433-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 11/11/2015] [Indexed: 05/13/2023]
Abstract
We provide evidence that AtDBP1 promotes flowering by regulating the transcript levels of several important integrators and floral meristem identity genes, including FLC, CO, SOC1, LFY, FT and FD. DNA-binding protein phosphatases (DBP) which exhibit both sequence specific DNA-binding and protein phosphatase 2C activities are important regulators that are involved in both the transcriptional and post-translational regulations. DBP factors are known to mediate susceptibility to potyviruses; however, whether they are involved in other processes is still unclear. In this study, under both long day (LD) and short day conditions, AtDBP1 overexpressing plants displayed early flowering, while the knock out mutants, atdbp1, exhibited a delay in flowering relative to the wild-type plants; both the overexpressing lines and atdbp1 mutants remained photoperiodic sensitive, indicating that AtDBP1 was involved in the autonomous pathway. AtDBP1 does not respond to vernalization at transcript level, and both AtDBP1 overexpressing plants and atdbp1 mutants remain responsive to vernalization, indicating that AtDBP1 may not be directly involved in vernalization. Real-time PCR analysis showed that AtDBP1 can suppress FLOWERING LOCUC C (FLC) expression, a key integrator of the autonomous and vernalization pathways, and enhance the expression levels of CONSTANS and FLOWERING LOCUC T, key regulators of the LD pathway. Furthermore, expression of floral meristem identity genes including SUPPRESSOR OF OVEREXPRESSION OF CO 1, LEAFY and FD was also promoted in AtDBP1 overexpressing plants. AtDBP1 transcription can be detected in root, leaf, stem, flower and silique. AtDBP1-GFP and YFP-AtDBP1 fusion protein were localized in the cytosol and nucleus. Our results provide the evidence demonstrating the effective role of AtDBP1 for flowering time regulation and report a novel function of DBP factors in planta besides in plant defense.
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Affiliation(s)
- Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Wenfeng Ning
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Hongyan Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Xingzheng Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Shixiang Lü
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
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40
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Vectors for Genetically-Encoded Tags for Electron Microscopy Contrast in Drosophila. Biol Proced Online 2016; 18:5. [PMID: 26839516 PMCID: PMC4736618 DOI: 10.1186/s12575-016-0034-1] [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: 07/07/2015] [Accepted: 01/25/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND One of the most notable recent advances in electron microscopy (EM) was the development of genetically-encoded EM tags, including the fluorescent flavoprotein Mini-SOG (Mini-Singlet Oxygen Generator). Mini-SOG generates good EM contrast, thus providing a viable alternative to technically-demanding methods such as immuno-electron microcopy (immuno-EM). Based on the Mini-SOG technology, in this paper, we describe the construction, validation and optimization of a series of vectors which allow expression of Mini-SOG in the Drosophila melanogaster genetic model system. FINDINGS We constructed a Mini-SOG tag that has been codon-optimized for expression in Drosophila (DMS tag) using PCR-mediated gene assembly. The photo-oxidation reaction triggered by DMS was then tested using these vectors in Drosophila cell lines. DMS tag did not affect the subcellular localization of the proteins we tested. More importantly, we demonstrated the utility of the DMS tag for EM in Drosophila by showing that it can produce robust photo-oxidation reactions in the presence of blue light and the substrate DAB; the resultant electron micrographs contain electron-dense regions corresponding to the protein of interest. The vectors we generated allow protein tagging at both termini, for constitutive and inducible protein expression, as well as the generation of transgenic lines by P-element transformation. CONCLUSIONS We demonstrated the feasibility of Mini-SOG tagging in Drosophila. The constructed vectors will no doubt be a useful molecular tool for genetic tagging to facilitate high-resolution localization of proteins in Drosophila by electron microscopy.
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Popova AA, Schillo SM, Demir K, Ueda E, Nesterov-Mueller A, Levkin PA. Droplet-Array (DA) Sandwich Chip: A Versatile Platform for High-Throughput Cell Screening Based on Superhydrophobic-Superhydrophilic Micropatterning. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:5217-5222. [PMID: 26255809 DOI: 10.1002/adma.201502115] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 06/30/2015] [Indexed: 06/04/2023]
Abstract
A droplet-array (DA) sandwich chip is a miniaturized platform for cell-based high-throughput screening. It is based on sandwiching of a glass slide with a preprinted library and a superhydrophobic-superhydrophilic pattern, which consists of thousands of simultaneously formed microdroplets containing cells. The DA sandwich chip allows for one-step cell seeding, simultaneous initiation of screening, and 1000 times less reagent consumption than a regular 96-well plate.
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Affiliation(s)
- Anna A Popova
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Sebastian M Schillo
- Karlsruhe Institute of Technology, Institute of Microstructure Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Konstantin Demir
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Erica Ueda
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - A Nesterov-Mueller
- Karlsruhe Institute of Technology, Institute of Microstructure Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Pavel A Levkin
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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42
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Carballeda JM, Maroniche G, Lucero MS, Richetta M, Gómez E, Chimeno Zoth S, Berinstein A. Infectious Bursal Disease Virus non-structural protein VP5 is not a transmembrane protein. Virology 2015; 483:312-7. [DOI: 10.1016/j.virol.2015.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 01/28/2015] [Accepted: 05/01/2015] [Indexed: 10/23/2022]
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Xiao S, Chen YC, Betenbaugh MJ, Martin SE, Shiloach J. MiRNA mimic screen for improved expression of functional neurotensin receptor from HEK293 cells. Biotechnol Bioeng 2015; 112:1632-43. [PMID: 25676429 DOI: 10.1002/bit.25567] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/23/2015] [Accepted: 02/05/2015] [Indexed: 01/17/2023]
Abstract
Obtaining adequate quantities of functional mammalian membrane proteins has been a bottleneck in their structural and functional studies because the expression of these proteins from mammalian cells is relatively low. To explore the possibility of enhancing expression of these proteins using miRNA, a stable T-REx-293 cell line expressing the neurotensin receptor type 1 (NTSR1), a hard-to-express G protein-coupled receptor (GPCR), was constructed. The cell line was then subjected to human miRNA mimic library screening. In parallel, an HEK293 cell line expressing luciferase was also screened with the same human miRNA mimic library. Five microRNA mimics: hsa-miR-22-5p, hsa-miR-18a-5p, hsa-miR-22-3p, hsa-miR-429, and hsa-miR-2110were identified from both screens. They led to 48% increase in the expression of functional NTSR1 and to 239% increase of luciferase expression. These miRNAs were also effective in enhancing the expression of secretedglypican-3 hFc-fusion protein from HEK293 cells.The results indicate that these molecules may have a wide role in enhancing the production of proteins with biomedical interest.
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Affiliation(s)
- Su Xiao
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892.,Departments of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Yu-Chi Chen
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of health, Rockville, Maryland, 20850
| | - Michael J Betenbaugh
- Departments of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Scott E Martin
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of health, Rockville, Maryland, 20850.
| | - Joseph Shiloach
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892.
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LaCava J, Molloy KR, Taylor MS, Domanski M, Chait BT, Rout MP. Affinity proteomics to study endogenous protein complexes: pointers, pitfalls, preferences and perspectives. Biotechniques 2015; 58:103-19. [PMID: 25757543 PMCID: PMC4465938 DOI: 10.2144/000114262] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 02/17/2015] [Indexed: 01/13/2023] Open
Abstract
Dissecting and studying cellular systems requires the ability to specifically isolate distinct proteins along with the co-assembled constituents of their associated complexes. Affinity capture techniques leverage high affinity, high specificity reagents to target and capture proteins of interest along with specifically associated proteins from cell extracts. Affinity capture coupled to mass spectrometry (MS)-based proteomic analyses has enabled the isolation and characterization of a wide range of endogenous protein complexes. Here, we outline effective procedures for the affinity capture of protein complexes, highlighting best practices and common pitfalls.
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Affiliation(s)
- John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
- Institute for Systems Genetics, New York University School of Medicine, New York, NY
| | - Kelly R. Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Martin S. Taylor
- High Throughput Biology Center and Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michal Domanski
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
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45
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Ma Z, Du L, Li M. Toward fluorescent probes for G-protein-coupled receptors (GPCRs). J Med Chem 2014; 57:8187-203. [PMID: 24983484 DOI: 10.1021/jm401823z] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
G-protein-coupled receptors (GPCRs), a superfamily of cell-surface receptors that are the targets of about 40% of prescription drugs on the market, can sense numerous critical extracellular signals. Recent breakthroughs in structural biology, especially in holo-form X-ray crystal structures, have contributed to our understanding of GPCR signaling. However, actions of GPCRs at the cellular and molecular level, interactions between GPCRs, and the role of protein dynamics in receptor activities still remain controversial. To overcome these dilemmas, fluorescent probes of GPCRs have been employed, which have advantages of in vivo safety and real-time monitoring. Various probes that depend on specific mechanisms and/or technologies have been used to study GPCRs. The present review focuses on surveying the design and applications of fluorescent probes for GPCRs that are derived from small molecules or using protein-labeling techniques, as well as discussing some design strategies for new probes.
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Affiliation(s)
- Zhao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Shandong University , Jinan, Shandong 250012, China
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46
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Rossi M, Genre A, Turina M. Genetic dissection of a putative nucleolar localization signal in the coat protein of ourmia melon virus. Arch Virol 2014; 159:1187-92. [PMID: 24248258 DOI: 10.1007/s00705-013-1923-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 11/07/2013] [Indexed: 10/26/2022]
Abstract
Ourmiaviruses became the object of recent attention for their unusual taxonomic placements among plant viruses. The ourmia melon virus (OuMV) RNA3 encodes a 22-kDa coat protein (CP). Besides its role in virion formation, the OuMV CP facilitates systemic virus spread. In Nicotiana benthamiana, an eGFP-CP fusion protein was localized in the nucleus and preferentially in the nucleolus. By bioinformatics analysis, we identified an arginine- and lysine-rich region at the N-terminus of the CP. Here, we demonstrate by deletion and alanine scanning mutagenesis that this region in the CP is responsible for its preferential accumulation in the nucleolus of host cells.
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Affiliation(s)
- M Rossi
- Sez. di Torino, CNR, Istituto di Virologia Vegetale, Strada delle Cacce 73, 10135, Torino, Italy
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47
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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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48
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Zhu M, Ni W, Dong Y, Wu ZY. EGFP tags affect cellular localization of ATP7B mutants. CNS Neurosci Ther 2013; 19:346-51. [PMID: 23607698 DOI: 10.1111/cns.12091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/03/2013] [Accepted: 02/04/2013] [Indexed: 01/22/2023] Open
Abstract
AIMS Wilson's disease is an autosomal recessive disorder of copper metabolism due to mutations within ATP7B gene. Clinical investigations indicate that ATP7B truncations are associated with an early age of onset when compared to its missense mutations. In vitro studies show that mislocalization of ATP7B mutants is involved in disease-causing mechanisms. Enhanced green fluorescent protein (EGFP) tags are commonly used in in vitro studies of cellular localization of ATP7B mutants. However, there is still much unknown about cellular localization of ATP7B truncations. METHODS Here, we subcloned full-length human wild-type, a missense mutation (T935M), and four truncating mutants (E332X, Q511X, Q547X, Q819X) of ATP7B into pEGFP-C1, pEGFP-N2 and pCMV-myc, and transfected Chinese hamster ovary (CHO) and SH-SY5Y cells with them, respectively. RESULTS ATP7B truncations all showed a diffuse and homogenous distribution pattern within the cytosol of CHO and SH-SY5Y cells, whereas its wild-type proteins and T935M mutation were clustered in the Golgi apparatus. Furthermore, we found that EGFP tags at N- or C-terminal would severely affect cellular localization of ATP7B truncations, and EGFP tags at N-terminal also have an influence on T935M localization. CONCLUSION EGFP tags may not be suitable for the detection of cellular localization of ATP7B mutants.
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Affiliation(s)
- Min Zhu
- Department of Neurology and Institute of Neurology, Huashan Hospital, Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai, China
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Šamajová O, Komis G, Šamaj J. Emerging topics in the cell biology of mitogen-activated protein kinases. TRENDS IN PLANT SCIENCE 2013; 18:140-8. [PMID: 23291243 DOI: 10.1016/j.tplants.2012.11.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 10/31/2012] [Accepted: 11/26/2012] [Indexed: 05/20/2023]
Abstract
Signaling through mitogen-activated protein kinase (MAPK) cascades is organized in complex interconnected subcellular networks. Upon MAPK activation, signals are transferred to targets in different subcellular compartments able to regulate various cellular processes. Therefore, subcellular dissection of individual MAPK modules is vital to understand how a single MAPK can simultaneously mediate many tasks and how a single stimulus can direct different MAPK modules to separated tasks. In this opinion article, we present a subcellular localization prediction of all members of Arabidopsis thaliana MAPK modules validated wherever possible with experimental data. Furthermore, we propose, that at least in part, the complexity of plant MAPK signaling can be explained by unique strategies of subcellular targeting, which will be worth investigating in the near future.
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Affiliation(s)
- Olga Šamajová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Department of Cell Biology, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
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50
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Petro EJ, Raben DM. Bacterial expression strategies for several Sus scrofa diacylglycerol kinase alpha constructs: solubility challenges. Sci Rep 2013; 3:1609. [PMID: 23558375 PMCID: PMC3617429 DOI: 10.1038/srep01609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 03/19/2013] [Indexed: 01/27/2023] Open
Abstract
We pursued several strategies for expressing either full-length Sus scrofa diacylglycerol kinase (DGK) alpha or the catalytic domain (alphacat) in Escherichia coli. Alphacat could be extracted, refolded, and purified from inclusion bodies, but when subjected to analytical gel filtration chromatography, it elutes in the void volume, in what we conclude are microscopic aggregates unsuitable for x-ray crystallography. Adding glutathione S-transferase, thioredoxin, or maltose binding protein as N-terminal fusion tags did not improve alphacat's solubility. Coexpressing with bacterial chaperones increased the yield of alphacat in the supernatant after high-speed centrifugation, but the protein still elutes in the void upon analytical gel filtration chromatography. We believe our work will be of interest to those interested in the structure of eukaryotic DGKs, so that they know which expression strategies have already been tried, as well as to those interested in protein folding and those interested in chaperone/target-protein interactions.
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Affiliation(s)
- Elizabeth J. Petro
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Daniel M. Raben
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD
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