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Wang F, Yan D, Han K, Gao Z, Ma C, Chen Y, Bao X, Li C. Identification and complete genome sequence of iris potyvirus A, which causes dwarfing and foliar chlorosis with mosaic or mottle disease symptoms on lily (Lilium lancifolium Thunb.) in China. Virus Res 2023; 334:199141. [PMID: 37355176 PMCID: PMC10410506 DOI: 10.1016/j.virusres.2023.199141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/26/2023]
Abstract
Lily plants (Lilium lancifolium Thunb.) exhibiting dwarfing and foliar chlorosis with mosaic or mottle disease symptoms were found in Anhui Province, China. We used high-throughput sequencing of small RNA to survey the virus in the lily cultivation region of Anhui Province. Here, we report the identification and complete genome sequence of the viral agent. It contains 9733 nucleotides, excluding the poly(A) tail, and encodes a polyprotein of 3063 amino acids. The complete polyprotein ORF shows 98.92% amino acid sequence identity with that of iris potyvirus A (GenBank MH898493). Phylogenetic analysis of coat protein sequences placed the viral agent close to members of the genus Potyvirus in the family Potyviridae, and it was therefore provisionally named iris potyvirus A isolate Anhui (IrPVA-Anhui). This is the first complete genome sequence of IrPVA-Anhui from lily plant, for which only a partial sequence from Iris domestica has been reported previously. Comparative analysis of this genome sequence with those of closely related potyviruses identified nine cleavage sites and the conserved motifs typical of potyviruses. Subsequent virus identification was performed using serological assays (ELISA and antibody-based lateral flow assays), molecular methods (RT-PCR), and a pathogenicity test. Virus particles with a length of about 700 nm, similar to viruses in the genus Potyvirus, were observed via transmission electron microscope (TEM). We back-inoculated healthy plants of multiple species to investigate the host range of the virus. It infected the original host, Iris domestica, and Nicotiana benthamiana but not Triticum aestivum, Pisum sativum, Chenopodium amaranticolor, or Datura stramonium. This is the first report of natural IrPVA-Anhui infection of lily plants in China, providing a scientific basis for IrPVA-Anhui control in future lily plantings.
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Affiliation(s)
- Fang Wang
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China
| | - Dankan Yan
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China
| | - Kelei Han
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China
| | - Zhengliang Gao
- Wanbei Branch, Anhui Academy of Agricultural Sciences, Fuyang, Anhui 236600, China
| | - Chao Ma
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China
| | - Ying Chen
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China
| | - Xianxun Bao
- Science and Technology Industry Department, Anhui Academy of Agricultural Sciences Hefei, Anhui 230031, China
| | - Cheng Li
- Research Management Department, Anhui Academy of Agricultural Sciences Hefei, Anhui 230031, China.
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Lin Q, Yan D, Hua M, Yin Y, Zheng H, Chen J, Yan F, Peng J, He Q, Lu Y. Complete genome sequence of iris potyvirus B infecting Lilium lancifolium in China. Arch Virol 2022; 167:2391-2393. [PMID: 35925395 DOI: 10.1007/s00705-022-05539-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/06/2022] [Indexed: 11/27/2022]
Abstract
The complete genome sequence of a virus from lily (Lilium lancifolium Thunb.) growing in Huoshan County, Anhui Province, China, was determined. The whole genome consists of 9558 nucleotides, excluding the poly(A) tail, and encodes a 3061-amino-acid polyprotein (GenBank number ON365558) typical of potyviruses. This is the first complete genome sequence of iris potyvirus B (IPB), for which only a partial sequence from Iris domestica was reported previously. Comparative analysis of this genome sequence with those of closely related potyviruses identified nine cleavage sites and the conserved motifs typical of potyviruses. The complete polyprotein ORF shares 73.6% nucleotide and 81.6% amino acid sequence identity with that of iris potyvirus A (IPA, GenBank number MH898493). Phylogenetic analysis showed that IPB is related to IPA and clusters in a group with lily yellow mosaic virus (LYMV). This is the first report of IPB infecting lily plants.
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Affiliation(s)
- Qi Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Dankan Yan
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Mengying Hua
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Yueyan Yin
- Institute of Alpine Economic Plants, Yunnan Academy of Agricultural Sciences, Lijiang, 674100, Yunnan, China
| | - Hongying Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Jiejun Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Qiongji He
- Institute of Alpine Economic Plants, Yunnan Academy of Agricultural Sciences, Lijiang, 674100, Yunnan, China.
| | - Yuwen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, 315211, Zhejiang, China.
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Hirai H, Takemata N, Tamura M, Ohta K. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3727-3744. [PMID: 35348762 PMCID: PMC9023297 DOI: 10.1093/nar/gkac175] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 03/01/2022] [Accepted: 03/05/2022] [Indexed: 11/16/2022] Open
Abstract
During the cellular adaptation to nutrient starvation, cells temporarily decelerate translation processes including ribosomal biogenesis. However, the mechanisms repressing robust gene expression from the ribosomal gene cluster (rDNA) are unclear. Here, we demonstrate that fission yeast cells facing glucose starvation assemble facultative heterochromatin in rDNA leading to its transcriptional repression. Glucose starvation induces quick dissociation of the ATF/CREB-family protein Atf1 from rDNA, where in turn the histone chaperone FACT is recruited to promote H3K9 methylation and heterochromatinization. We also identify the histone acetyltransferase Gcn5 as a repressor of rDNA heterochromatinization in glucose-rich conditions, and this protein dissociates from rDNA upon glucose starvation. Facultative heterochromatin formation in rDNA requires histone deacetylases Clr3 and both the RNAi-dependent and -independent gene silencing pathways. This is essential in adaptation to starvation since mutants lacking heterochromatin formation in rDNA lead to untimely cell death during glucose starvation.
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Affiliation(s)
- Hayato Hirai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Tokyo 153-8902, Japan
| | - Naomichi Takemata
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Tokyo 153-8902, Japan
| | - Miki Tamura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Tokyo 153-8902, Japan
| | - Kunihiro Ohta
- To whom correspondence should be addressed. Tel: +81 3 5465 8834;
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Yin H, Dong Z, Wang X, Lu S, Xia F, Abuduwaili A, Bi Y, Li Y. Metagenomic Analysis of Marigold: Mixed Infection Including Two New Viruses. Viruses 2021; 13:1254. [PMID: 34203118 PMCID: PMC8310094 DOI: 10.3390/v13071254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/25/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022] Open
Abstract
Marigold plants with symptoms of mosaic, crinkle, leaf curl and necrosis were observed and small RNA and ribo-depleted total RNA deep sequencing were conducted to identify the associated viruses. Broad bean wilt virus 2, cucumber mosaic virus, turnip mosaic virus, a new potyvirus tentatively named marigold mosaic virus (MMV) and a new partitivirus named as marigold cryptic virus (MCV) were finally identified. Complete genome sequence analysis showed MMV was 9811 nt in length, encoding a large polyprotein with highest aa sequence identity (57%) with the putative potyvirus polygonatumkingianum virus 1. Phylogenetic analysis with the definite potyviruses based on the polyprotein sequence showed MMV clustered closest to plum pox virus. The complete genome of MCV comprised of dsRNA1 (1583 bp) and dsRNA2 (1459 bp), encoding the RNA-dependent RNA polymerase (RdRp), and coat protein (CP), respectively. MCV RdRp shared the highest (75.7%) aa sequence identity with the unclassified partitivirus ambrosia cryptic virus 2, and 59.0%, 57.1%, 56.1%, 54.5% and 33.7% with the corresponding region of the definite delta-partitiviruses, pepper cryptic virus 2, beet cryptic virus 3, beet cryptic virus 2, pepper cryptic virus 1 and fig cryptic virus, respectively. Phylogenetic analysis based on the RdRp aa sequence showed MCV clustered into the delta-partitivirus group. These findings enriched our knowledge of viruses infecting marigold, but the association of the observed symptom and the identified viruses and the biological characterization of the new viruses should be further investigated.
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Affiliation(s)
- Hang Yin
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing 102206, China; (H.Y.); (Z.D.); (X.W.); (S.L.); (A.A.); (Y.B.)
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Department of Plant Protection, Beijing University of Agriculture, Beijing 102206, China
| | - Zheng Dong
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing 102206, China; (H.Y.); (Z.D.); (X.W.); (S.L.); (A.A.); (Y.B.)
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Department of Plant Protection, Beijing University of Agriculture, Beijing 102206, China
| | - Xulong Wang
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing 102206, China; (H.Y.); (Z.D.); (X.W.); (S.L.); (A.A.); (Y.B.)
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Department of Plant Protection, Beijing University of Agriculture, Beijing 102206, China
| | - Shuhao Lu
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing 102206, China; (H.Y.); (Z.D.); (X.W.); (S.L.); (A.A.); (Y.B.)
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Department of Plant Protection, Beijing University of Agriculture, Beijing 102206, China
| | - Fei Xia
- Beijing Institute of Landscape Architecture, Beijing 100102, China;
| | - Annihaer Abuduwaili
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing 102206, China; (H.Y.); (Z.D.); (X.W.); (S.L.); (A.A.); (Y.B.)
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Department of Plant Protection, Beijing University of Agriculture, Beijing 102206, China
| | - Yang Bi
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing 102206, China; (H.Y.); (Z.D.); (X.W.); (S.L.); (A.A.); (Y.B.)
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Department of Plant Protection, Beijing University of Agriculture, Beijing 102206, China
| | - Yongqiang Li
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing 102206, China; (H.Y.); (Z.D.); (X.W.); (S.L.); (A.A.); (Y.B.)
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Department of Plant Protection, Beijing University of Agriculture, Beijing 102206, China
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Vlachakis D. Genetic and structural analyses of ssRNA viruses pave the way for the discovery of novel antiviral pharmacological targets. Mol Omics 2021; 17:357-364. [PMID: 33725065 DOI: 10.1039/d0mo00173b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In the era of big data and artificial intelligence, a lot of new discoveries have influenced the fields of antiviral drug design and pharmacophore identification. Viruses have always been a threat to society in terms of public health and economic stability. Viruses not only affect humans but also livestock and agriculture with a direct impact on food safety, economy and environmental imprint. Most recently, with the pandemic of COVID-19, it was made clear that a single virus can have a devastating impact on global well-being and economy. In this direction, there is an emerging need for the identification of promising pharmacological targets in viruses. Herein, an effort has been made to discuss the current knowledge, state-of-the-art applications and future implications for the main pharmacological targets of single-stranded RNA viruses.
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Affiliation(s)
- Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied BIology and Biotechnology, Agricultural University of Athens, Athens, Greece.
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Mishra V. Affinity Tags for Protein Purification. Curr Protein Pept Sci 2021; 21:821-830. [PMID: 32504500 DOI: 10.2174/1389203721666200606220109] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/09/2020] [Accepted: 05/06/2020] [Indexed: 11/22/2022]
Abstract
The affinity tags are unique proteins/peptides that are attached at the N- or C-terminus of the recombinant proteins. These tags help in protein purification. Additionally, some affinity tags also serve a dual purpose as solubility enhancers for challenging protein targets. By applying a combinatorial approach, carefully chosen affinity tags designed in tandem have proven to be very successful in the purification of single proteins or multi-protein complexes. In this mini-review, the key features of the most commonly used affinity tags are discussed. The affinity tags have been classified into two significant categories, epitope tags, and protein/domain tags. The epitope tags are generally small peptides with high affinity towards a chromatography resin. The protein/domain tags often perform double duty as solubility enhancers as well as aid in affinity purification. Finally, protease-based affinity tag removal strategies after purification are discussed.
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Affiliation(s)
- Vibhor Mishra
- Department of Biology, Indiana University, Bloomington, IN 47405, USA,Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA
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7
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Sun L, Liu XM, Li WZ, Yi YY, He X, Wang Y, Jin QW. The molecular chaperone Hsp90 regulates heterochromatin assembly through stabilizing multiple complexes in fission yeast. J Cell Sci 2020; 133:jcs244863. [PMID: 32499408 DOI: 10.1242/jcs.244863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/18/2020] [Indexed: 12/18/2022] Open
Abstract
In the fission yeast Schizosaccharomyces pombe, both RNAi machinery and RNAi-independent factors mediate transcriptional and posttranscriptional silencing and heterochromatin formation. Here, we show that the silencing of reporter genes at major native heterochromatic loci (centromeres, telomeres, mating-type locus and rDNA regions) and an artificially induced heterochromatin locus is alleviated in a fission yeast hsp90 mutant, hsp90-G84C Also, H3K9me2 enrichment at heterochromatin regions, especially at the mating-type locus and subtelomeres, is compromised, suggesting heterochromatin assembly defects. We further discovered that Hsp90 is required for stabilization or assembly of the RNA-induced transcriptional silencing (RITS) and Argonaute siRNA chaperone (ARC) RNAi effector complexes, the RNAi-independent factor Fft3, the shelterin complex subunit Poz1 and the Snf2/HDAC-containing repressor complex (SHREC). Our ChIP data suggest that Hsp90 regulates the efficient recruitment of the methyltransferase/ubiquitin ligase complex CLRC by shelterin to chromosome ends and targeting of the SHREC and Fft3 to mating type locus and/or rDNA region. Finally, our genetic analyses demonstrated that increased heterochromatin spreading restores silencing at subtelomeres in the hsp90-G84C mutant. Thus, this work uncovers a conserved factor critical for promoting RNAi-dependent and -independent heterochromatin assembly and gene silencing through stabilizing multiple effectors and effector complexes.
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Affiliation(s)
- Li Sun
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Xiao-Min Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Wen-Zhu Li
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yuan-Yuan Yi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Xiangwei He
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yamei Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Quan-Wen Jin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
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Yuan P, Yang Z, Song H, Wang K, Yang Y, Xie L, Huang S, Liu J, Ran L, Song Z. Three Main Inducers of Alphacoronavirus Infection of Enterocytes: Sialic Acid, Proteases, and Low pH. Intervirology 2018; 61:53-63. [PMID: 30176660 PMCID: PMC7179561 DOI: 10.1159/000492424] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 07/19/2018] [Indexed: 12/19/2022] Open
Abstract
Transmissible gastroenteritis virus (TGEV) and porcine epidemic diarrhea virus (PEDV) are similar coronaviruses, causing diseases characterized by vomiting, diarrhea, and death from severe dehydration in piglets. Thus, they have caused huge losses to the swine-breeding industry worldwide. Nowadays, they are easily transmitted among the continents via vehicles, equipment, and cargo. Both viruses establish an infection in porcine enterocytes in the small intestine, and their spike (S) proteins play a key role in the virus-cell binding process under unfavorable conditions when the intestine with a low pH is filled with a thick layer of mucus and proteases. Sialic acid, proteases, and low pH are three main inducers of coronavirus infection. However, the details of how sialic acid and low pH affect virus binding to the host cell are not determined, and the functions of the proteases are unknown. This review emphasizes the role of three factors in the invasion of TGEV and PEDV into porcine enterocytes and offers more insights into Alphacoronavirus infection in the intestinal environment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Zhenhui Song
- *Zhenhui Song, PhD, Department of Veterinary Medicine, College of Animal Science, Southwest University, Chongqing 402460 (People's Republic of China), E-Mail
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Nautiyal K, Kuroda Y. A SEP tag enhances the expression, solubility and yield of recombinant TEV protease without altering its activity. N Biotechnol 2018; 42:77-84. [DOI: 10.1016/j.nbt.2018.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/16/2018] [Accepted: 02/09/2018] [Indexed: 10/18/2022]
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Li Y, Jia A, Qiao Y, Xiang J, Zhang Y, Wang W. Virome analysis of lily plants reveals a new potyvirus. Arch Virol 2017; 163:1079-1082. [PMID: 29280016 DOI: 10.1007/s00705-017-3690-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/11/2017] [Indexed: 11/26/2022]
Abstract
Lily plants exhibiting virus-like symptoms of leaf yellowing, twisting and brownish necrotic spots were collected, and next-generation sequencing of small RNAs was conducted to identify the associated viruses. Cucumber mosaic virus, lily symptomless virus and a hitherto unrecorded potyvirus, tentatively named "lily yellow mosaic virus" (LYMV), were detected. The genomic RNA of LYMV was 9811 nt in length, encoding a large polyprotein of 3,124 amino acids with a predicted Mr of 353.3 kDa. BLAST analysis showed that LYMV shared a high degree of amino acid sequence identity with Thunberg fritillary mosaic virus (55%), bean yellow mosaic virus (52%), clover yellow vein virus (51%), leek yellow stripe virus (51%), and lily mottle virus (52%), and these viruses clustered together in a phylogenetic tree.
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Affiliation(s)
- Yongqiang Li
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Anning Jia
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Yan Qiao
- Beijing Plant Protection Station, Beijing, 100029, China
| | - Jun Xiang
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Yongjiang Zhang
- Chinese Academy of Inspection and Quarantine, Beijing, China.
| | - Wenhe Wang
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China.
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit Trees, Beijing, China.
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Targeting protein function: the expanding toolkit for conditional disruption. Biochem J 2017; 473:2573-89. [PMID: 27574023 PMCID: PMC5003692 DOI: 10.1042/bcj20160240] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/20/2016] [Indexed: 01/06/2023]
Abstract
A major objective in biological research is to understand spatial and temporal requirements for any given gene, especially in dynamic processes acting over short periods, such as catalytically driven reactions, subcellular transport, cell division, cell rearrangement and cell migration. The interrogation of such processes requires the use of rapid and flexible methods of interfering with gene function. However, many of the most widely used interventional approaches, such as RNAi or CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated 9), operate at the level of the gene or its transcripts, meaning that the effects of gene perturbation are exhibited over longer time frames than the process under investigation. There has been much activity over the last few years to address this fundamental problem. In the present review, we describe recent advances in disruption technologies acting at the level of the expressed protein, involving inducible methods of protein cleavage, (in)activation, protein sequestration or degradation. Drawing on examples from model organisms we illustrate the utility of fast-acting techniques and discuss how different components of the molecular toolkit can be employed to dissect previously intractable biochemical processes and cellular behaviours.
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Mann KS, Walker M, Sanfaçon H. Identification of Cleavage Sites Recognized by the 3C-Like Cysteine Protease within the Two Polyproteins of Strawberry Mottle Virus. Front Microbiol 2017; 8:745. [PMID: 28496438 PMCID: PMC5407059 DOI: 10.3389/fmicb.2017.00745] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 04/10/2017] [Indexed: 01/10/2023] Open
Abstract
Strawberry mottle virus (SMoV, family Secoviridae, order Picornavirales) is one of several viruses found in association with strawberry decline disease in Eastern Canada. The SMoV genome consists of two positive-sense single-stranded RNAs, each encoding one large polyprotein. The RNA1 polyprotein (P1) includes the domains for a putative helicase, a VPg, a 3C-like cysteine protease and an RNA-dependent RNA polymerase at its C-terminus, and one or two protein domains at its N-terminus. The RNA2 polyprotein (P2) is predicted to contain the domains for a movement protein (MP) and one or several coat proteins at its N-terminus, and one or more additional domains for proteins of unknown function at its C-terminus. The RNA1-encoded 3C-like protease is presumed to cleave the two polyproteins in cis (P1) and in trans (P2). Using in vitro processing assays, we systematically scanned the two polyproteins for cleavage sites recognized by this protease. We identified five cis-cleavage sites in P1, with cleavage between the putative helicase and VPg domains being the most efficient. The presence of six protein domains in the SMoV P1, including two upstream of the putative helicase domain, is a feature shared with nepoviruses but not with comoviruses. Results from trans-cleavage assays indicate that the RNA1-encoded 3C-like protease recognized a single cleavage site, which was between the predicted MP and coat protein domains in the P2 polyprotein. The cleavage site consensus sequence for the SMoV 3C-like protease is AxE (E or Q)/(G or S).
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Affiliation(s)
| | | | - Hélène Sanfaçon
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, SummerlandBC, Canada
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Sandersjöö L, Jonsson A, Löfblom J. Protease substrate profiling using bacterial display of self-blocking affinity proteins and flow-cytometric sorting. Biotechnol J 2016; 12. [DOI: 10.1002/biot.201600365] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 10/20/2016] [Accepted: 10/25/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Lisa Sandersjöö
- Division of Protein Technology, School of Biotechnology, KTH - Royal Institute of Technology; AlbaNova University Center; Stockholm Sweden
| | - Andreas Jonsson
- Division of Protein Technology, School of Biotechnology, KTH - Royal Institute of Technology; AlbaNova University Center; Stockholm Sweden
| | - John Löfblom
- Division of Protein Technology, School of Biotechnology, KTH - Royal Institute of Technology; AlbaNova University Center; Stockholm Sweden
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Li L, Sanchez CP, Slaughter BD, Zhao Y, Khan MR, Unruh JR, Rubinstein B, Si K. A Putative Biochemical Engram of Long-Term Memory. Curr Biol 2016; 26:3143-3156. [PMID: 27818176 DOI: 10.1016/j.cub.2016.09.054] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/22/2016] [Accepted: 09/26/2016] [Indexed: 12/15/2022]
Abstract
How a transient experience creates an enduring yet dynamic memory remains an unresolved issue in studies of memory. Experience-dependent aggregation of the RNA-binding protein CPEB/Orb2 is one of the candidate mechanisms of memory maintenance. Here, using tools that allow rapid and reversible inactivation of Orb2 protein in neurons, we find that Orb2 activity is required for encoding and recall of memory. From a screen, we have identified a DNA-J family chaperone, JJJ2, which facilitates Orb2 aggregation, and ectopic expression of JJJ2 enhances the animal's capacity to form long-term memory. Finally, we have developed tools to visualize training-dependent aggregation of Orb2. We find that aggregated Orb2 in a subset of mushroom body neurons can serve as a "molecular signature" of memory and predict memory strength. Our data indicate that self-sustaining aggregates of Orb2 may serve as a physical substrate of memory and provide a molecular basis for the perduring yet malleable nature of memory.
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Affiliation(s)
- Liying Li
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Consuelo Perez Sanchez
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Brian D Slaughter
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Yubai Zhao
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Mohammed Repon Khan
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Jay R Unruh
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Boris Rubinstein
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Kausik Si
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA.
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15
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Cesaratto F, Burrone OR, Petris G. Tobacco Etch Virus protease: A shortcut across biotechnologies. J Biotechnol 2016; 231:239-249. [PMID: 27312702 DOI: 10.1016/j.jbiotec.2016.06.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/31/2016] [Accepted: 06/10/2016] [Indexed: 11/29/2022]
Abstract
About thirty years ago, studies on the RNA genome of Tobacco Etch Virus revealed the presence of an efficient and specific protease, called Tobacco Etch Virus protease (TEVp), that was part of the Nuclear Inclusion a (NIa) enzyme. TEVp is an efficient and specific protease of 27kDa that has become a valuable biotechnological tool. Nowadays TEVp is a unique endopeptidase largely exploited in biotechnology from industrial applications to in vitro and in vivo cellular studies. A number of TEVp mutants with different rate of cleavage, stability and specificity have been reported. Similarly, a panel of different target cleavage sites, derived from the canonical ENLYFQ-G/S site, has been established. In this review we describe these aspects of TEVp and some of its multiple applications. A particular focus is on the use and molecular biology of TEVp in living cells and organisms.
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Affiliation(s)
- Francesca Cesaratto
- International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
| | - Oscar R Burrone
- International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy.
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16
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Zhu F, Sun Y, Wang Y, Pan H, Wang F, Zhang X, Zhang Y, Liu J. Molecular Characterization of the Complete Genome of Three Basal-BR Isolates of Turnip mosaic virus Infecting Raphanus sativus in China. Int J Mol Sci 2016; 17:E888. [PMID: 27271614 PMCID: PMC4926422 DOI: 10.3390/ijms17060888] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/16/2016] [Accepted: 05/27/2016] [Indexed: 11/23/2022] Open
Abstract
Turnip mosaic virus (TuMV) infects crops of plant species in the family Brassicaceae worldwide. TuMV isolates were clustered to five lineages corresponding to basal-B, basal-BR, Asian-BR, world-B and OMs. Here, we determined the complete genome sequences of three TuMV basal-BR isolates infecting radish from Shandong and Jilin Provinces in China. Their genomes were all composed of 9833 nucleotides, excluding the 3'-terminal poly(A) tail. They contained two open reading frames (ORFs), with the large one encoding a polyprotein of 3164 amino acids and the small overlapping ORF encoding a PIPO protein of 61 amino acids, which contained the typically conserved motifs found in members of the genus Potyvirus. In pairwise comparison with 30 other TuMV genome sequences, these three isolates shared their highest identities with isolates from Eurasian countries (Germany, Italy, Turkey and China). Recombination analysis showed that the three isolates in this study had no "clear" recombination. The analyses of conserved amino acids changed between groups showed that the codons in the TuMV out group (OGp) and OMs group were the same at three codon sites (852, 1006, 1548), and the other TuMV groups (basal-B, basal-BR, Asian-BR, world-B) were different. This pattern suggests that the codon in the OMs progenitor did not change but that in the other TuMV groups the progenitor sequence did change at divergence. Genetic diversity analyses indicate that the PIPO gene was under the highest selection pressure and the selection pressure on P3N-PIPO and P3 was almost the same. It suggests that most of the selection pressure on P3 was probably imposed through P3N-PIPO.
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Affiliation(s)
- Fuxiang Zhu
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Ying Sun
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Yan Wang
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Hongyu Pan
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Fengting Wang
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Xianghui Zhang
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Yanhua Zhang
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Jinliang Liu
- College of Plant Sciences, Jilin University, Changchun 130062, China.
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17
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A protease-based biosensor for the detection of schistosome cercariae. Sci Rep 2016; 6:24725. [PMID: 27090566 PMCID: PMC4835807 DOI: 10.1038/srep24725] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/30/2016] [Indexed: 01/18/2023] Open
Abstract
Parasitic diseases affect millions of people worldwide, causing debilitating illnesses and death. Rapid and cost-effective approaches to detect parasites are needed, especially in resource-limited settings. A common signature of parasitic diseases is the release of specific proteases by the parasites at multiple stages during their life cycles. To this end, we engineered several modular Escherichia coli and Bacillus subtilis whole-cell-based biosensors which incorporate an interchangeable protease recognition motif into their designs. Herein, we describe how several of our engineered biosensors have been applied to detect the presence and activity of elastase, an enzyme released by the cercarial larvae stage of Schistosoma mansoni. Collectively, S. mansoni and several other schistosomes are responsible for the infection of an estimated 200 million people worldwide. Since our biosensors are maintained in lyophilised cells, they could be applied for the detection of S. mansoni and other parasites in settings without reliable cold chain access.
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18
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Kakui Y, Sunaga T, Arai K, Dodgson J, Ji L, Csikász-Nagy A, Carazo-Salas R, Sato M. Module-based construction of plasmids for chromosomal integration of the fission yeast Schizosaccharomyces pombe. Open Biol 2016; 5:150054. [PMID: 26108218 PMCID: PMC4632507 DOI: 10.1098/rsob.150054] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Integration of an external gene into a fission yeast chromosome is useful to investigate the effect of the gene product. An easy way to knock-in a gene construct is use of an integration plasmid, which can be targeted and inserted to a chromosome through homologous recombination. Despite the advantage of integration, construction of integration plasmids is energy- and time-consuming, because there is no systematic library of integration plasmids with various promoters, fluorescent protein tags, terminators and selection markers; therefore, researchers are often forced to make appropriate ones through multiple rounds of cloning procedures. Here, we establish materials and methods to easily construct integration plasmids. We introduce a convenient cloning system based on Golden Gate DNA shuffling, which enables the connection of multiple DNA fragments at once: any kind of promoters and terminators, the gene of interest, in combination with any fluorescent protein tag genes and any selection markers. Each of those DNA fragments, called a ‘module’, can be tandemly ligated in the order we desire in a single reaction, which yields a circular plasmid in a one-step manner. The resulting plasmids can be integrated through standard methods for transformation. Thus, these materials and methods help easy construction of knock-in strains, and this will further increase the value of fission yeast as a model organism.
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Affiliation(s)
- Yasutaka Kakui
- Chromosome Segregation Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Tomonari Sunaga
- Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University TWIns, 2-2 Wakamatsucho, Shinjuku, Tokyo 162-0056, Japan
| | - Kunio Arai
- Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University TWIns, 2-2 Wakamatsucho, Shinjuku, Tokyo 162-0056, Japan Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
| | - James Dodgson
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Liang Ji
- Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University TWIns, 2-2 Wakamatsucho, Shinjuku, Tokyo 162-0056, Japan Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
| | - Attila Csikász-Nagy
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige 38010, Italy Randall Division of Cell and Molecular Biophysics and Institute for Mathematical and Molecular Biomedicine, King's College London, London SE1 1UL, UK
| | - Rafael Carazo-Salas
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Masamitsu Sato
- Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University TWIns, 2-2 Wakamatsucho, Shinjuku, Tokyo 162-0056, Japan Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
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19
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Pitner RA, Scarpelli AH, Leonard JN. Regulation of Bacterial Gene Expression by Protease-Alleviated Spatial Sequestration (PASS). ACS Synth Biol 2015; 4:966-74. [PMID: 25822588 DOI: 10.1021/sb500302y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In natural microbial systems, conditional spatial sequestration of transcription factors enables cells to respond rapidly to changes in their environment or intracellular state by releasing presynthesized regulatory proteins. Although such a mechanism may be useful for engineering synthetic biology technologies ranging from cell-based biosensors to biosynthetic platforms, to date it remains unknown how or whether such conditional spatial sequestration may be engineered. In particular, based upon seemingly contradictory reports in the literature, it is not clear whether subcellular spatial localization of a transcription factor within the cytoplasm is sufficient to preclude regulation of cognate promoters on plasmid-borne or chromosomal loci. Here, we describe a modular, orthogonal platform for investigating and implementing this mechanism using protease-alleviated spatial sequestration (PASS). In this system, expression of an exogenous protease mediates the proteolytic release of engineered transcriptional regulators from the inner face of the Escherichia coli cytoplasmic membrane. We demonstrate that PASS mediates robust, conditional regulation of either transcriptional repression, via tetR, or transcriptional activation, by the λ phage CI protein. This work provides new insights into a biologically important facet of microbial gene expression and establishes a new strategy for engineering conditional transcriptional regulation for the microbial synthetic biology toolbox.
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Affiliation(s)
- Ragan A. Pitner
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Andrew H. Scarpelli
- Interdepartmental
Biosciences Graduate Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Joshua N. Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry
of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois 60208, United States
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20
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Detert Oude Weme RGJ, Kovács ÁT, de Jong SJG, Veening JW, Siebring J, Kuipers OP. Single cell FRET analysis for the identification of optimal FRET-pairs in Bacillus subtilis using a prototype MEM-FLIM system. PLoS One 2015; 10:e0123239. [PMID: 25886351 PMCID: PMC4401445 DOI: 10.1371/journal.pone.0123239] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/01/2015] [Indexed: 11/21/2022] Open
Abstract
Protein-protein interactions can be studied in vitro, e.g. with bacterial or yeast two-hybrid systems or surface plasmon resonance. In contrast to in vitro techniques, in vivo studies of protein-protein interactions allow examination of spatial and temporal behavior of such interactions in their native environment. One approach to study protein-protein interactions in vivo is via Förster Resonance Energy Transfer (FRET). Here, FRET efficiency of selected FRET-pairs was studied at the single cell level using sensitized emission and Frequency Domain-Fluorescence Lifetime Imaging Microscopy (FD-FLIM). For FRET-FLIM, a prototype Modulated Electron-Multiplied FLIM system was used, which is, to the best of our knowledge, the first account of Frequency Domain FLIM to analyze FRET in single bacterial cells. To perform FRET-FLIM, we first determined and benchmarked the best fluorescent protein-pair for FRET in Bacillus subtilis using a novel BglBrick-compatible integration vector. We show that GFP-tagRFP is an excellent donor-acceptor pair for B. subtilis in vivo FRET studies. As a proof of concept, selected donor and acceptor fluorescent proteins were fused using a linker that contained a tobacco etch virus (TEV)-protease recognition sequence. Induction of TEV-protease results in loss of FRET efficiency and increase in fluorescence lifetime. The loss of FRET efficiency after TEV induction can be followed in time in single cells via time-lapse microscopy. This work will facilitate future studies of in vivo dynamics of protein complexes in single B. subtilis cells.
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Affiliation(s)
- Ruud G. J. Detert Oude Weme
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Ákos T. Kovács
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | | | - Jan-Willem Veening
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Jeroen Siebring
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Oscar P. Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, 9747 AG Groningen, The Netherlands
- * E-mail:
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21
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Sarker S, Ghorashi SA, Swarbrick CM, Khandokar YB, Himiari Z, Forwood JK, Raidal SR. An efficient approach for recombinant expression and purification of the viral capsid protein from beak and feather disease virus (BFDV) in Escherichia coli. J Virol Methods 2015; 215-216:1-8. [DOI: 10.1016/j.jviromet.2015.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 02/09/2015] [Accepted: 02/09/2015] [Indexed: 11/28/2022]
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22
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Kakui Y, Sato M, Okada N, Toda T, Yamamoto M. Microtubules and Alp7-Alp14 (TACC-TOG) reposition chromosomes before meiotic segregation. Nat Cell Biol 2013; 15:786-96. [PMID: 23770679 DOI: 10.1038/ncb2782] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 05/10/2013] [Indexed: 12/11/2022]
Abstract
Tethering kinetochores at spindle poles facilitates their efficient capture and segregation by microtubules at mitotic onset in yeast. During meiotic prophase of fission yeast, however, kinetochores are detached from the poles, which facilitates meiotic recombination but may cause a risk of chromosome mis-segregation during meiosis. How cells circumvent this dilemma remains unclear. Here we show that an extensive microtubule array assembles from the poles at meiosis I onset and retrieves scattered kinetochores towards the poles to prevent chromosome drift. Moreover, the microtubule-associated protein complex Alp7-Alp14 (the fission yeast orthologues of mammalian TACC-TOG) is phosphorylated by Polo kinase, which promotes its meiosis-specific association to the outer kinetochore complex Nuf2-Ndc80 of scattered kinetochores, thereby assisting in capturing remote kinetochores. Although TOG was recently characterized as a microtubule polymerase, Dis1 (the other TOG orthologue in fission yeast), together with the Dam1 complex, plays a role in microtubule shortening to pull kinetochores polewards. Thus, microtubules and their binding proteins uniquely reconstitute chromosome configuration during meiosis.
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Affiliation(s)
- Yasutaka Kakui
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Tokyo 113-0032, Japan
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23
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24
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Magalhães GS, Novo JB, Clissa PB, Della Casa MS, Butera D, da Silva AMM. Engineered mammalian vector to express EGFP-tagged proteins as biomarkers. Mol Biotechnol 2012; 51:119-27. [PMID: 21847674 DOI: 10.1007/s12033-011-9444-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Due to its specialized post-translational machinery, mammalian cells represent an interesting and not fully explored system to express snake toxins. Therefore, in this work, we built up a new mammalian expression vector that enhances the feasibility to use mammalian cells to express proteins as biomarkers. Among the modifications, an Igκ signal peptide and a 6xHis tag were inserted into this vector in order to drive the protein to the supernatant and simplify its purification, respectively. In addition, to facilitate selection of high producing clones and also tag proteins which may function as a biomarker, the sequence of enhanced green fluorescent protein (EGFP) was added. The efficiency of the resulting vector (pToxEGFP) was tested by cloning and expressing the viper venom disintegrin echistatin (Ech) that due to its affinity to integrin αvβ3 was tested as a molecular marker. Expression of EGFP-Ech was achieved in CHO-DXB11 cells resulting in a yield of 22 mg/L. The binding activity of this chimera protein was successfully achieved on human umbilical vein endothelial cells which highly express αvβ3. The results indicate that pToxEGFP may constitute an efficient and versatile expression vector to express tagged proteins with potential biomarker activity.
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Affiliation(s)
- Geraldo Santana Magalhães
- Laboratório de Imunopatologia, Instituto Butantan, Av. Vital Brasil, 1500, São Paulo, SP 05503-900, Brazil.
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25
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Simplifying protein expression with ligation-free, traceless and tag-switching plasmids. Protein Expr Purif 2012; 85:9-17. [DOI: 10.1016/j.pep.2012.06.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 06/01/2012] [Accepted: 06/08/2012] [Indexed: 01/30/2023]
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26
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Young CL, Britton ZT, Robinson AS. Recombinant protein expression and purification: A comprehensive review of affinity tags and microbial applications. Biotechnol J 2012; 7:620-34. [DOI: 10.1002/biot.201100155] [Citation(s) in RCA: 312] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 11/23/2011] [Accepted: 11/29/2011] [Indexed: 12/27/2022]
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27
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An overview of enzymatic reagents for the removal of affinity tags. Protein Expr Purif 2011; 80:283-93. [PMID: 21871965 PMCID: PMC3195948 DOI: 10.1016/j.pep.2011.08.005] [Citation(s) in RCA: 252] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 08/04/2011] [Accepted: 08/05/2011] [Indexed: 11/20/2022]
Abstract
Although they are often exploited to facilitate the expression and purification of recombinant proteins, every affinity tag, whether large or small, has the potential to interfere with the structure and function of its fusion partner. For this reason, reliable methods for removing affinity tags are needed. Only enzymes have the requisite specificity to be generally useful reagents for this purpose. In this review, the advantages and disadvantages of some commonly used endo- and exoproteases are discussed in light of the latest information.
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28
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Vandamme J, Völkel P, Rosnoblet C, Le Faou P, Angrand PO. Interaction proteomics analysis of polycomb proteins defines distinct PRC1 complexes in mammalian cells. Mol Cell Proteomics 2011; 10:M110.002642. [PMID: 21282530 DOI: 10.1074/mcp.m110.002642] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Polycomb group (PcG) proteins maintain transcriptional repression of hundreds of genes involved in development, signaling or cancer using chromatin-based epigenetic mechanisms. Biochemical studies in Drosophila have revealed that PcG proteins associate in at least two classes of protein complexes known as Polycomb repressive complexes 1 and 2 (PRC1 and PRC2). Drosophila core PRC1 is composed of four subunits, Polycomb (Pc), Sex combs extra (Sce), Polyhomeotic (Ph), and Posterior sex combs (Psc). Each of these proteins has multiple orthologs in vertebrates classified respectively as the CBX, RING1/RNF2, PHC, and BMI1/PCGF families. Mammalian genomes encode five CBX family members (CBX2, CBX4, CBX6, CBX7, and CBX8) that are believed to have distinct biological functions. Here, we applied a tandem affinity purification (TAP) approach coupled with tandem mass spectrometry (MS/MS) methodologies in order to identify interacting partners of CBX family proteins under the same experimental conditions. Our analysis identified with high confidence about 20 proteins co-eluted with CBX2 and CBX7 tagged proteins, about 40 with CBX4, and around 60 with CBX6 and CBX8. We provide evidences that the CBX family proteins are mutually exclusive and define distinct PRC1-like protein complexes. CBX proteins also interact with different efficiencies with the other PRC1 components. Among the novel CBX interacting partners, protein kinase 2 associates with all CBX-PRC1 protein complexes, whereas 14-3-3 proteins specifically bind to CBX4. 14-3-3 protein binding to CBX4 appears to modulate the interaction between CBX4 and the BMI1/PCGF components of PRC1, but has no effect on CBX4-RING1/RNF2 interaction. Finally, we suggest that differences in CBX protein interactions would account, at least in part, for distinct subnuclear localization of the CBX family members.
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Affiliation(s)
- Julien Vandamme
- Chromatinomics, Interdisciplinary Research Institute, Univ. Lille Nord de France, Université de Lille 1 Sciences et Technologies/CNRS USR 3078, 50 Avenue Halley, Parc Scientifique de la Haute Borne, F-59658 Villeneuve d'Ascq Cedex, France
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29
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Kostallas G, Löfdahl PÅ, Samuelson P. Substrate profiling of tobacco etch virus protease using a novel fluorescence-assisted whole-cell assay. PLoS One 2011; 6:e16136. [PMID: 21267463 PMCID: PMC3022733 DOI: 10.1371/journal.pone.0016136] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 12/14/2010] [Indexed: 11/18/2022] Open
Abstract
Site-specific proteolysis of proteins plays an important role in many cellular functions and is often key to the virulence of infectious organisms. Efficient methods for characterization of proteases and their substrates will therefore help us understand these fundamental processes and thereby hopefully point towards new therapeutic strategies. Here, a novel whole-cell in vivo method was used to investigate the substrate preference of the sequence specific tobacco etch virus protease (TEVp). The assay, which utilizes protease-mediated intracellular rescue of genetically encoded short-lived fluorescent substrate reporters to enhance the fluorescence of the entire cell, allowed subtle differences in the processing efficiency of closely related substrate peptides to be detected. Quantitative screening of large combinatorial substrate libraries, through flow cytometry analysis and cell sorting, enabled identification of optimal substrates for TEVp. The peptide, ENLYFQG, identical to the protease's natural substrate peptide, emerged as a strong consensus cleavage sequence, and position P3 (tyrosine, Y) and P1 (glutamine, Q) within the substrate peptide were confirmed as being the most important specificity determinants. In position P1′, glycine (G), serine (S), cysteine (C), alanine (A) and arginine (R) were among the most prevalent residues observed, all known to generate functional TEVp substrates and largely in line with other published studies stating that there is a strong preference for short aliphatic residues in this position. Interestingly, given the complex hydrogen-bonding network that the P6 glutamate (E) is engaged in within the substrate-enzyme complex, an unexpectedly relaxed residue preference was revealed for this position, which has not been reported earlier. Thus, in the light of our results, we believe that our assay, besides enabling protease substrate profiling, also may serve as a highly competitive platform for directed evolution of proteases and their substrates.
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Affiliation(s)
- George Kostallas
- Department of Molecular Biotechnology, School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Per-Åke Löfdahl
- Department of Molecular Biotechnology, School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Patrik Samuelson
- Department of Molecular Biotechnology, School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden
- * E-mail:
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30
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Charlton A, Zachariou M. Tag removal by site-specific cleavage of recombinant fusion proteins. Methods Mol Biol 2011; 681:349-367. [PMID: 20978975 DOI: 10.1007/978-1-60761-913-0_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Where an affinity tag has served its purpose it may become desirable to remove it from the protein of interest. This chapter describes the removal of such fusion partners from the intended protein product by cleavage with site-specific endoproteases. Methods to achieve proteolytic cleavage of the fusion proteins are provided, along with techniques for optimising the yield of authentic product.
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Affiliation(s)
- Adam Charlton
- Commonwealth Serum Laboratories Ltd, Parkville, VIC, Australia
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31
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Application of “Homogeneous Assay for Fluorescence Concentrated on Membrane” to the Analysis of the Substrate Specificity of Protease. Biosci Biotechnol Biochem 2010; 74:869-71. [DOI: 10.1271/bbb.90822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Properties of a homogeneous C-lobe prepared by introduction of a TEV cleavage site between the lobes of human transferrin. Protein Expr Purif 2010; 72:32-41. [PMID: 20064616 DOI: 10.1016/j.pep.2010.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 01/04/2010] [Accepted: 01/05/2010] [Indexed: 11/20/2022]
Abstract
Essential to iron transport and delivery, human serum transferrin (hTF) is a bilobal glycoprotein capable of reversibly binding one ferric ion in each lobe (the N- and C-lobes). A complete description of iron release from hTF, as well as insight into the physiological significance of the bilobal structure, demands characterization of the isolated lobes. Although production of large amounts of isolated N-lobe and full-length hTF has been well documented, attempts to produce the C-lobe (by recombinant and/or proteolytic approaches) have met with more limited success. Our new strategy involves replacing the hepta-peptide, PEAPTDE (comprising the bridge between the lobes) with the sequence ENLYFQ/G in a His-tagged non-glycosylated monoferric hTF construct, designated Fe(C)hTF. The new bridge sequence of this construct, designated Fe(C)TEV hTF, is readily cleaved by the tobacco etch virus (TEV) protease yielding non-glycosylated C-lobe. Following nickel column chromatography (to remove the N-lobe and the TEV protease which are both His tagged), the homogeneity of the C-lobe has been confirmed by mass spectroscopy. Differing reactivity with a monoclonal antibody specific to the C-lobe indicates that introduction of the TEV cleavage site into the bridge alters its conformation. The spectral and kinetic properties of the isolated C-lobe differ significantly from those of the isolated N-lobe.
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33
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Taliansky ME, Brown JWS, Rajamäki ML, Valkonen JPT, Kalinina NO. Involvement of the plant nucleolus in virus and viroid infections: parallels with animal pathosystems. Adv Virus Res 2010; 77:119-58. [PMID: 20951872 PMCID: PMC7149663 DOI: 10.1016/b978-0-12-385034-8.00005-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The nucleolus is a dynamic subnuclear body with roles in ribosome subunit biogenesis, mediation of cell-stress responses, and regulation of cell growth. An increasing number of reports reveal that similar to the proteins of animal viruses, many plant virus proteins localize in the nucleolus to divert host nucleolar proteins from their natural functions in order to exert novel role(s) in the virus infection cycle. This chapter will highlight studies showing how plant viruses recruit nucleolar functions to facilitate virus translation and replication, virus movement and assembly of virus-specific ribonucleoprotein (RNP) particles, and to counteract plant host defense responses. Plant viruses also provide a valuable tool to gain new insights into novel nucleolar functions and processes. Investigating the interactions between plant viruses and the nucleolus will facilitate the design of novel strategies to control plant virus infections.
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Affiliation(s)
- M E Taliansky
- Scottish Crop Research Institute, Invergowrie, Dundee, United Kingdom
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34
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Hartmann BM, Kaar W, Yoo IK, Lua LHL, Falconer RJ, Middelberg APJ. The chromatography-free release, isolation and purification of recombinant peptide for fibril self-assembly. Biotechnol Bioeng 2009; 104:973-85. [PMID: 19530081 DOI: 10.1002/bit.22447] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
One of the major expenses associated with recombinant peptide production is the use of chromatography in the isolation and purification stages of a bioprocess. Here we report a chromatography-free isolation and purification process for recombinant peptide expressed in Escherichia coli (E. coli). Initial peptide release is by homogenization and then by enzymatic cleavage of the peptide-containing fusion protein, directly in the E. coli homogenate. Release is followed by selective solvent precipitation (SSP) to isolate and purify the peptide away from larger cell contaminants. Specifically, we expressed in E. coli the self-assembling beta-sheet forming peptide P(11)-2 in fusion to thioredoxin. Homogenate was heat treated (55 degrees C, 15 min) and then incubated with tobacco etch virus protease (TEVp) to release P(11)-2 having a native N-terminus. SSP with ethanol at room temperature then removed contaminating proteins in an integrated isolation-purification step; it proved necessary to add 250 mM NaCl to homogenate to prevent P(11)-2 from partitioning to the precipitate. This process structure gave recombinant P(11)-2 peptide at 97% polypeptide purity and 40% overall yield, without a single chromatography step. Following buffer-exchange of the 97% pure product by bind-elute chromatography into defined chemical conditions, the resulting peptide was shown to be functionally active and able to form self-assembled fibrils. To the best of our knowledge, this manuscript reports the first published process for chromatography-free recombinant peptide release, isolation and purification. The process proved able to deliver functional recombinant peptide at high purity and potentially low cost, opening cost-sensitive materials applications for peptide-based materials.
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Affiliation(s)
- B M Hartmann
- Centre for Biomolecular Engineering, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia
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35
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Wang HY, Liu JL, Gao R, Chen J, Shao YH, Li XD. Complete genomic sequence analyses of Turnip mosaic virus basal-BR isolates from China. Virus Genes 2009; 38:421-8. [PMID: 19238532 DOI: 10.1007/s11262-009-0335-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2008] [Accepted: 02/04/2009] [Indexed: 11/28/2022]
Abstract
Isolates of Turnip mosaic virus (TuMV) are divided into four molecular lineages based on host range and geographical origins. Basal-BR is one of the four lineages and represented a new emergent lineage in East Asia. In one previous paper, we report the occurrence of basal-BR isolates in China. Here, we presented the first two complete genomic sequences of Chinese TuMV basal-BR isolates, WFLB06 and TANX2. The genomes of both isolates were 9833 nucleotides excluding the poly(A) tail, and had identical genomic structure. Most of their genes shared the highest identities with Japanese isolates. Recombination analysis showed that WFLB06 was an interlineage recombinant of basal-BR and Asian-BR parents, while TANX2 was an intralineage recombinant of basal-BR parents, and these two isolates represented two novel recombination patterns of TuMV. The ratio of nonsynonymous and synonymous substitution for the P1 gene of Chinese TuMV population was the highest and amounted to 12 times higher than that for the NIa-Pro gene, which implies that the selection pressure on the P1 gene was the highest among the genes present in the genome.
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Affiliation(s)
- Hong-Yan Wang
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
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36
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Kaar W, Hartmann B, Fan Y, Zeng B, Lua L, Dexter A, Falconer R, Middelberg A. Microbial bio-production of a recombinant stimuli-responsive biosurfactant. Biotechnol Bioeng 2009; 102:176-87. [DOI: 10.1002/bit.22037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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37
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Wigdal SS, Anderson JL, Vidugiris GJ, Shultz J, Wood KV, Fan F. A novel bioluminescent protease assay using engineered firefly luciferase. CURRENT CHEMICAL GENOMICS 2008; 2:16-28. [PMID: 20161840 PMCID: PMC2803436 DOI: 10.2174/1875397300802010016] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Revised: 08/20/2008] [Accepted: 08/23/2008] [Indexed: 11/22/2022]
Abstract
Proteases play important roles in a variety of disease processes. Understanding their biological functions underpins the efforts of drug discovery. We have developed a bioluminescent protease assay using a circularly permuted form of firefly luciferase, wherein the native enzyme termini were joined by a peptide containing a protease site of interest. Protease cleavage of these mutant luciferases greatly activates the enzyme, typically over 100 fold. The mutant luciferase substrates are easily generated by molecular cloning and cell-free translation reactions and thus the protease substrates do not need to be chemically synthesized or purchased. The assay has broad applicability using a variety of proteases and their cognate sites and can sensitively detect protease activity. In this report we further demonstrate its utility for the evaluation of protease recognition sequence specificity and subsequent establishment of an optimized assay for the identification and characterization of protease inhibitors using high throughput screening.
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Affiliation(s)
- Susan S Wigdal
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711, USA
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38
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Harder B, Schomburg A, Pflanz R, Küstner K, Gerlach N, Schuh R. TEV protease-mediated cleavage in Drosophila as a tool to analyze protein functions in living organisms. Biotechniques 2008; 44:765-72. [PMID: 18476830 DOI: 10.2144/000112884] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Drosophila provides a powerful experimental system to analyze gene functions in a multi-cellular organism. Here we describe an in vivo method that interferes with the integrity of selected proteins through site-specific cleavage in Drosophila. The technique is based on the highly specific seven-amino-acid recognition site of the tobacco etch virus (TEV) protease. We established transgenic fly lines that direct TEV protease expression in various tissues without affecting fly viability. The insertion of the TEV protease recognition site in defined positions of target proteins mediates their sequence-specific cleavage after controlled TEV protease expression in the fly. Thereby, this technique is a powerful tool that allows the in vivo manipulation of selected proteins in a time- and tissue-specific manner.
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Affiliation(s)
- Ben Harder
- Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany
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39
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Li W, Hilf ME, Webb SE, Baker CA, Adkins S. Presence of P1b and absence of HC-Pro in Squash vein yellowing virus suggests a general feature of the genus Ipomovirus in the family Potyviridae. Virus Res 2008; 135:213-9. [DOI: 10.1016/j.virusres.2008.03.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 03/21/2008] [Accepted: 03/21/2008] [Indexed: 10/22/2022]
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40
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Charlton A. Site-specific cleavage of fusion proteins. Methods Mol Biol 2008; 421:211-228. [PMID: 18826057 DOI: 10.1007/978-1-59745-582-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Where an affinity tag has served its purpose, it may become desirable to remove it from the protein of interest. This chapter describes the removal of such fusion partners from the intended protein product by cleavage with site-specific endoproteases. Methods to achieve proteolytic cleavage of the fusion proteins are provided, along with techniques for optimizing the yield of authentic product.
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Affiliation(s)
- Adam Charlton
- Industrial Biotechnology, CSIRO Molecular and Health Technology, Australia
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41
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Yu XQ, Lan YF, Wang HY, Liu JL, Zhu XP, Valkonen JPT, Li XD. The complete genomic sequence of Tobacco vein banding mosaic virus and its similarities with other potyviruses. Virus Genes 2007; 35:801-6. [PMID: 17668310 DOI: 10.1007/s11262-007-0135-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2007] [Accepted: 06/27/2007] [Indexed: 10/23/2022]
Abstract
The complete genomic sequence of an isolate of Tobacco vein banding mosaic virus (TVBMV-YND) from Yunnan, China was determined by sequencing overlapping cDNA fragments obtained by RT-PCR with degenerate and/or specific primers. The genome is composed of 9,570 nucleotides (nt) excluding the 3'-terminal poly (A) tail and contains one single open reading frame of 9,240 nt encoding a large polyprotein of 3,079 amino acids with predicted Mr of 348.6 kDa. Phylogenetic analysis of complete genomic sequences confirmed that TVBMV is a distinct species of the genus Potyvirus. Different parts of TVBMV-YND genome shared different levels of identity with other species of potyviruses, while most parts showed greatest identity with Chilli veinal mottle virus among the potyviruses with available complete genomic sequences. TVBMV-YND had a rare Q/N cleavage site for NIb/CP and uncommon RITC motif in HC-Pro that is crucial for aphid transmission of potyviruses.
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Affiliation(s)
- Xiao-Qing Yu
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, PR China
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42
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Rawlings ND, Morton FR. The MEROPS batch BLAST: a tool to detect peptidases and their non-peptidase homologues in a genome. Biochimie 2007; 90:243-59. [PMID: 17980477 DOI: 10.1016/j.biochi.2007.09.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Accepted: 09/21/2007] [Indexed: 11/29/2022]
Abstract
Many of the 181 families of peptidases contain homologues that are known to have functions other than peptide bond hydrolysis. Distinguishing an active peptidase from a homologue that is not a peptidase requires specialist knowledge of the important active site residues, because replacement or lack of one of these catalytic residues is an important clue that the homologue in question is unlikely to hydrolyse peptide bonds. Now that the rate at which proteins are characterized is outstripped by the rate that genome sequences are determined, many genes are being incorrectly annotated because only sequence similarity is taken into consideration. We present a tool called the MEROPS batch BLAST which not only performs a comparison against the MEROPS sequence collection, but also does a pair-wise alignment with the closest homologue detected and calculates the position of the active site residues. A non-peptidase homologue can be distinguished by the absence or unacceptable replacement of any of these residues. An analysis of peptidase homologues in the genome of the bacterium Erythrobacter litoralis is presented as an example.
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Affiliation(s)
- Neil D Rawlings
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
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43
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Kurz M, Cowieson NP, Robin G, Hume DA, Martin JL, Kobe B, Listwan P. Incorporating a TEV cleavage site reduces the solubility of nine recombinant mouse proteins. Protein Expr Purif 2006; 50:68-73. [PMID: 16798010 DOI: 10.1016/j.pep.2006.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Revised: 05/12/2006] [Accepted: 05/14/2006] [Indexed: 11/22/2022]
Abstract
Failure to express soluble proteins in bacteria is mainly attributed to the properties of the target protein itself, as well as the choice of the vector, the purification tag and the linker between the tag and protein, and codon usage. The expression of proteins with fusion tags to facilitate subsequent purification steps is a widely used procedure in the production of recombinant proteins. However, the additional residues can affect the properties of the protein; therefore, it is often desirable to remove the tag after purification. This is usually done by engineering a cleavage site between the tag and the encoded protein that is recognised by a site-specific protease, such as the one from tobacco etch virus (TEV). In this study, we investigated the effect of four different tags on the bacterial expression and solubility of nine mouse proteins. Two of the four engineered constructs contained hexahistidine tags with either a long or short linker. The other two constructs contained a TEV cleavage site engineered into the linker region. Our data show that inclusion of the TEV recognition site directly downstream of the recombination site of the Invitrogen Gateway vector resulted in a loss of solubility of the nine mouse proteins. Our work suggests that one needs to be very careful when making modifications to expression vectors and combining different affinity and fusion tags and cleavage sites.
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Affiliation(s)
- Mareike Kurz
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
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44
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Liang WX, Song LM, Tian GZ, Li HF, Fan ZF. The genomic sequence of Wisteria vein mosaic virus and its similarities with other potyviruses. Arch Virol 2006; 151:2311-9. [PMID: 16732423 DOI: 10.1007/s00705-006-0780-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Accepted: 03/31/2006] [Indexed: 10/24/2022]
Abstract
The complete nucleotide sequence of a Beijing isolate of Wisteria vein mosaic virus was determined to be 9695 nucleotides in length excluding the poly(A) tail. Sequence analysis predicted a single large open reading frame of 9279 nucleotides potentially encodes a polyprotein of 3092 amino acids. Phylogenetic analysis based on the genomic and deduced amino acid sequences support the current status of Wisteria vein mosaic virus (WVMV) as a distinct virus of the genus Potyvirus and a member of the Bean common mosaic virus (BCMV) subgroup. Sequence comparisons of WVMV and other members of the BCMV subgroup showed that WVMV is most closely related to both soybean mosaic virus and watermelon mosaic virus.
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Affiliation(s)
- W X Liang
- Department of Plant Pathology and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, PR China
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45
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Hakansson-McReynolds S, Jiang S, Rong L, Caffrey M. Solution structure of the severe acute respiratory syndrome-coronavirus heptad repeat 2 domain in the prefusion state. J Biol Chem 2006; 281:11965-71. [PMID: 16507566 PMCID: PMC8099417 DOI: 10.1074/jbc.m601174200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The envelope glycoprotein, termed the spike protein, of severe acute respiratory syndrome coronavirus (SARS-CoV) is known to mediate viral entry. Similar to other class 1 viral fusion proteins, the heptad repeat regions of SARS-CoV spike are thought to undergo conformational changes from a prefusion form to a subsequent post-fusion form that enables fusion of the viral and host membranes. Recently, the structure of a post-fusion form of SARS-CoV spike, which consists of isolated domains of heptad repeats 1 and 2 (HR1 and HR2), has been determined by x-ray crystallography. To date there is no structural information for the prefusion conformations of SARS-CoV HR1 and HR2. In this work we present the NMR structure of the HR2 domain (residues 1141-1193) from SARS-CoV (termed S2-HR2) in the presence of the co-solvent trifluoroethanol. We find that in the absence of HR1, S2-HR2 forms a coiled coil symmetric trimer with a complex molecular mass of 18 kDa. The S2-HR2 structure, which is the first example of the prefusion form of coronavirus envelope, supports the current model of viral membrane fusion and gives insight into the design of structure-based antagonists of SARS.
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Affiliation(s)
- Susanna Hakansson-McReynolds
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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46
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van den Berg S, Löfdahl PA, Härd T, Berglund H. Improved solubility of TEV protease by directed evolution. J Biotechnol 2005; 121:291-8. [PMID: 16150509 DOI: 10.1016/j.jbiotec.2005.08.006] [Citation(s) in RCA: 245] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2005] [Accepted: 08/04/2005] [Indexed: 11/28/2022]
Abstract
The efficiency and high specificity of tobacco etch virus (TEV) protease has made it widely used for cleavage of recombinant fusion proteins. However, the production of TEV protease in E. coli is hampered by low solubility. We have subjected the gene encoding TEV protease to directed evolution to improve the yield of soluble protein. Libraries of mutated genes obtained by error-prone PCR and gene shuffling were introduced into the Gateway cloning system for facilitated transfer between vectors for screening, purification, or other applications. Fluorescence based in vivo solubility screening was carried out by cloning the libraries into a plasmid encoding a C-terminal GFP fusion. Mutant genes giving rise to high GFP fluorescence intensity indicating high levels of soluble TEV-GFP were subsequently transferred to a vector providing a C-terminal histidine tag for expression, purification, and activity tests of mutated TEV. We identified a mutant, TEV(SH), in which three amino acid substitutions result in a five-fold increase in the yield of purified protease with retained activity.
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Affiliation(s)
- Susanne van den Berg
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE 171 77 Stockholm, Sweden
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47
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Wen R, Zhang SC, Michaud D, Sanfaçon H. Inhibitory effects of cystatins on proteolytic activities of the Plum pox potyvirus cysteine proteinases. Virus Res 2005; 105:175-82. [PMID: 15351491 DOI: 10.1016/j.virusres.2004.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2004] [Revised: 05/28/2004] [Accepted: 05/28/2004] [Indexed: 11/17/2022]
Abstract
In an effort to develop new antiviral strategies effective against potyviruses, several cystatins were evaluated for their ability to inhibit the cysteine proteinases of Plum pox potyvirus (PPV) using in vitro proteolytic assays. The following cystatins were purified as GST fusion proteins and shown to be active against papain:oryzacystatins I and II (OCI and OCII), corn cystatin II (CCII), human stefin A (HSA), the domain 8 of tomato multicystatin (TMC-8) and a large 24kDa tomato cystatin (LTCyst). These cystatins did not inhibit the activity of purified recombinant PPV NIa proteinase, a serine-like cysteine proteinases related to the 3C proteinases of picornaviruses and to chymotrypsin. The cystatins were shown to inhibit slightly the activity of the PPV HC-Pro proteinase with CCII being the best inhibitor. However a large excess of the cystatins was required to observe any inhibition. Based on these results and on the documented pleiotropic effects of cystatins on the metabolism of plants, we conclude that they are not the best candidates for antiviral strategies targeted to viral cysteine proteinases. The availability of soluble active recombinant PPV NIa proteinase will be instrumental for the selection of other proteinase inhibitors with increased affinity and specificity for this proteinase.
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Affiliation(s)
- Rui Wen
- Pacific Agri-Food Research Centre, 4200 Highway 97, Summerland, BC, Canada V0H 1Z0
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48
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Maoka T, Hataya T. The Complete Nucleotide Sequence and Biotype Variability of Papaya leaf distortion mosaic virus. PHYTOPATHOLOGY 2005; 95:128-135. [PMID: 18943981 DOI: 10.1094/phyto-95-0128] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
ABSTRACT The complete nucleotide sequence of the genome of Papaya leaf distortion mosaic virus (PLDMV) was determined. The viral RNA genome of strain LDM (leaf distortion mosaic) comprised 10,153 nucleotides, excluding the poly(A) tail, and contained one long open reading frame encoding a polyprotein of 3,269 amino acids (molecular weight 373,347). The polyprotein contained nine putative proteolytic cleavage sites and some motifs conserved in other potyviral polyproteins with 44 to 50% identities, indicating that PLDMV is a distinct species in the genus Potyvirus. Like the W biotype of Papaya ringspot virus (PRSV), the non-papaya-infecting biotype of PLDMV (PLDMV-C) was found in plants of the family Cucurbitaceae. The coat protein (CP) sequence of PLDMV-C in naturally infected-Trichosanthes bracteata was compared with those of three strains of the P biotype (PLDMV-P), LDM and two additional strains M (mosaic) and YM (yellow mosaic), which are biologically different from each other. The CP sequences of three strains of PLDMV-P share high identities of 95 to 97%, while they share lower identities of 88 to 89% with that of PLDMV-C. Significant changes in hydrophobicity and a deletion of two amino acids at the N-terminal region of the CP of PLDMV-C were observed. The finding of two biotypes of PLDMV implies the possibility that the papaya-infecting biotype evolved from the cucurbitaceae-infecting potyvirus, as has been previously suggested for PRSV. In addition, a similar evolutionary event acquiring infectivity to papaya may arise frequently in viruses in the family Cucurbitaceae.
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49
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Nair DM, Purdue PE, Lazarow PB. Pex7p translocates in and out of peroxisomes in Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2004; 167:599-604. [PMID: 15545321 PMCID: PMC2172567 DOI: 10.1083/jcb.200407119] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Pex7p is the soluble receptor responsible for importing into peroxisomes newly synthesized proteins bearing a type 2 peroxisomal targeting sequence. We observe that appending GFP to Pex7p's COOH terminus shifts Pex7p's intracellular distribution from predominantly cytosolic to predominantly peroxisomal in Saccharomyces cerevisiae. Cleavage of the link between Pex7p and GFP within peroxisomes liberates GFP, which remains inside the organelle, and Pex7p, which exits to the cytosol. The reexported Pex7p is functional, resulting in import of thiolase into peroxisomes and improved growth of the yeast on oleic acid. These results support the “extended shuttle” model of peroxisome import receptor function and open the way to future studies of receptor export.
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Affiliation(s)
- Devi M Nair
- Mount Sinai School of Medicine, New York, NY 10029, USA
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50
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Scholle MD, Collart FR, Kay BK. In vivo biotinylated proteins as targets for phage-display selection experiments. Protein Expr Purif 2004; 37:243-52. [PMID: 15294305 DOI: 10.1016/j.pep.2004.05.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2004] [Revised: 05/07/2004] [Indexed: 10/26/2022]
Abstract
Screening phage-displayed combinatorial libraries represents an attractive method for identifying affinity reagents to target proteins. Two critical components of a successful selection experiment are having a pure target protein and its immobilization in a native conformation. To achieve both of these requirements in a single step, we have devised cytoplasmic expression vectors for expression of proteins that are tagged at the amino- or carboxy-terminus (pMCSG16 and 15) via the AviTag, which is biotinylated in vivo with concurrent expression of the BirA biotin ligase. To facilitate implementation in high-throughput applications, the engineered vectors, pMCSG15 and pMCSG16, also contain a ligase-independent cloning site (LIC), which permits up to 100% cloning efficiency. The expressed protein can be purified from bacterial cell lysates with immobilized metal affinity chromatography or streptavidin-coated magnetic beads, and the beads used directly to select phage from combinatorial libraries. From selections using the N-terminally biotinylated version of one target protein, a peptide ligand (Kd= 9 microM) was recovered that bound in a format-dependent manner. To demonstrate the utility of pMCSG16, a set of 192 open reading frames were cloned, and protein was expressed and immobilized for use in high-throughput selections of phage-display libraries.
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Affiliation(s)
- Michael D Scholle
- Combinatorial Biology, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
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