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      Identification of nuclear localization signal and nuclear export signal of VP1 from the chicken anemia virus and effects on VP2 shuttling in cells

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          Abstract

          Background

          VP1 of the chicken anemia virus (CAV) is a structural protein that is required for virus encapsulation. VP1 proteins are present both in the nucleus and cytoplasm; however, the functional nuclear localization signal (NLS) and nuclear export signal (NES) of VP1 are still unknown. This study aimed to characterize the NLS and NES motifs of VP1 using bioinformatics methods and multiple-site fragment deletions, and investigate shuttling of VP2 from nucleus to cytoplasm by co-transfection with VP1.

          Methods

          Two putative NLS motifs were predicted by the WoLF PSORT and NLStradamus programs from the amino acid sequence of VP1. Three NES motifs of VP1 were predicted by the NetNES 1.1 Server and ELM server programs. All mutants were created by multiple-site fragment deletion mutagenesis. VP1 and VP2 were co-expressed in cells using plasmid transfection.

          Results

          A functional NLS motif was identified at amino acid residues 3 to 10 (RRARRPRG) of VP1. Critical amino acids 3 to 10 were significantly involved in nuclear import in cells and were evaluated using systematic deletion mutagenesis. Three NES motifs of VP1 were predicted by the NetNES 1.1 Server and ELM server programs. A functional NES was identified at amino acid residues 375 to 388 (ELDTNFFTLYVAQ). Leptomycin B (LMB) treatment demonstrated that VP1 export from nucleus to cytoplasm occurred through a chromosome region maintenance 1 (CRM1)-dependent pathway. With co-expression of VP1 and VP2 in cells, we observed that VP1 may transport VP2 from nucleus to cytoplasm.

          Conclusion

          Our data showed that VP1 of CAV contained functional NLS and NES motifs that modulated nuclear import and export through a CRM1-dependent pathway. Further, VP1 may play a role in the transport of VP2 from nucleus to cytoplasm.

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          Most cited references34

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          NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction

          Background Nuclear localization signals (NLSs) are stretches of residues within a protein that are important for the regulated nuclear import of the protein. Of the many import pathways that exist in yeast, the best characterized is termed the 'classical' NLS pathway. The classical NLS contains specific patterns of basic residues and computational methods have been designed to predict the location of these motifs on proteins. The consensus sequences, or patterns, for the other import pathways are less well-understood. Results In this paper, we present an analysis of characterized NLSs in yeast, and find, despite the large number of nuclear import pathways, that NLSs seem to show similar patterns of amino acid residues. We test current prediction methods and observe a low true positive rate. We therefore suggest an approach using hidden Markov models (HMMs) to predict novel NLSs in proteins. We show that our method is able to consistently find 37% of the NLSs with a low false positive rate and that our method retains its true positive rate outside of the yeast data set used for the training parameters. Conclusion Our implementation of this model, NLStradamus, is made available at:
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            The HIV-1 Rev activation domain is a nuclear export signal that accesses an export pathway used by specific cellular RNAs.

            HIV-1 Rev protein directs nuclear export of pre-mRNAs and mRNAs containing its binding site, the Rev response element (RRE). To define how Rev acts, we used conjugates between bovine serum albumin (BSA) and peptides comprising the Rev activation domain (BSA-R). BSA-R inhibited Rev-mediated nuclear RNA export, whereas a mutant activation domain peptide conjugate did not. BSA-R did not affect the export of mRNA, tRNA, or ribosomal subunits, but did inhibit export of 5S rRNA and spliceosomal U snRNAs. BSA-R was itself exported from the nucleus in an active, saturable manner. Thus, the Rev activation domain constitutes a nuclear export signal that redirects RRE-containing viral RNAs to a non-mRNA export pathway.
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              MView: a web-compatible database search or multiple alignment viewer.

              MView is a tool for converting the results of a sequence database search into the form of a coloured multiple alignment of hits stacked against the query. Alternatively, an existing multiple alignment can be processed. In either case, the output is simply HTML, so the result is platform independent and does not require a separate application or applet to be loaded. Free from http://www.sander.ebi.ac.uk/mview/ subject to copyright restrictions. brown@ebi.ac.uk
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                Author and article information

                Contributors
                +886-7-731-7123 , cjh1106@cgmh.org.tw
                just_dfm@hotmail.com
                yylien@mail.npust.edu.tw
                fcsun@mail.dyu.edu.tw
                hsishanlin@yahoo.com.tw
                +886-4-2205-3366 , leemengshiou@mail.cmu.edu.tw
                Journal
                Virol J
                Virol. J
                Virology Journal
                BioMed Central (London )
                1743-422X
                5 April 2019
                5 April 2019
                2019
                : 16
                : 45
                Affiliations
                [1 ]GRID grid.145695.a, Center for Shockwave Medicine and Tissue Engineering, Department of Medical Research, , Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, ; 123 Tai-Pei Road, Niao Sung District, Kaohsiung, Taiwan 833
                [2 ]ISNI 0000 0004 0532 3749, GRID grid.260542.7, Graduate Institute of Biotechnology, College of Agriculture and Natural Resources, , National Chung Hsing University, ; Taichung, 40402 Taiwan
                [3 ]ISNI 0000 0000 9767 1257, GRID grid.412083.c, Department of Veterinary Medicine, , National Pingtung University of Science and Technology, ; Pingtung, Taiwan
                [4 ]ISNI 0000 0000 9767 1257, GRID grid.412083.c, Research Center of Animal Biologics, , National Pingtung University of Science and Technology, ; Pingtung, Taiwan
                [5 ]Department of Bioresources, Da-Yeh University, Changhua, Taiwan
                [6 ]ISNI 0000 0000 9230 8977, GRID grid.411396.8, Department of Orthopedic Surgery, Center for Shockwave Medicine and Tissue Engineering, , Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine; Fooyin University, School of Nursing, ; Kaohsiung, Taiwan
                [7 ]ISNI 0000 0001 0083 6092, GRID grid.254145.3, Department of Chinese Pharmaceutical Science and Chinese Medicine Resources, , China Medical University, ; 91, Hsueh-Shih Road, Taichung, Taiwan
                Author information
                http://orcid.org/0000-0003-3667-2741
                Article
                1153
                10.1186/s12985-019-1153-5
                6451244
                30953524
                783ad926-75ab-4764-8c91-c390e7324175
                © The Author(s). 2019

                Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 1 August 2018
                : 25 March 2019
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100004606, Chang Gung Medical Foundation;
                Award ID: CMRPG8F1131
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100004663, Ministry of Science and Technology, Taiwan;
                Award ID: NSC-95-2313-B-039-004-; NSC-96-2313-B-276-001-MY3
                Award Recipient :
                Categories
                Research
                Custom metadata
                © The Author(s) 2019

                Microbiology & Virology
                chicken anemia virus,vp1,vp2,nuclear localization signal,nuclear export signal,crm1-dependent pathway

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