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Optimization of non-denaturing protein extraction conditions for plant PPR proteins

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Optimization of non-denaturing protein extraction conditions for plant PPR proteins

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dc.contributor.author Andrés-Colás, Nuria es_ES
dc.contributor.author Van Der Straeten, Dominique es_ES
dc.date.accessioned 2020-10-23T03:31:01Z
dc.date.available 2020-10-23T03:31:01Z
dc.date.issued 2017-11-07 es_ES
dc.identifier.issn 1932-6203 es_ES
dc.identifier.uri http://hdl.handle.net/10251/153034
dc.description.abstract [EN] Pentatricopeptide repeat proteins are one of the major protein families in flowering plants, containing around 450 members. They participate in RNA editing and are related to plant growth, development and reproduction, as well as to responses to ABA and abiotic stresses. Their characteristics have been described in silico; however, relatively little is known about their biochemical properties. Different types of PPR proteins, with different tasks in RNA editing, have been suggested to interact in an editosome to complete RNA editing. Other non-PPR editing factors, such as the multiple organellar RNA editing factors and the organelle RNA recognition motif-containing protein family, for example, have also been described in plants. However, while evidence on protein interactions between non-PPR RNA editing proteins is accumulating, very few PPR protein interactions have been reported; possibly due to their high instability. In this manuscript, we aimed to optimize the conditions for non denaturing protein extraction of PPR proteins allowing in vivo protein analyses, such as interaction assays by co-immunoprecipitation. The unusually high protein degradation rate, the aggregation properties and the high pl, as well as the ATP-dependence of some PPR proteins, are key aspects to be considered when extracting PPR proteins in a non-denatured state. During extraction of PPR proteins, the use of proteasome and phosphatase inhibitors is critical. The use of the ATP-cofactor reduces considerably the degradation of PPR proteins. A short centrifugation step to discard cell debris is essential to avoid PPR precipitation; while in some cases, addition of a reductant is needed, probably caused by the pl/pH context. This work provides an easy and rapid optimized non-denaturing total protein extraction protocol from plant tissue, suitable for polypeptides of the PPR family. es_ES
dc.description.sponsorship This work was supported by Research Foundation Flanders (FWO) (project G.0C84.14N). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.r D.V.D.S. gratefully acknowledges Ghent University and the Research Foundation Flanders (FWO) for financial support (project G.0084.14N). N.A.-C. and D.V.D.S. acknowledge Maria Helena S. Goldman for the N. benthamiana seeds, helpful suggestions regarding experimental design and data interpretation, and critical reading of the manuscript. es_ES
dc.language Inglés es_ES
dc.publisher Public Library of Science es_ES
dc.relation FWO/G.0C84.14N es_ES
dc.relation.ispartof PLoS ONE es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Pentatricopeptide repeat proteins es_ES
dc.subject Arabidopsis-Thaliana es_ES
dc.subject RNA es_ES
dc.subject Mitochondria es_ES
dc.subject Recognition es_ES
dc.subject Fertility es_ES
dc.subject Substrate es_ES
dc.subject Vectors es_ES
dc.subject Complex es_ES
dc.subject System es_ES
dc.subject.classification BIOQUIMICA Y BIOLOGIA MOLECULAR es_ES
dc.title Optimization of non-denaturing protein extraction conditions for plant PPR proteins es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1371/journal.pone.0187753 es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia es_ES
dc.description.bibliographicCitation Andrés-Colás, N.; Van Der Straeten, D. (2017). Optimization of non-denaturing protein extraction conditions for plant PPR proteins. PLoS ONE. 12(11):1-15. https://doi.org/10.1371/journal.pone.0187753 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1371/journal.pone.0187753 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 15 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 12 es_ES
dc.description.issue 11 es_ES
dc.identifier.pmid 29112961 es_ES
dc.identifier.pmcid PMC5675432 es_ES
dc.relation.pasarela S\378287 es_ES
dc.contributor.funder Ghent University es_ES
dc.contributor.funder Research Foundation Flanders es_ES
dc.description.references Barkan, A., & Small, I. (2014). Pentatricopeptide Repeat Proteins in Plants. Annual Review of Plant Biology, 65(1), 415-442. doi:10.1146/annurev-arplant-050213-040159 es_ES
dc.description.references Saha, D., Prasad, A. M., & Srinivasan, R. (2007). Pentatricopeptide repeat proteins and their emerging roles in plants. Plant Physiology and Biochemistry, 45(8), 521-534. doi:10.1016/j.plaphy.2007.03.026 es_ES
dc.description.references SCHMITZLINNEWEBER, C., & SMALL, I. (2008). Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends in Plant Science, 13(12), 663-670. doi:10.1016/j.tplants.2008.10.001 es_ES
dc.description.references De Longevialle, A. F., Meyer, E. H., Andrés, C., Taylor, N. L., Lurin, C., Millar, A. H., & Small, I. D. (2007). The Pentatricopeptide Repeat Gene OTP43 Is Required for trans-Splicing of the Mitochondrial nad1 Intron 1 in Arabidopsis thaliana. The Plant Cell, 19(10), 3256-3265. doi:10.1105/tpc.107.054841 es_ES
dc.description.references Liu, Y., He, J., Chen, Z., Ren, X., Hong, X., & Gong, Z. (2010). ABA overly-sensitive 5 (ABO5), encoding a pentatricopeptide repeat protein required for cis-splicing of mitochondrial nad2 intron 3, is involved in the abscisic acid response in Arabidopsis. The Plant Journal, 63(5), 749-765. doi:10.1111/j.1365-313x.2010.04280.x es_ES
dc.description.references Sung, T.-Y., Tseng, C.-C., & Hsieh, M.-H. (2010). The SLO1 PPR protein is required for RNA editing at multiple sites with similar upstream sequences in Arabidopsis mitochondria. The Plant Journal, 63(3), 499-511. doi:10.1111/j.1365-313x.2010.04258.x es_ES
dc.description.references Zhu, Q., Dugardeyn, J., Zhang, C., Takenaka, M., Kühn, K., Craddock, C., … Van Der Straeten, D. (2012). SLO2, a mitochondrial pentatricopeptide repeat protein affecting several RNA editing sites, is required for energy metabolism. The Plant Journal, 71(5), 836-849. doi:10.1111/j.1365-313x.2012.05036.x es_ES
dc.description.references Zhu, Q., Dugardeyn, J., Zhang, C., Mühlenbock, P., Eastmond, P. J., Valcke, R., … Van Der Straeten, D. (2014). The Arabidopsis thaliana RNA Editing Factor SLO2, which Affects the Mitochondrial Electron Transport Chain, Participates in Multiple Stress and Hormone Responses. Molecular Plant, 7(2), 290-310. doi:10.1093/mp/sst102 es_ES
dc.description.references Colcombet, J., Lopez-Obando, M., Heurtevin, L., Bernard, C., Martin, K., Berthomé, R., & Lurin, C. (2013). Systematic study of subcellular localization of Arabidopsis PPR proteins confirms a massive targeting to organelles. RNA Biology, 10(9), 1557-1575. doi:10.4161/rna.26128 es_ES
dc.description.references Ichinose, M., & Sugita, M. (2016). RNA Editing and Its Molecular Mechanism in Plant Organelles. Genes, 8(1), 5. doi:10.3390/genes8010005 es_ES
dc.description.references Sun, T., Bentolila, S., & Hanson, M. R. (2016). The Unexpected Diversity of Plant Organelle RNA Editosomes. Trends in Plant Science, 21(11), 962-973. doi:10.1016/j.tplants.2016.07.005 es_ES
dc.description.references Yagi, Y., Tachikawa, M., Noguchi, H., Satoh, S., Obokata, J., & Nakamura, T. (2013). Pentatricopeptide repeat proteins involved in plant organellar RNA editing. RNA Biology, 10(9), 1419-1425. doi:10.4161/rna.24908 es_ES
dc.description.references Lurin, C., Andrés, C., Aubourg, S., Bellaoui, M., Bitton, F., Bruyère, C., … Small, I. (2004). Genome-Wide Analysis of Arabidopsis Pentatricopeptide Repeat Proteins Reveals Their Essential Role in Organelle Biogenesis. The Plant Cell, 16(8), 2089-2103. doi:10.1105/tpc.104.022236 es_ES
dc.description.references Bentolila, S., Heller, W. P., Sun, T., Babina, A. M., Friso, G., van Wijk, K. J., & Hanson, M. R. (2012). RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing. Proceedings of the National Academy of Sciences, 109(22), E1453-E1461. doi:10.1073/pnas.1121465109 es_ES
dc.description.references Glass, F., Härtel, B., Zehrmann, A., Verbitskiy, D., & Takenaka, M. (2015). MEF13 Requires MORF3 and MORF8 for RNA Editing at Eight Targets in Mitochondrial mRNAs in Arabidopsis thaliana. Molecular Plant, 8(10), 1466-1477. doi:10.1016/j.molp.2015.05.008 es_ES
dc.description.references Härtel, B., Zehrmann, A., Verbitskiy, D., van der Merwe, J. A., Brennicke, A., & Takenaka, M. (2013). MEF10 is required for RNA editing at nad2-842 in mitochondria of Arabidopsis thaliana and interacts with MORF8. Plant Molecular Biology, 81(4-5), 337-346. doi:10.1007/s11103-012-0003-2 es_ES
dc.description.references Hu, J., Wang, K., Huang, W., Liu, G., Gao, Y., Wang, J., … Zhu, Y. (2012). The Rice Pentatricopeptide Repeat Protein RF5 Restores Fertility in Hong-Lian Cytoplasmic Male-Sterile Lines via a Complex with the Glycine-Rich Protein GRP162. The Plant Cell, 24(1), 109-122. doi:10.1105/tpc.111.093211 es_ES
dc.description.references Sun, T., Germain, A., Giloteaux, L., Hammani, K., Barkan, A., Hanson, M. R., & Bentolila, S. (2013). An RNA recognition motif-containing protein is required for plastid RNA editing in Arabidopsis and maize. Proceedings of the National Academy of Sciences, 110(12), E1169-E1178. doi:10.1073/pnas.1220162110 es_ES
dc.description.references Sun, T., Shi, X., Friso, G., Van Wijk, K., Bentolila, S., & Hanson, M. R. (2015). A Zinc Finger Motif-Containing Protein Is Essential for Chloroplast RNA Editing. PLOS Genetics, 11(3), e1005028. doi:10.1371/journal.pgen.1005028 es_ES
dc.description.references Takenaka, M., Zehrmann, A., Verbitskiy, D., Kugelmann, M., Hartel, B., & Brennicke, A. (2012). Multiple organellar RNA editing factor (MORF) family proteins are required for RNA editing in mitochondria and plastids of plants. Proceedings of the National Academy of Sciences, 109(13), 5104-5109. doi:10.1073/pnas.1202452109 es_ES
dc.description.references Boussardon, C., Salone, V., Avon, A., Berthomé, R., Hammani, K., Okuda, K., … Lurin, C. (2012). Two Interacting Proteins Are Necessary for the Editing of the NdhD-1 Site in Arabidopsis Plastids. The Plant Cell, 24(9), 3684-3694. doi:10.1105/tpc.112.099507 es_ES
dc.description.references Coquille, S., Filipovska, A., Chia, T., Rajappa, L., Lingford, J. P., Razif, M. F. M., … Rackham, O. (2014). An artificial PPR scaffold for programmable RNA recognition. Nature Communications, 5(1). doi:10.1038/ncomms6729 es_ES
dc.description.references Uyttewaal, M., Arnal, N., Quadrado, M., Martin-Canadell, A., Vrielynck, N., Hiard, S., … Mireau, H. (2008). Characterization of Raphanus sativus Pentatricopeptide Repeat Proteins Encoded by the Fertility Restorer Locus for Ogura Cytoplasmic Male Sterility. The Plant Cell, 20(12), 3331-3345. doi:10.1105/tpc.107.057208 es_ES
dc.description.references Kobayashi, T., Yagi, Y., & Nakamura, T. (2016). Development of Genome Engineering Tools from Plant-Specific PPR Proteins Using Animal Cultured Cells. Chromosome and Genomic Engineering in Plants, 147-155. doi:10.1007/978-1-4939-4931-1_11 es_ES
dc.description.references Kun, W., Feng, G., Renshan, Z., Shaoqing, L., & Yingguo, Z. (2010). Expression, Purification, and Secondary Structure Prediction of Pentatricopeptide Repeat Protein RF1A from Rice. Plant Molecular Biology Reporter, 29(3), 739-744. doi:10.1007/s11105-010-0260-7 es_ES
dc.description.references Yin, P., Li, Q., Yan, C., Liu, Y., Liu, J., Yu, F., … Yan, N. (2013). Structural basis for the modular recognition of single-stranded RNA by PPR proteins. Nature, 504(7478), 168-171. doi:10.1038/nature12651 es_ES
dc.description.references Law, Y.-S., Zhang, R., Guan, X., Cheng, S., Sun, F., Duncan, O., … Lim, B. L. (2015). Phosphorylation and Dephosphorylation of the Presequence of Precursor MULTIPLE ORGANELLAR RNA EDITING FACTOR3 during Import into Mitochondria from Arabidopsis. Plant Physiology, 169(2), 1344-1355. doi:10.1104/pp.15.01115 es_ES
dc.description.references Hershko, A., & Ciechanover, A. (1998). THE UBIQUITIN SYSTEM. Annual Review of Biochemistry, 67(1), 425-479. doi:10.1146/annurev.biochem.67.1.425 es_ES
dc.description.references Hegeman, C. E., Hayes, M. L., & Hanson, M. R. (2005). Substrate and cofactor requirements for RNA editing of chloroplast transcripts in Arabidopsis in vitro. The Plant Journal, 42(1), 124-132. doi:10.1111/j.1365-313x.2005.02360.x es_ES
dc.description.references Hooper, C. M., Castleden, I. R., Tanz, S. K., Aryamanesh, N., & Millar, A. H. (2016). SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations. Nucleic Acids Research, 45(D1), D1064-D1074. doi:10.1093/nar/gkw1041 es_ES
dc.description.references Jaedicke, K., Lichtenthäler, A. L., Meyberg, R., Zeidler, M., & Hughes, J. (2012). A phytochrome–phototropin light signaling complex at the plasma membrane. Proceedings of the National Academy of Sciences, 109(30), 12231-12236. doi:10.1073/pnas.1120203109 es_ES
dc.description.references Singh, R., Lee, M.-O., Lee, J.-E., Choi, J., Park, J. H., Kim, E. H., … Jwa, N.-S. (2012). Rice Mitogen-Activated Protein Kinase Interactome Analysis Using the Yeast Two-Hybrid System. Plant Physiology, 160(1), 477-487. doi:10.1104/pp.112.200071 es_ES
dc.description.references Irigoyen, M. L., Iniesto, E., Rodriguez, L., Puga, M. I., Yanagawa, Y., Pick, E., … Rubio, V. (2014). Targeted Degradation of Abscisic Acid Receptors Is Mediated by the Ubiquitin Ligase Substrate Adaptor DDA1 in Arabidopsis. The Plant Cell, 26(2), 712-728. doi:10.1105/tpc.113.122234 es_ES
dc.description.references Magori, S., & Citovsky, V. (2011). Agrobacterium Counteracts Host-Induced Degradation of Its Effector F-Box Protein. Science Signaling, 4(195), ra69-ra69. doi:10.1126/scisignal.2002124 es_ES
dc.description.references Zhou, X., Graumann, K., Evans, D. E., & Meier, I. (2012). Novel plant SUN–KASH bridges are involved in RanGAP anchoring and nuclear shape determination. Journal of Cell Biology, 196(2), 203-211. doi:10.1083/jcb.201108098 es_ES
dc.description.references Bracha‐Drori, K., Shichrur, K., Katz, A., Oliva, M., Angelovici, R., Yalovsky, S., & Ohad, N. (2004). Detection of protein–protein interactions in plants using bimolecular fluorescence complementation. The Plant Journal, 40(3), 419-427. doi:10.1111/j.1365-313x.2004.02206.x es_ES
dc.description.references Krasileva, K. V., Dahlbeck, D., & Staskawicz, B. J. (2010). Activation of an Arabidopsis Resistance Protein Is Specified by the in Planta Association of Its Leucine-Rich Repeat Domain with the Cognate Oomycete Effector. The Plant Cell, 22(7), 2444-2458. doi:10.1105/tpc.110.075358 es_ES
dc.description.references Klenova, E. (2002). Immunoprecipitation techniques for the analysis of transcription factor complexes. Methods, 26(3), 254-259. doi:10.1016/s1046-2023(02)00029-4 es_ES
dc.description.references Manavski, N., Guyon, V., Meurer, J., Wienand, U., & Brettschneider, R. (2012). An Essential Pentatricopeptide Repeat Protein Facilitates 5′ Maturation and Translation Initiation of rps3 mRNA in Maize Mitochondria. The Plant Cell, 24(7), 3087-3105. doi:10.1105/tpc.112.099051 es_ES
dc.description.references Andrés-Colás, N., Zhu, Q., Takenaka, M., De Rybel, B., Weijers, D., & Van Der Straeten, D. (2017). Multiple PPR protein interactions are involved in the RNA editing system in Arabidopsis mitochondria and plastids. Proceedings of the National Academy of Sciences, 114(33), 8883-8888. doi:10.1073/pnas.1705815114 es_ES
dc.description.references Karimi, M., Inzé, D., & Depicker, A. (2002). GATEWAY™ vectors for Agrobacterium-mediated plant transformation. Trends in Plant Science, 7(5), 193-195. doi:10.1016/s1360-1385(02)02251-3 es_ES
dc.description.references NAKAGAWA, T., SUZUKI, T., MURATA, S., NAKAMURA, S., HINO, T., MAEO, K., … ISHIGURO, S. (2007). Improved Gateway Binary Vectors: High-Performance Vectors for Creation of Fusion Constructs in Transgenic Analysis of Plants. Bioscience, Biotechnology, and Biochemistry, 71(8), 2095-2100. doi:10.1271/bbb.70216 es_ES
dc.description.references Voinnet, O., Rivas, S., Mestre, P., & Baulcombe, D. (2003). Retracted: An enhanced transient expression system in plants based on suppression of gene silencing by the p19 protein of tomato bushy stunt virus. The Plant Journal, 33(5), 949-956. doi:10.1046/j.1365-313x.2003.01676.x es_ES
dc.description.references Pukac, L. A., Carter, J. E., Morrison, K. S., & Karnovsky, M. J. (1997). Enhancement of Diaminobenzidine Colorimetric Signal in Immunoblotting. BioTechniques, 23(3), 385-388. doi:10.2144/97233bm08 es_ES


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